Starting phenix.real_space_refine on Fri Jul 3 01:59:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9be5_44470/07_2026/9be5_44470.cif Found real_map, /net/cci-nas-00/data/ceres_data/9be5_44470/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9be5_44470/07_2026/9be5_44470.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9be5_44470/07_2026/9be5_44470.map" model { file = "/net/cci-nas-00/data/ceres_data/9be5_44470/07_2026/9be5_44470.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9be5_44470/07_2026/9be5_44470.cif" } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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: 2.15, per 1000 atoms: 0.18 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: 0.64 Conformation dependent library (CDL) restraints added in 216.1 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: 1.64 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: 1.82 Time building geometry restraints manager: 0.98 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: 17075 1.42 - 2.85: 1251 2.85 - 4.27: 59 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: 2.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.590 Find NCS groups from input model: 0.080 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:0.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.970 ------------------------------------------------------------------------------- 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 : 0.746 7.123 18400 Z= 0.663 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 0.74555 / 0.66 (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 : 0.187 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: 0.1083 time to fit residues: 9.6702 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 : 0.289 ------------------------------------------------------------------------------- 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 = 0.4251 r_free = 0.4251 target = 0.186675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.122297 restraints weight = 13748.847| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 1.63 r_work: 0.3301 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.0800 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= 0.158 Angle : 0.629 10.347 18400 Z= 0.374 Chirality : 0.043 0.264 2097 Planarity : 0.004 0.043 1325 Dihedral : 31.454 177.316 4008 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.12 % Allowed : 4.00 % Favored : 94.88 % 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: 2.05 (0.30), residues: 735 helix: 2.01 (0.21), residues: 547 sheet: None (None), residues: 0 loop : -0.57 (0.41), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 116 TYR 0.018 0.002 TYR H 118 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 0.00271 / 0.16 (12700) covalent geometry : angle 0.62855 / 0.37 (18400) hydrogen bonds : bond 0.05131 / 3.38 ( 733) hydrogen bonds : angle 3.05374 / 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 : 0.225 Fit side-chains REVERT: E 81 ASP cc_start: 0.8407 (t0) cc_final: 0.8113 (t0) outliers start: 7 outliers final: 5 residues processed: 64 average time/residue: 0.1191 time to fit residues: 10.5971 Evaluate side-chains 58 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.205 ------------------------------------------------------------------------------- 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: 0.8980 chunk 57 optimal weight: 1.9990 chunk 53 optimal weight: 0.0770 chunk 14 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 overall best weight: 1.1542 ------------------------------------------------------------------------------- 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 = 0.4231 r_free = 0.4231 target = 0.184703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.119456 restraints weight = 13890.310| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 1.62 r_work: 0.3255 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1153 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= 0.173 Angle : 0.622 10.825 18400 Z= 0.363 Chirality : 0.043 0.276 2097 Planarity : 0.004 0.043 1325 Dihedral : 31.736 178.265 4008 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.44 % Allowed : 5.60 % Favored : 92.96 % 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: 2.09 (0.30), residues: 735 helix: 2.04 (0.21), residues: 547 sheet: None (None), residues: 0 loop : -0.57 (0.41), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 83 TYR 0.015 0.001 TYR C 57 PHE 0.015 0.002 PHE C 25 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.17 (12700) covalent geometry : angle 0.62240 / 0.36 (18400) hydrogen bonds : bond 0.04807 / 3.18 ( 733) hydrogen bonds : angle 2.96058 / 2.12 ( 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 69 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.296 Fit side-chains REVERT: C 74 LYS cc_start: 0.7731 (mmmt) cc_final: 0.7222 (mtmm) REVERT: D 48 ASP cc_start: 0.7381 (t70) cc_final: 0.7154 (t0) REVERT: E 81 ASP cc_start: 0.8556 (t0) cc_final: 0.8170 (t0) outliers start: 9 outliers final: 7 residues processed: 63 average time/residue: 0.1025 time to fit residues: 9.3392 Evaluate side-chains 63 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.194 ------------------------------------------------------------------------------- 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: 1.9990 chunk 24 optimal weight: 0.9990 chunk 72 optimal weight: 20.0000 chunk 