Starting phenix.real_space_refine on Wed Aug 5 19:29:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q16_18061/08_2026/8q16_18061.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q16_18061/08_2026/8q16_18061.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8q16_18061/08_2026/8q16_18061.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q16_18061/08_2026/8q16_18061.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8q16_18061/08_2026/8q16_18061.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q16_18061/08_2026/8q16_18061.map" } resolution = 3.6 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= 0.002 sd= 0.052 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 294 5.49 5 S 13 5.16 5 C 6516 2.51 5 N 2175 2.21 5 O 2775 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s 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: 11773 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 776 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "B" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 763 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "C" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "D" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 710 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 87} Chain: "E" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 776 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "F" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 737 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "G" Number of atoms: 628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 628 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "H" Number of atoms: 623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 623 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "I" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Time building chain proxies: 2.47, per 1000 atoms: 0.21 Number of scatterers: 11773 At special positions: 0 Unit cell: (74.881, 124.317, 118.501, 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 13 16.00 P 294 15.00 O 2775 8.00 N 2175 7.00 C 6516 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: 0.82 Conformation dependent library (CDL) restraints added in 222.4 milliseconds 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1362 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 10 sheets defined 75.7% alpha, 2.7% beta 147 base pairs and 240 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'A' and resid 18 through 24 Processing helix chain 'A' and resid 28 through 39 Processing helix chain 'A' and resid 47 through 75 removed outlier: 4.585A pdb=" N VAL A 51 " --> pdb=" O ALA A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 92 removed outlier: 3.575A pdb=" N ASP A 92 " --> pdb=" O ALA A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 99 Processing helix chain 'A' and resid 114 through 118 Processing helix chain 'B' and resid 19 through 24 Processing helix chain 'B' and resid 28 through 39 Processing helix chain 'B' and resid 48 through 75 Processing helix chain 'B' and resid 81 through 92 Processing helix chain 'B' and resid 92 through 99 Processing helix chain 'C' and resid 66 through 78 Processing helix chain 'C' and resid 84 through 113 Processing helix chain 'C' and resid 119 through 131 Processing helix chain 'C' and resid 133 through 152 removed outlier: 3.651A pdb=" N SER C 152 " --> pdb=" O THR C 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 78 Processing helix chain 'D' and resid 84 through 113 Processing helix chain 'D' and resid 119 through 131 Processing helix chain 'D' and resid 133 through 153 Processing helix chain 'E' and resid 45 through 58 removed outlier: 3.647A pdb=" N LEU E 49 " --> pdb=" O GLY E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 80 removed outlier: 4.057A pdb=" N ASP E 78 " --> pdb=" O GLU E 74 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N PHE E 79 " --> pdb=" O ILE E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 115 Processing helix chain 'E' and resid 121 through 133 Processing helix chain 'F' and resid 46 through 58 Processing helix chain 'F' and resid 64 through 80 removed outlier: 4.016A pdb=" N ASP F 78 " --> pdb=" O GLU F 74 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N PHE F 79 " --> pdb=" O ILE F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 115 Processing helix chain 'F' and resid 121 through 132 Processing helix chain 'G' and resid 25 through 30 removed outlier: 4.006A pdb=" N GLN G 28 " --> pdb=" O GLY G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 31 through 42 