Starting phenix.real_space_refine on Wed Aug 5 19:53:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9be5_44470/08_2026/9be5_44470.cif Found real_map, /net/cci-nas-00/data/ceres_data/9be5_44470/08_2026/9be5_44470.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9be5_44470/08_2026/9be5_44470.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9be5_44470/08_2026/9be5_44470.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9be5_44470/08_2026/9be5_44470.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9be5_44470/08_2026/9be5_44470.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.028 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 288 5.49 5 S 12 5.16 5 C 6576 2.51 5 N 2231 2.21 5 O 2791 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11898 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 795 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2952 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2987 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Time building chain proxies: 2.32, per 1000 atoms: 0.19 Number of scatterers: 11898 At special positions: 0 Unit cell: (73.08, 123.54, 118.32, 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 12 16.00 P 288 15.00 O 2791 8.00 N 2231 7.00 C 6576 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: 0.78 Conformation dependent library (CDL) restraints added in 210.4 milliseconds 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1406 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 10 sheets defined 73.1% alpha, 2.9% beta 128 base pairs and 234 stacking pairs defined. Time for finding SS restraints: 1.65 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.746A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.675A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.539A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 121 Processing helix chain 'E' and resid 44 through 56 removed outlier: 3.716A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.832A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.521A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.584A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 121 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.769A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.478A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.442A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.760A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.904A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.332A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 406 hydrogen bonds defined for protein. 1200 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 327 hydrogen bonds 654 hydrogen bond angles 0 basepair planarities 128 basepair parallelities 234 stacking parallelities Total time for adding SS restraints: 1.75 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2432 1.33 - 1.45: 4054 1.45 - 1.57: 5616 1.57 - 1.69: 576 1.69 - 1.81: 22 Bond restraints: 12700 Sorted by residual: bond pdb=" C3' DC I 4 " pdb=" C2' DC I 4 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.18e+01 bond pdb=" C3' DC J -58 " pdb=" C2' DC J -58 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.14e+01 bond pdb=" C3' DT J -17 " pdb=" C2' DT J -17 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.13e+01 bond pdb=" C3' DT J -29 " pdb=" C2' DT J -29 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.07e+01 bond pdb=" C3' DC J 34 " pdb=" C2' DC J 34 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.05e+01 ... (remaining 12695 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 17054 1.42 - 2.85: 1270 2.85 - 4.27: 61 4.27 - 5.70: 14 5.70 - 7.12: 1 Bond angle restraints: 18400 Sorted by residual: angle pdb=" O4' DG I -68 " pdb=" C4' DG I -68 " pdb=" C3' DG I -68 " ideal model delta sigma weight residual 106.00 103.09 2.91 6.00e-01 2.78e+00 2.35e+01 angle pdb=" O4' DG J -8 " pdb=" C4' DG J -8 " pdb=" C3' DG J -8 " ideal model delta sigma weight residual 106.00 103.22 2.78 6.00e-01 2.78e+00 2.14e+01 angle pdb=" O4' DA I -67 " pdb=" C4' DA I -67 " pdb=" C3' DA I -67 " ideal model delta sigma weight residual 106.00 103.26 2.74 6.00e-01 2.78e+00 2.08e+01 angle pdb=" N3 DT I -71 " pdb=" C4 DT I -71 " pdb=" O4 DT I -71 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.94e+01 angle pdb=" N3 DT I -39 " pdb=" C4 DT I -39 " pdb=" O4 DT I -39 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.92e+01 ... (remaining 18395 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.01: 