1 optimal weight: 0.9980 chunk 26 optimal weight: 0.0470 chunk 78 optimal weight: 9.9990 chunk 87 optimal weight: 20.0000 chunk 10 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 overall best weight: 0.9882 ------------------------------------------------------------------------------- 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 = 0.4301 r_free = 0.4301 target = 0.189480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.125449 restraints weight = 14152.317| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.65 r_work: 0.3342 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12700 Z= 0.156 Angle : 0.605 12.996 18400 Z= 0.352 Chirality : 0.042 0.272 2097 Planarity : 0.004 0.042 1325 Dihedral : 31.793 179.560 4008 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.44 % Allowed : 7.52 % Favored : 91.04 % 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: 2.22 (0.30), residues: 735 helix: 2.13 (0.21), residues: 547 sheet: None (None), residues: 0 loop : -0.51 (0.42), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 83 TYR 0.014 0.001 TYR C 57 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 0.00297 / 0.16 (12700) covalent geometry : angle 0.60466 / 0.35 (18400) hydrogen bonds : bond 0.04443 / 2.93 ( 733) hydrogen bonds : angle 2.84215 / 2.04 ( 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 63 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.179 Fit side-chains REVERT: A 56 LYS cc_start: 0.7528 (ttpt) cc_final: 0.6551 (mttt) REVERT: C 33 LEU cc_start: 0.8457 (mt) cc_final: 0.8239 (mt) REVERT: C 72 ASP cc_start: 0.7469 (m-30) cc_final: 0.7166 (m-30) REVERT: D 48 ASP cc_start: 0.7575 (t70) cc_final: 0.7306 (t0) REVERT: E 81 ASP cc_start: 0.8556 (t0) cc_final: 0.8135 (t0) outliers start: 9 outliers final: 8 residues processed: 57 average time/residue: 0.0868 time to fit residues: 7.2730 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 : 0.286 ------------------------------------------------------------------------------- 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: 2.9990 chunk 54 optimal weight: 2.9990 chunk 83 optimal weight: 20.0000 chunk 42 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 87 optimal weight: 20.0000 chunk 46 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 25 optimal weight: 0.5980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.4200 r_free = 0.4200 target = 0.185902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.123159 restraints weight = 13339.653| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.65 r_work: 0.3193 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1575 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= 0.158 Angle : 0.601 10.903 18400 Z= 0.348 Chirality : 0.042 0.265 2097 Planarity : 0.004 0.041 1325 Dihedral : 31.885 178.746 4008 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.76 % Allowed : 8.32 % Favored : 89.92 % 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: 2.30 (0.30), residues: 735 helix: 2.20 (0.21), residues: 544 sheet: None (None), residues: 0 loop : -0.45 (0.42), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 92 TYR 0.023 0.002 TYR H 118 PHE 0.018 0.002 PHE C 25 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.16 (12700) covalent geometry : angle 0.60081 / 0.35 (18400) hydrogen bonds : bond 0.04395 / 2.90 ( 733) hydrogen bonds : angle 2.82514 / 2.03 ( 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 68 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.289 Fit side-chains REVERT: A 56 LYS cc_start: 0.7196 (ttpt) cc_final: 0.6153 (mttt) REVERT: C 74 LYS cc_start: 0.7567 (mmmm) cc_final: 0.7084 (mtmm) REVERT: E 81 ASP cc_start: 0.8607 (t0) cc_final: 0.8169 (t0) REVERT: E 90 MET cc_start: 0.7717 (tpp) cc_final: 0.7206 (mmt) outliers start: 11 outliers final: 8 residues processed: 62 average time/residue: 0.0859 time to fit residues: 7.9532 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 : 0.183 ------------------------------------------------------------------------------- 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 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 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: 0.0670 chunk 70 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 chunk 87 optimal weight: 20.0000 chunk 17 optimal weight: 4.9990 chunk 92 optimal weight: 10.0000 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4214 r_free = 0.4214 target = 0.187345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.124978 restraints weight = 13366.463| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.65 r_work: 0.3234 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1723 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= 0.137 Angle : 0.581 13.594 18400 Z= 0.339 Chirality : 0.040 0.255 2097 Planarity : 0.004 0.041 1325 Dihedral : 31.782 177.424 4008 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.60 % Allowed : 9.92 % Favored : 88.48 % 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: 2.55 (0.30), residues: 735 helix: 2.36 (0.21), residues: 545 sheet: None (None), residues: 0 loop : -0.30 (0.42), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 92 TYR 0.012 0.001 TYR C 57 PHE 0.009 0.001 PHE E 67 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.14 (12700) covalent geometry : angle 0.58109 / 0.34 (18400) hydrogen bonds : bond 0.04141 / 2.73 ( 733) hydrogen bonds : angle 2.68883 / 