Processing helix chain 'G' and resid 50 through 77 removed outlier: 3.804A pdb=" N GLU G 54 " --> pdb=" O LEU G 50 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ARG G 56 " --> pdb=" O TYR G 52 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 94 removed outlier: 3.537A pdb=" N GLN G 94 " --> pdb=" O ALA G 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 30 removed outlier: 3.719A pdb=" N GLN H 28 " --> pdb=" O GLY H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 31 through 42 removed outlier: 3.535A pdb=" N ILE H 35 " --> pdb=" O ALA H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 50 through 77 removed outlier: 3.963A pdb=" N GLU H 54 " --> pdb=" O LEU H 50 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 94 Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 45 removed outlier: 7.316A pdb=" N ARG A 44 " --> pdb=" O ILE D 118 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 80 Processing sheet with id=AA3, first strand: chain 'A' and resid 103 through 104 removed outlier: 7.187A pdb=" N THR A 103 " --> pdb=" O TYR H 99 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 44 through 45 removed outlier: 7.250A pdb=" N ARG B 44 " --> pdb=" O ILE C 118 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 79 through 80 Processing sheet with id=AA6, first strand: chain 'B' and resid 103 through 104 removed outlier: 6.942A pdb=" N THR B 103 " --> pdb=" O TYR G 99 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 84 through 85 removed outlier: 6.777A pdb=" N ARG E 84 " --> pdb=" O VAL H 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 119 through 120 Processing sheet with id=AA9, first strand: chain 'F' and resid 84 through 85 removed outlier: 7.022A pdb=" N ARG F 84 " --> pdb=" O VAL G 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'F' and resid 119 through 120 406 hydrogen bonds defined for protein. 1200 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 376 hydrogen bonds 748 hydrogen bond angles 0 basepair planarities 147 basepair parallelities 240 stacking parallelities Total time for adding SS restraints: 1.92 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1894 1.33 - 1.45: 4330 1.45 - 1.57: 5749 1.57 - 1.68: 586 1.68 - 1.80: 24 Bond restraints: 12583 Sorted by residual: bond pdb=" C3' DT J 14 " pdb=" C2' DT J 14 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.30e+01 bond pdb=" C3' DT J 30 " pdb=" C2' DT J 30 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.07e+01 bond pdb=" C3' DT J -6 " pdb=" C2' DT J -6 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.02e+01 bond pdb=" C3' DG I -22 " pdb=" C2' DG I -22 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.54e+00 bond pdb=" C3' DT I -29 " pdb=" C2' DT I -29 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.35e+00 ... (remaining 12578 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.11: 16133 1.11 - 2.22: 1694 2.22 - 3.33: 404 3.33 - 4.44: 13 4.44 - 5.55: 8 Bond angle restraints: 18252 Sorted by residual: angle pdb=" N3 DT I -23 " pdb=" C4 DT I -23 " pdb=" O4 DT I -23 " ideal model delta sigma weight residual 119.90 122.63 -2.73 6.00e-01 2.78e+00 2.07e+01 angle pdb=" N3 DT I -17 " pdb=" C4 DT I -17 " pdb=" O4 DT I -17 " ideal model delta sigma weight residual 119.90 122.63 -2.73 6.00e-01 2.78e+00 2.07e+01 angle pdb=" N3 DT I -39 " pdb=" C4 DT I -39 " pdb=" O4 DT I -39 " ideal model delta sigma weight residual 119.90 122.60 -2.70 6.00e-01 2.78e+00 2.03e+01 angle pdb=" N3 DT I 33 " pdb=" C4 DT I 33 " pdb=" O4 DT I 33 " ideal model delta sigma weight residual 119.90 122.58 -2.68 6.00e-01 2.78e+00 2.00e+01 angle pdb=" N3 DT I 31 " pdb=" C4 DT I 31 " pdb=" O4 DT I 31 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.94e+01 ... (remaining 18247 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 5560 35.95 - 71.90: 1215 71.90 - 107.85: 8 107.85 - 143.80: 2 143.80 - 179.75: 1 Dihedral angle restraints: 6786 sinusoidal: 4674 harmonic: 2112 Sorted by residual: dihedral pdb=" C4' DT I -59 " pdb=" C3' DT I -59 " pdb=" O3' DT I -59 " pdb=" P DC I -58 " ideal model delta sinusoidal sigma weight residual -140.00 39.75 -179.75 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG I 20 " pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DG I 21 " ideal model delta sinusoidal sigma weight residual 220.00 81.92 138.08 1 3.50e+01 8.16e-04 1.37e+01 dihedral pdb=" C4' DC I 52 " pdb=" C3' DC I 52 " pdb=" O3' DC I 52 " pdb=" P DC I 53 " ideal model delta sinusoidal sigma weight residual 220.00 86.16 133.84 1 3.50e+01 8.16e-04 1.33e+01 ... (remaining 6783 