5519 35.01 - 70.02: 1347 70.02 - 105.03: 24 105.03 - 140.04: 3 140.04 - 175.05: 1 Dihedral angle restraints: 6894 sinusoidal: 4715 harmonic: 2179 Sorted by residual: dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual 220.00 44.95 175.05 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DC J 34 " pdb=" C3' DC J 34 " pdb=" O3' DC J 34 " pdb=" P DT J 35 " ideal model delta sinusoidal sigma weight residual 220.00 81.39 138.61 1 3.50e+01 8.16e-04 1.37e+01 dihedral pdb=" C4' DA J -38 " pdb=" C3' DA J -38 " pdb=" O3' DA J -38 " pdb=" P DG J -37 " ideal model delta sinusoidal sigma weight residual 220.00 92.22 127.78 1 3.50e+01 8.16e-04 1.26e+01 ... (remaining 6891 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1817 0.066 - 0.133: 275 0.133 - 0.199: 3 0.199 - 0.265: 0 0.265 - 0.332: 2 Chirality restraints: 2097 Sorted by residual: chirality pdb=" CB ILE H 86 " pdb=" CA ILE H 86 " pdb=" CG1 ILE H 86 " pdb=" CG2 ILE H 86 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" CB ILE D 86 " pdb=" CA ILE D 86 " pdb=" CG1 ILE D 86 " pdb=" CG2 ILE D 86 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" C3' DT J -17 " pdb=" C4' DT J -17 " pdb=" O3' DT J -17 " pdb=" C2' DT J -17 " both_signs ideal model delta sigma weight residual False -2.73 -2.58 -0.15 2.00e-01 2.50e+01 5.59e-01 ... (remaining 2094 not shown) Planarity restraints: 1325 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " -0.029 5.00e-02 4.00e+02 4.44e-02 3.15e+00 pdb=" N PRO C 80 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA I -35 " 0.022 2.00e-02 2.50e+03 9.32e-03 2.39e+00 pdb=" N9 DA I -35 " -0.017 2.00e-02 2.50e+03 pdb=" C8 DA I -35 " -0.006 2.00e-02 2.50e+03 pdb=" N7 DA I -35 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DA I -35 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DA I -35 " 0.002 2.00e-02 2.50e+03 pdb=" N6 DA I -35 " 0.008 2.00e-02 2.50e+03 pdb=" N1 DA I -35 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DA I -35 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DA I -35 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DA I -35 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " -0.026 5.00e-02 4.00e+02 3.86e-02 2.38e+00 pdb=" N PRO G 80 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " -0.022 5.00e-02 4.00e+02 ... (remaining 1322 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 644 2.71 - 3.26: 11030 3.26 - 3.81: 23956 3.81 - 4.35: 28509 4.35 - 4.90: 41145 Nonbonded interactions: 105284 Sorted by model distance: nonbonded pdb=" O TYR G 39 " pdb=" OG SER H 75 " model vdw 2.167 3.040 nonbonded pdb=" NH1 ARG D 83 " pdb=" OE2 GLU D 90 " model vdw 2.192 3.120 nonbonded pdb=" OH TYR B 98 " pdb=" OD2 ASP H 65 " model vdw 2.220 3.040 nonbonded pdb=" OG1 THR D 87 " pdb=" OE1 GLU D 90 " model vdw 2.244 3.040 nonbonded pdb=" NE2 GLN G 24 " pdb=" OE1 GLN H 44 " model vdw 2.269 3.120 ... (remaining 105279 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 39 through 134) selection = (chain 'E' and resid 39 through 134) } ncs_group { reference = (chain 'B' and resid 25 through 102) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 16 through 118) } ncs_group { reference = (chain 'D' and resid 29 through 121) selection = chain 'H' } 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: 2.100 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.080 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 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 : 0.006 0.037 12700 Z= 0.522 Angle : 0.753 7.123 18400 Z= 0.668 Chirality : 0.045 0.332 2097 Planarity : 0.004 0.044 1325 Dihedral : 28.066 175.051 5488 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.30), residues: 735 helix: 1.65 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -0.74 (0.41), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 95 TYR 0.014 0.001 TYR C 57 PHE 0.026 0.002 PHE C 25 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00582 / 0.52 (12700) covalent geometry : angle 0.75251 / 0.67 (18400) hydrogen bonds : bond 0.11947 / 8.07 ( 733) hydrogen bonds : angle 4.73008 / 3.41 ( 1854) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.285 Fit side-chains REVERT: C 33 LEU cc_start: 0.8149 (mt) cc_final: 0.7915 (mt) REVERT: D 56 MET cc_start: 0.7779 (tpp) cc_final: 0.7440 (mmm) REVERT: H 59 MET cc_start: 0.8332 (mmp) cc_final: 0.7877 (mmp) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.1190 time to fit residues: 10.6978 Evaluate side-chains 53 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN E 108 ASN