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 64 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.267 Fit side-chains REVERT: A 56 LYS cc_start: 0.7238 (ttpt) cc_final: 0.6199 (mttt) REVERT: C 72 ASP cc_start: 0.7252 (m-30) cc_final: 0.6931 (m-30) REVERT: C 74 LYS cc_start: 0.7389 (mmmm) cc_final: 0.6982 (mtmm) REVERT: E 81 ASP cc_start: 0.8610 (t0) cc_final: 0.8174 (t0) REVERT: E 90 MET cc_start: 0.7709 (tpp) cc_final: 0.7417 (mmm) outliers start: 10 outliers final: 9 residues processed: 58 average time/residue: 0.1102 time to fit residues: 8.9991 Evaluate side-chains 60 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.266 ------------------------------------------------------------------------------- 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 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 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: 0.9980 chunk 59 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 98 optimal weight: 20.0000 chunk 86 optimal weight: 20.0000 chunk 14 optimal weight: 0.6980 chunk 94 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 96 optimal weight: 20.0000 chunk 29 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4190 r_free = 0.4190 target = 0.184685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.121781 restraints weight = 13359.831| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.64 r_work: 0.3193 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12700 Z= 0.175 Angle : 0.617 13.431 18400 Z= 0.351 Chirality : 0.042 0.256 2097 Planarity : 0.004 0.040 1325 Dihedral : 31.920 177.042 4008 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % 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: 2.27 (0.30), residues: 735 helix: 2.16 (0.21), residues: 544 sheet: None (None), residues: 0 loop : -0.40 (0.42), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 92 TYR 0.014 0.001 TYR C 57 PHE 0.015 0.002 PHE C 25 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.18 (12700) covalent geometry : angle 0.61749 / 0.35 (18400) hydrogen bonds : bond 0.04410 / 2.93 ( 733) hydrogen bonds : angle 2.83654 / 2.04 ( 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 69 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.274 Fit side-chains REVERT: A 56 LYS cc_start: 0.7335 (ttpt) cc_final: 0.6301 (mttt) REVERT: C 72 ASP cc_start: 0.7308 (m-30) cc_final: 0.6978 (m-30) REVERT: C 74 LYS cc_start: 0.7544 (mmmm) cc_final: 0.7106 (mtmm) REVERT: E 81 ASP cc_start: 0.8607 (t0) cc_final: 0.8211 (t0) REVERT: E 90 MET cc_start: 0.7780 (tpp) cc_final: 0.7510 (mmm) REVERT: G 19 SER cc_start: 0.7565 (m) cc_final: 0.7063 (p) outliers start: 11 outliers final: 11 residues processed: 63 average time/residue: 0.1029 time to fit residues: 9.4444 Evaluate side-chains 68 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 108 LEU 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 D residue 93 THR Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain F residue 30 THR 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: 0.5980 chunk 93 optimal weight: 9.9990 chunk 70 optimal weight: 0.8980 chunk 76 optimal weight: 20.0000 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: 0.1980 chunk 65 optimal weight: 2.9990 chunk 91 optimal weight: 10.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4214 r_free = 0.4214 target = 0.187224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.124862 restraints weight = 13299.765| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.64 r_work: 0.3254 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1936 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= 0.134 Angle : 0.577 12.589 18400 Z= 0.335 Chirality : 0.040 0.245 2097 Planarity : 0.004 0.041 1325 Dihedral : 31.771 175.788 4008 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.60 % Allowed : 12.16 % Favored : 86.24 % 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: 2.62 (0.30), residues: 735 helix: 2.40 (0.21), residues: 545 sheet: None (None), residues: 0 loop : -0.22 (0.42), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 92 TYR 0.012 0.001 TYR G 57 PHE 0.008 0.001 PHE E 67 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.13 (12700) covalent geometry : angle 0.57660 / 0.34 (18400) hydrogen bonds : bond 0.04087 / 2.70 ( 733) hydrogen bonds : angle 2.68481 / 1.93 ( 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 69 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.226 Fit side-chains REVERT: A 56 LYS cc_start: 0.7297 (ttpt) cc_final: 0.6272 (mttt) REVERT: C 72 ASP cc_start: 0.7253 (m-30) cc_final: 0.6933 (m-30) REVERT: C 74 LYS cc_start: 0.7502 (mmmm) cc_final: 0.7075 (mtmm) REVERT: E 81 ASP cc_start: 0.8565 (t0) cc_final: 0.8183 (t0) REVERT: E 90 MET cc_start: 0.7741 (tpp) cc_final: 0.7475 (mmm) REVERT: G 19 SER cc_start: 0.7580 (m) cc_final: 0.7101 (p) outliers start: 10 outliers final: 9 residues processed: 64 average time/residue: 0.0959 time to fit residues: 8.8912 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 : 0.177 ------------------------------------------------------------------------------- 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 32 GLU 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 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: 10.0000 chunk 35 optimal weight: 2.9990 chunk 86 optimal weight: 20.0000 chunk 44 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 94 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 