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1199 0.034 - 0.067: 592 0.067 - 0.101: 197 0.101 - 0.134: 97 0.134 - 0.168: 2 Chirality restraints: 2087 Sorted by residual: chirality pdb=" C3' DG I 10 " pdb=" C4' DG I 10 " pdb=" O3' DG I 10 " pdb=" C2' DG I 10 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 7.02e-01 chirality pdb=" C3' DT I -59 " pdb=" C4' DT I -59 " pdb=" O3' DT I -59 " pdb=" C2' DT I -59 " both_signs ideal model delta sigma weight residual False -2.73 -2.60 -0.14 2.00e-01 2.50e+01 4.59e-01 chirality pdb=" CA ILE C 118 " pdb=" N ILE C 118 " pdb=" C ILE C 118 " pdb=" CB ILE C 118 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.46e-01 ... (remaining 2084 not shown) Planarity restraints: 1280 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA I -13 " 0.021 2.00e-02 2.50e+03 9.23e-03 2.34e+00 pdb=" N9 DA I -13 " -0.019 2.00e-02 2.50e+03 pdb=" C8 DA I -13 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DA I -13 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DA I -13 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DA I -13 " 0.003 2.00e-02 2.50e+03 pdb=" N6 DA I -13 " 0.008 2.00e-02 2.50e+03 pdb=" N1 DA I -13 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA I -13 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DA I -13 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DA I -13 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 47 " -0.022 2.00e-02 2.50e+03 8.94e-03 2.20e+00 pdb=" N9 DA I 47 " 0.016 2.00e-02 2.50e+03 pdb=" C8 DA I 47 " 0.004 2.00e-02 2.50e+03 pdb=" N7 DA I 47 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DA I 47 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DA I 47 " -0.003 2.00e-02 2.50e+03 pdb=" N6 DA I 47 " -0.009 2.00e-02 2.50e+03 pdb=" N1 DA I 47 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 47 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DA I 47 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DA I 47 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 131 " -0.024 5.00e-02 4.00e+02 3.66e-02 2.14e+00 pdb=" N PRO D 132 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO D 132 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 132 " -0.020 5.00e-02 4.00e+02 ... (remaining 1277 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 746 2.72 - 3.27: 10591 3.27 - 3.81: 23042 3.81 - 4.36: 26420 4.36 - 4.90: 38709 Nonbonded interactions: 99508 Sorted by model distance: nonbonded pdb=" N2 DG I -10 " pdb=" O2 DC J 10 " model vdw 2.181 2.496 nonbonded pdb=" OG1 THR E 119 " pdb=" NH1 ARG H 46 " model vdw 2.230 3.120 nonbonded pdb=" OG1 THR G 74 " pdb=" OD2 ASP G 86 " model vdw 2.294 3.040 nonbonded pdb=" O SER A 18 " pdb=" OG SER A 21 " model vdw 2.295 3.040 nonbonded pdb=" NH2 ARG B 34 " pdb=" OE1 GLU C 64 " model vdw 2.307 3.120 ... (remaining 99503 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 18 through 118) selection = chain 'B' } ncs_group { reference = (chain 'C' and resid 63 through 152) selection = (chain 'D' and resid 63 through 152) } ncs_group { reference = (chain 'E' and resid 45 through 134) selection = (chain 'F' and resid 45 through 134) } ncs_group { reference = (chain 'G' and resid 25 through 102) 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.670 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.860 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 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 0.049 12583 Z= 0.540 Angle : 0.728 5.553 18252 Z= 0.651 Chirality : 0.046 0.168 2087 Planarity : 0.004 0.037 1280 Dihedral : 26.753 179.755 5424 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.50 % Allowed : 2.50 % Favored : 97.00 % 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: 2.53 (0.31), residues: 716 helix: 2.56 (0.22), residues: 528 sheet: None (None), residues: 0 loop : -1.03 (0.40), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 117 TYR 0.009 0.001 TYR B 59 PHE 0.009 0.001 PHE E 42 HIS 0.002 0.001 HIS H 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00632 / 0.54 (12583) covalent geometry : angle 0.72793 / 0.65 (18252) hydrogen bonds : bond 0.11397 / 7.77 ( 782) hydrogen bonds : angle 3.74409 / 2.70 ( 1948) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 117 time to evaluate : 0.299 Fit side-chains REVERT: A 25 LEU cc_start: 0.8403 (mt) cc_final: 0.7919 (mt) REVERT: A 26 GLN cc_start: 0.8150 (mm-40) cc_final: 0.7809 (mm110) REVERT: B 106 SER cc_start: 0.9147 (m) cc_final: 0.8763 (t) REVERT: B 112 ASN cc_start: 0.8459 (t0) cc_final: 0.7993 (p0) REVERT: D 75 LYS cc_start: 0.8783 (mmtt) cc_final: 