G 38 ASN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.186055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.122857 restraints weight = 13955.488| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 1.63 r_work: 0.3294 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.0802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12700 Z= 0.157 Angle : 0.648 10.393 18400 Z= 0.379 Chirality : 0.044 0.296 2097 Planarity : 0.005 0.044 1325 Dihedral : 31.373 176.955 4008 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.12 % Allowed : 3.84 % Favored : 95.04 % 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: 2.04 (0.30), residues: 735 helix: 2.00 (0.21), residues: 547 sheet: None (None), residues: 0 loop : -0.58 (0.41), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 67 TYR 0.019 0.002 TYR H 80 PHE 0.017 0.002 PHE C 25 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.16 (12700) covalent geometry : angle 0.64760 / 0.38 (18400) hydrogen bonds : bond 0.05105 / 3.37 ( 733) hydrogen bonds : angle 3.04880 / 2.17 ( 1854) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.253 Fit side-chains REVERT: E 81 ASP cc_start: 0.8445 (t0) cc_final: 0.8155 (t0) outliers start: 7 outliers final: 5 residues processed: 64 average time/residue: 0.1167 time to fit residues: 10.3244 Evaluate side-chains 59 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain G residue 114 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 28 optimal weight: 1.9990 chunk 71 optimal weight: 20.0000 chunk 12 optimal weight: 1.9990 chunk 87 optimal weight: 20.0000 chunk 24 optimal weight: 2.9990 chunk 81 optimal weight: 20.0000 chunk 29 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 53 optimal weight: 0.1980 chunk 14 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 HIS ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 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 = 0.4226 r_free = 0.4226 target = 0.184324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.120624 restraints weight = 14000.222| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.61 r_work: 0.3269 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12700 Z= 0.159 Angle : 0.626 10.699 18400 Z= 0.363 Chirality : 0.043 0.298 2097 Planarity : 0.004 0.043 1325 Dihedral : 31.607 177.770 4008 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.44 % Allowed : 5.76 % Favored : 92.80 % 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: 2.18 (0.30), residues: 735 helix: 2.11 (0.21), residues: 547 sheet: None (None), residues: 0 loop : -0.53 (0.41), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 83 TYR 0.021 0.002 TYR H 80 PHE 0.017 0.002 PHE C 25 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.16 (12700) covalent geometry : angle 0.62602 / 0.36 (18400) hydrogen bonds : bond 0.04746 / 3.15 ( 733) hydrogen bonds : angle 2.92955 / 2.10 ( 1854) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.238 Fit side-chains REVERT: C 74 LYS cc_start: 0.7721 (mmmt) cc_final: 0.7225 (mtmm) REVERT: E 81 ASP cc_start: 0.8523 (t0) cc_final: 0.8116 (t0) outliers start: 9 outliers final: 7 residues processed: 61 average time/residue: 0.0995 time to fit residues: 8.8209 Evaluate side-chains 62 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 86 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 90 optimal weight: 9.9990 chunk 67 optimal weight: 4.9990 chunk 47 optimal weight: 0.3980 chunk 24 optimal weight: 0.5980 chunk 72 optimal weight: 20.0000 chunk 1 optimal weight: 0.9980 chunk 26 optimal weight: 0.4980 chunk 78 optimal weight: 9.9990 chunk 87 optimal weight: 20.0000 chunk 10 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 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 = 0.4313 r_free = 0.4313 target = 0.190772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.126977 restraints weight = 14139.557| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 1.67 r_work: 0.3362 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12700 Z= 0.141 Angle : 0.604 12.562 18400 Z= 0.351 Chirality : 0.042 0.292 2097 Planarity : 0.004 0.042 1325 Dihedral : 31.629 179.732 4008 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.44 % Allowed : 6.88 % Favored : 91.68 % 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: 2.38 (0.30), residues: 735 helix: 2.25 (0.21), residues: 547 sheet: None (None), residues: 0 loop : -0.45 (0.42), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 83 TYR 0.013 0.001 TYR C 57 PHE 0.016 0.002 PHE C 25 