45 optimal weight: 0.0570 chunk 83 optimal weight: 20.0000 chunk 25 optimal weight: 0.8980 overall best weight: 0.9502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 25 ASN G 31 HIS ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.186117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.123578 restraints weight = 13213.670| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.64 r_work: 0.3228 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12700 Z= 0.151 Angle : 0.591 12.963 18400 Z= 0.339 Chirality : 0.041 0.245 2097 Planarity : 0.004 0.041 1325 Dihedral : 31.810 175.341 4008 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.76 % Allowed : 12.32 % Favored : 85.92 % 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: 2.50 (0.30), residues: 735 helix: 2.31 (0.21), residues: 544 sheet: None (None), residues: 0 loop : -0.26 (0.42), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 92 TYR 0.013 0.001 TYR C 57 PHE 0.012 0.001 PHE G 25 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.15 (12700) covalent geometry : angle 0.59101 / 0.34 (18400) hydrogen bonds : bond 0.04208 / 2.79 ( 733) hydrogen bonds : angle 2.74630 / 1.97 ( 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 : 0.225 Fit side-chains REVERT: A 56 LYS cc_start: 0.7288 (ttpt) cc_final: 0.6259 (mttt) REVERT: C 72 ASP cc_start: 0.7260 (m-30) cc_final: 0.6954 (m-30) REVERT: C 74 LYS cc_start: 0.7518 (mmmm) cc_final: 0.7083 (mtmm) REVERT: E 81 ASP cc_start: 0.8580 (t0) cc_final: 0.8206 (t0) REVERT: E 90 MET cc_start: 0.7694 (tpp) cc_final: 0.7418 (mmm) REVERT: G 19 SER cc_start: 0.7555 (m) cc_final: 0.7048 (p) outliers start: 11 outliers final: 11 residues processed: 60 average time/residue: 0.1017 time to fit residues: 8.8248 Evaluate side-chains 66 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.283 ------------------------------------------------------------------------------- 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 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 F residue 30 THR 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: 0.0870 chunk 74 optimal weight: 10.9990 chunk 26 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 94 optimal weight: 10.0000 chunk 7 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 25 ASN G 38 ASN H 44 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.187060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.124764 restraints weight = 13288.880| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.65 r_work: 0.3241 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2063 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= 0.132 Angle : 0.578 12.558 18400 Z= 0.334 Chirality : 0.040 0.241 2097 Planarity : 0.004 0.040 1325 Dihedral : 31.760 175.123 4008 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.60 % Allowed : 12.64 % Favored : 85.76 % 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: 2.62 (0.30), residues: 735 helix: 2.39 (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 0.005 0.000 ARG F 92 TYR 0.013 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 0.00233 / 0.13 (12700) covalent geometry : angle 0.57808 / 0.33 (18400) hydrogen bonds : bond 0.04080 / 2.70 ( 733) hydrogen bonds : angle 2.69260 / 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 65 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.297 Fit side-chains REVERT: A 56 LYS cc_start: 0.7273 (ttpt) cc_final: 0.6250 (mttt) REVERT: C 72 ASP cc_start: 0.7239 (m-30) cc_final: 0.6938 (m-30) REVERT: C 74 LYS cc_start: 0.7502 (mmmm) cc_final: 0.7087 (mtmm) REVERT: E 81 ASP cc_start: 0.8567 (t0) cc_final: 0.8198 (t0) REVERT: E 90 MET cc_start: 0.7671 (tpp) cc_final: 0.7398 (mmm) REVERT: G 19 SER cc_start: 0.7546 (m) cc_final: 0.7047 (p) outliers start: 10 outliers final: 10 residues processed: 59 average time/residue: 0.1010 time to fit residues: 8.8569 Evaluate side-chains 63 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.293 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 62 optimal weight: 0.2980 chunk 80 optimal weight: 20.0000 chunk 0 optimal weight: 7.9990 chunk 2 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 56 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN F 25 ASN G 38 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.187068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.124839 restraints weight = 13279.902| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.64 r_work: 0.3243 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2099 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= 0.137 Angle : 0.580 12.515 18400 Z= 0.335 Chirality : 0.040 0.241 2097 Planarity : 0.004 0.040 1325 Dihedral : 31.744 174.858 4008 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.76 % Allowed : 12.48 % Favored : 85.76 % 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: 2.62 (0.30), residues: 735 helix: 2.39 (0.21), residues: 545 sheet: None (None), residues: 0 loop : -0.22 (0.42), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 92 TYR 0.028 0.001 TYR H 80 PHE 0.009 0.001 PHE A 67 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.14 (12700) covalent geometry : angle 0.57977 / 0.34 (18400) hydrogen bonds : bond 0.04087 / 2.71 ( 733) hydrogen bonds : angle 2.69185 / 1.93 ( 1854) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1968.85 seconds wall clock time: 34 minutes 25.40 seconds (2065.40 seconds total)