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.14 (12700) covalent geometry : angle 0.60405 / 0.35 (18400) hydrogen bonds : bond 0.04339 / 2.86 ( 733) hydrogen bonds : angle 2.77822 / 1.99 ( 1854) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.234 Fit side-chains REVERT: A 56 LYS cc_start: 0.7525 (ttpt) cc_final: 0.6559 (mttt) REVERT: C 72 ASP cc_start: 0.7484 (m-30) cc_final: 0.7201 (m-30) REVERT: D 48 ASP cc_start: 0.7355 (t0) cc_final: 0.7058 (t0) REVERT: E 133 GLU cc_start: 0.7964 (mp0) cc_final: 0.7755 (mp0) outliers start: 9 outliers final: 8 residues processed: 58 average time/residue: 0.0933 time to fit residues: 7.9214 Evaluate side-chains 61 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 86 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 2 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 83 optimal weight: 20.0000 chunk 42 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 87 optimal weight: 20.0000 chunk 46 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 25 optimal weight: 0.2980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.187611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.125193 restraints weight = 13305.194| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 1.65 r_work: 0.3229 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12700 Z= 0.144 Angle : 0.600 10.586 18400 Z= 0.347 Chirality : 0.041 0.285 2097 Planarity : 0.004 0.042 1325 Dihedral : 31.720 179.419 4008 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.28 % Allowed : 8.16 % Favored : 90.56 % 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: 2.50 (0.30), residues: 735 helix: 2.34 (0.21), residues: 544 sheet: None (None), residues: 0 loop : -0.37 (0.42), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 92 TYR 0.021 0.001 TYR H 118 PHE 0.019 0.002 PHE C 25 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.14 (12700) covalent geometry : angle 0.60049 / 0.35 (18400) hydrogen bonds : bond 0.04277 / 2.82 ( 733) hydrogen bonds : angle 2.74462 / 1.97 ( 1854) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.208 Fit side-chains REVERT: A 56 LYS cc_start: 0.7191 (ttpt) cc_final: 0.6155 (mttt) REVERT: C 33 LEU cc_start: 0.8208 (mt) cc_final: 0.7984 (mt) REVERT: C 74 LYS cc_start: 0.7446 (mmmm) cc_final: 0.7027 (mtmm) REVERT: D 48 ASP cc_start: 0.7410 (t0) cc_final: 0.7112 (t0) REVERT: E 90 MET cc_start: 0.7722 (tpp) cc_final: 0.7211 (mmt) outliers start: 8 outliers final: 7 residues processed: 61 average time/residue: 0.0835 time to fit residues: 7.6517 Evaluate side-chains 59 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 86 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 14 optimal weight: 0.6980 chunk 70 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 87 optimal weight: 20.0000 chunk 17 optimal weight: 3.9990 chunk 92 optimal weight: 20.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 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 = 0.4220 r_free = 0.4220 target = 0.188073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.125651 restraints weight = 13343.773| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.65 r_work: 0.3238 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12700 Z= 0.138 Angle : 0.593 13.060 18400 Z= 0.342 Chirality : 0.041 0.277 2097 Planarity : 0.004 0.041 1325 Dihedral : 31.697 178.230 4008 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.28 % Allowed : 9.12 % Favored : 89.60 % 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: 2.59 (0.30), residues: 735 helix: 2.38 (0.21), residues: 545 sheet: None (None), residues: 0 loop : -0.26 (0.42), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 92 TYR 0.013 0.001 TYR H 118 PHE 0.012 0.001 PHE G 25 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.14 (12700) covalent geometry : angle 0.59307 / 0.34 (18400) hydrogen bonds : bond 0.04153 / 2.74 ( 733) hydrogen bonds : angle 2.68726 / 1.93 ( 1854) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.272 Fit side-chains REVERT: A 56 LYS cc_start: 0.7264 (ttpt) cc_final: 0.6234 (mttt) REVERT: D 48 ASP cc_start: 0.7453 (t0) cc_final: 0.7175 (t0) REVERT: E 90 MET cc_start: 0.7715 (tpp) cc_final: 0.7216 (mmt) outliers start: 8 outliers final: 8 residues processed: 55 average time/residue: 0.0916 time to fit residues: 7.3839 Evaluate side-chains 57 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 86 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 31 optimal weight: 0.7980 chunk 59 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 98 optimal weight: 20.0000 chunk 86 optimal weight: 20.0000 chunk 14 optimal weight: 0.5980 chunk 94 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 29 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 38 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.187718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.125367 restraints weight = 13289.689| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.65 r_work: 0.3258 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12700 Z= 0.139 Angle : 0.592 13.404 18400 Z= 0.339 Chirality : 0.041 0.269 2097 Planarity : 0.004 0.041 1325 Dihedral : 31.690 176.947 4008 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.44 % Allowed : 9.76 % Favored : 88.80 % 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: 2.63 (0.30), residues: 735 helix: 2.38 (0.21), residues: 545 sheet: None (None), residues: 0 loop : -0.15 (0.42), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 92 TYR 0.016 0.001 TYR H 118 PHE 0.015 0.001 PHE C 25 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.14 (12700) covalent geometry : angle 0.59164 / 0.34 (18400) hydrogen bonds : bond 0.04166 / 2.76 ( 733) hydrogen bonds : angle 2.69471 / 1.93 ( 1854) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.192 Fit side-chains REVERT: A 56 LYS cc_start: 0.7294 (ttpt) cc_final: 0.6267 (mttt) REVERT: C 33 LEU cc_start: 0.8239 (mt) cc_final: 0.8022 (mt) REVERT: C 74 LYS cc_start: 0.7388 (mmmm) cc_final: 0.7061 (mtmm) REVERT: D 48 ASP cc_start: 0.7567 (t0) cc_final: 0.7304 (t0) REVERT: E 90 MET cc_start: 0.7746 (tpp) cc_final: 0.7252 (mmt) outliers start: 9 outliers final: 8 residues processed: 59 average time/residue: 0.0992 time to fit residues: 8.2175 Evaluate side-chains 61 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 86 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 41 optimal weight: 0.7980 chunk 93 optimal weight: 9.9990 chunk 70 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 80 optimal weight: 20.0000 chunk 27 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 91 optimal weight: 10.0000 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 25 ASN G 38 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.185498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.122615 restraints weight = 13333.378| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.65 r_work: 0.3208 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12700 Z= 0.168 Angle : 0.617 12.356 18400 Z= 0.348 Chirality : 0.042 0.270 2097 Planarity : 0.004 0.040 1325 Dihedral : 31.788 176.024 4008 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.60 % Allowed : 10.72 % Favored : 87.68 % 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: 2.38 (0.30), residues: 735 helix: 2.21 (0.21), residues: 544 sheet: None (None), residues: 0 loop : -0.28 (0.42), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 92 TYR 0.019 0.002 TYR H 80 PHE 0.014 0.002 PHE G 25 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.17 (12700) covalent geometry : angle 0.61743 / 0.35 (18400) hydrogen bonds : bond 0.04329 / 2.89 ( 733) hydrogen bonds : angle 2.80465 / 2.01 ( 1854) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.269 Fit side-chains REVERT: A 56 LYS cc_start: 0.7196 (ttpt) cc_final: 0.6150 (mttt) REVERT: C 72 ASP cc_start: 0.7275 (m-30) cc_final: 0.6964 (m-30) REVERT: C 74 LYS cc_start: 0.7365 (mmmm) cc_final: 0.6972 (mtmm) REVERT: E 90 MET cc_start: 0.7765 (tpp) cc_final: 0.7489 (mmm) REVERT: G 19 SER cc_start: 0.7501 (m) cc_final: 0.7014 (p) outliers start: 10 outliers final: 10 residues processed: 61 average time/residue: 0.1001 time to fit residues: 8.8195 Evaluate side-chains 67 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 86 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 96 optimal weight: 20.0000 chunk 35 optimal weight: 0.7980 chunk 86 optimal weight: 30.0000 chunk 44 optimal weight: 0.3980 chunk 3 optimal weight: 0.6980 chunk 60 optimal weight: 0.5980 chunk 94 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 45 optimal weight: 0.0980 chunk 83 optimal weight: 20.0000 chunk 25 optimal weight: 0.3980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 25 ASN G 38 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.187699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.125459 restraints weight = 13204.733| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.63 r_work: 0.3269 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12700 Z= 0.126 Angle : 0.588 12.694 18400 Z= 0.336 Chirality : 0.040 0.263 2097 Planarity : 0.004 0.040 1325 Dihedral : 31.683 175.224 4008 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.76 % Allowed : 10.88 % Favored : 87.36 % 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: 2.64 (0.30), residues: 735 helix: 2.40 (0.21), residues: 545 sheet: None (None), residues: 0 loop : -0.18 (0.42), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 92 TYR 0.018 0.001 TYR H 80 PHE 0.009 0.001 PHE G 25 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.13 (12700) covalent geometry : angle 0.58805 / 0.34 (18400) hydrogen bonds : bond 0.04078 / 2.70 ( 733) hydrogen bonds : angle 2.68795 / 1.93 ( 1854) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.278 Fit side-chains REVERT: A 56 LYS cc_start: 0.7286 (ttpt) cc_final: 0.6257 (mttt) REVERT: C 72 ASP cc_start: 0.7285 (m-30) cc_final: 0.6995 (m-30) REVERT: C 74 LYS cc_start: 0.7455 (mmmm) cc_final: 0.7063 (mtmm) REVERT: E 90 MET cc_start: 0.7742 (tpp) cc_final: 0.7473 (mmm) outliers start: 11 outliers final: 10 residues processed: 60 average time/residue: 0.1024 time to fit residues: 8.9812 Evaluate side-chains 64 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 86 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 36 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 chunk 26 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 chunk 94 optimal weight: 9.9990 chunk 7 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 25 ASN G 38 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.187304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.125046 restraints weight = 13285.048| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.64 r_work: 0.3243 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12700 Z= 0.138 Angle : 0.592 13.068 18400 Z= 0.337 Chirality : 0.040 0.263 2097 Planarity : 0.004 0.041 1325 Dihedral : 31.670 175.063 4008 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.76 % Allowed : 11.20 % Favored : 87.04 % 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: 2.64 (0.30), residues: 735 helix: 2.41 (0.21), residues: 545 sheet: None (None), residues: 0 loop : -0.21 (0.42), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 92 TYR 0.024 0.001 TYR H 80 PHE 0.009 0.001 PHE G 25 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.14 (12700) covalent geometry : angle 0.59215 / 0.34 (18400) hydrogen bonds : bond 0.04109 / 2.73 ( 733) hydrogen bonds : angle 2.68891 / 1.93 ( 1854) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.302 Fit side-chains REVERT: A 56 LYS cc_start: 0.7253 (ttpt) cc_final: 0.6217 (mttt) REVERT: C 72 ASP cc_start: 0.7267 (m-30) cc_final: 0.6978 (m-30) REVERT: C 74 LYS cc_start: 0.7423 (mmmm) cc_final: 0.7046 (mtmm) REVERT: E 90 MET cc_start: 0.7715 (tpp) cc_final: 0.7445 (mmm) outliers start: 11 outliers final: 11 residues processed: 57 average time/residue: 0.1064 time to fit residues: 8.8622 Evaluate side-chains 63 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 86 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 54 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 80 optimal weight: 20.0000 chunk 0 optimal weight: 8.9990 chunk 2 optimal weight: 0.0970 chunk 36 optimal weight: 0.1980 chunk 4 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 94 ASN F 25 ASN G 31 HIS G 38 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.187661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.125533 restraints weight = 13275.830| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.64 r_work: 0.3252 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12700 Z= 0.130 Angle : 0.585 13.198 18400 Z= 0.335 Chirality : 0.040 0.261 2097 Planarity : 0.004 0.041 1325 Dihedral : 31.638 174.837 4008 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.60 % Allowed : 11.52 % Favored : 86.88 % 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 are not related in a simple way. whole: 2.72 (0.30), residues: 735 helix: 2.46 (0.21), residues: 545 sheet: None (None), residues: 0 loop : -0.18 (0.42), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 92 TYR 0.035 0.001 TYR H 80 PHE 0.009 0.001 PHE A 67 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.13 (12700) covalent geometry : angle 0.58505 / 0.33 (18400) hydrogen bonds : bond 0.04059 / 2.69 ( 733) hydrogen bonds : angle 2.66564 / 1.91 ( 1854) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1890.78 seconds wall clock time: 33 minutes 3.23 seconds (1983.23 seconds total)