0.8543 (mmtm) REVERT: D 88 MET cc_start: 0.8337 (tpp) cc_final: 0.7646 (tpp) REVERT: F 74 GLU cc_start: 0.7919 (tt0) cc_final: 0.7672 (tt0) REVERT: H 98 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8628 (tt) outliers start: 3 outliers final: 0 residues processed: 119 average time/residue: 0.1716 time to fit residues: 25.0795 Evaluate side-chains 80 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 79 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 98 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 40.0000 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.3980 chunk 45 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 124 GLN D 78 HIS D 124 GLN E 69 GLN ** G 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.155870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.102669 restraints weight = 15577.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.105085 restraints weight = 10423.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.106641 restraints weight = 8233.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.107490 restraints weight = 7250.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.108032 restraints weight = 6786.132| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12583 Z= 0.149 Angle : 0.600 6.711 18252 Z= 0.365 Chirality : 0.042 0.235 2087 Planarity : 0.004 0.046 1280 Dihedral : 30.329 178.683 4011 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.17 % Allowed : 9.50 % Favored : 89.33 % 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: 2.92 (0.31), residues: 716 helix: 2.79 (0.22), residues: 537 sheet: None (None), residues: 0 loop : -0.88 (0.40), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 53 TYR 0.009 0.001 TYR B 59 PHE 0.009 0.001 PHE E 42 HIS 0.004 0.001 HIS G 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.15 (12583) covalent geometry : angle 0.59967 / 0.37 (18252) hydrogen bonds : bond 0.05726 / 4.02 ( 782) hydrogen bonds : angle 3.00279 / 2.21 ( 1948) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.191 Fit side-chains REVERT: A 25 LEU cc_start: 0.8309 (mt) cc_final: 0.8065 (mp) REVERT: A 26 GLN cc_start: 0.7964 (mm-40) cc_final: 0.7610 (mm110) REVERT: A 76 LYS cc_start: 0.8973 (tppt) cc_final: 0.8628 (mttp) REVERT: B 106 SER cc_start: 0.8982 (m) cc_final: 0.8736 (t) REVERT: D 88 MET cc_start: 0.8260 (tpp) cc_final: 0.7489 (tpp) REVERT: F 53 ARG cc_start: 0.8202 (ttm-80) cc_final: 0.7925 (mtt90) outliers start: 7 outliers final: 6 residues processed: 86 average time/residue: 0.1503 time to fit residues: 16.4939 Evaluate side-chains 83 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 98 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 65 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 52 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 9 optimal weight: 10.0000 chunk 47 optimal weight: 0.9980 chunk 84 optimal weight: 20.0000 chunk 20 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 76 HIS ** 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 = 0.3939 r_free = 0.3939 target = 0.155966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.102833 restraints weight = 15776.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.105157 restraints weight = 10452.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.106652 restraints weight = 8275.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.107272 restraints weight = 7313.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.108016 restraints weight = 6898.218| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12583 Z= 0.146 Angle : 0.575 6.443 18252 Z= 0.350 Chirality : 0.040 0.236 2087 Planarity : 0.004 0.033 1280 Dihedral : 30.439 178.178 4011 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.00 % Allowed : 9.83 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.04 (0.31), residues: 716 helix: 2.89 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -0.89 (0.40), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 129 TYR 0.009 0.001 TYR B 59 PHE 0.010 0.001 PHE E 42 HIS 0.003 0.001 HIS F 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.15 (12583) covalent geometry : angle 0.57520 / 0.35 (18252) hydrogen bonds : bond 0.05234 / 3.70 ( 782) hydrogen bonds : angle 2.83196 / 2.09 ( 1948) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.234 Fit side-chains REVERT: A 26 GLN cc_start: 0.7974 (mm-40) cc_final: 0.7623 (mm110) REVERT: B 106 SER cc_start: 0.8978 (m) cc_final: 0.8742 (t) REVERT: C 75 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8693 (mmtm) REVERT: C 128 ARG cc_start: 0.8327 (mtt90) cc_final: 0.8100 (mtt90) REVERT: D 88 MET cc_start: 0.8220 (tpp) cc_final: 0.7470 (tpp) REVERT: H 94 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.7162 (mp10) outliers start: 12 outliers final: 8 residues processed: 86 average time/residue: 0.1360 time to fit residues: 15.1791 Evaluate side-chains 86 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 94 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 81 optimal weight: 20.0000 chunk 24 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 75 optimal weight: 10.9990 chunk 22 optimal weight: 3.9990 chunk 79 optimal weight: 10.0000 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 28 GLN G 76 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.156353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.103133 restraints weight = 15688.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.105545 restraints weight = 10473.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.107032 restraints weight = 8285.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.108012 restraints weight = 7296.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.108017 restraints weight = 6840.443| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 12583 Z= 0.140 Angle : 0.567 6.166 18252 Z= 0.344 Chirality : 0.040 0.238 2087 Planarity : 0.004 0.031 1280 Dihedral : 30.480 178.008 4009 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.00 % Allowed : 10.33 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.13 (0.31), residues: 716 helix: 2.96 (0.21), residues: 538 sheet: None (None), residues: 0 loop : -0.87 (0.40), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 53 TYR 0.009 0.001 TYR B 59 PHE 0.010 0.001 PHE E 42 HIS 0.003 0.001 HIS F 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.14 (12583) covalent geometry : angle 0.56692 / 0.34 (18252) hydrogen bonds : bond 0.05040 / 3.57 ( 782) hydrogen bonds : angle 2.73705 / 2.01 ( 1948) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.223 Fit side-chains REVERT: A 26 GLN cc_start: 0.7843 (mm-40) cc_final: 0.7510 (mm-40) REVERT: B 106 SER cc_start: 0.8982 (m) cc_final: 0.8744 (t) REVERT: C 75 LYS cc_start: 0.8967 (OUTLIER) cc_final: 0.8723 (mmtm) REVERT: C 100 GLU cc_start: 0.7731 (tp30) cc_final: 0.7500 (tp30) REVERT: D 88 MET cc_start: 0.8244 (tpp) cc_final: 0.7470 (tpp) REVERT: F 53 ARG cc_start: 0.8387 (ttm-80) cc_final: 0.7948 (mtt90) REVERT: H 94 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.7218 (mp10) outliers start: 12 outliers final: 7 residues processed: 90 average time/residue: 0.1412 time to fit residues: 16.3896 Evaluate side-chains 86 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 94 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 68 optimal weight: 0.4980 chunk 75 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 73 optimal weight: 20.0000 chunk 63 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 72 optimal weight: 20.0000 chunk 91 optimal weight: 10.0000 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.154691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.101551 restraints weight = 15741.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.104277 restraints weight = 11112.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.105185 restraints weight = 7944.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.105403 restraints weight = 8160.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.105416 restraints weight = 7345.011| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12583 Z= 0.173 Angle : 0.596 5.683 18252 Z= 0.353 Chirality : 0.041 0.239 2087 Planarity : 0.004 0.031 1280 Dihedral : 30.607 178.262 4009 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.33 % Allowed : 12.50 % Favored : 85.17 % 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: 2.95 (0.30), residues: 716 helix: 2.83 (0.21), residues: 538 sheet: None (None), residues: 0 loop : -0.96 (0.40), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 128 TYR 0.008 0.001 TYR B 59 PHE 0.010 0.001 PHE E 42 HIS 0.003 0.001 HIS H 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.17 (12583) covalent geometry : angle 0.59621 / 0.35 (18252) hydrogen bonds : bond 0.05262 / 3.70 ( 782) hydrogen bonds : angle 2.82709 / 2.09 ( 1948) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 0.282 Fit side-chains REVERT: A 26 GLN cc_start: 0.7896 (mm-40) cc_final: 0.7538 (mm-40) REVERT: B 106 SER cc_start: 0.9069 (m) cc_final: 0.8839 (t) REVERT: C 75 LYS cc_start: 0.9035 (OUTLIER) cc_final: 0.8806 (mmtm) REVERT: C 100 GLU cc_start: 0.7759 (tp30) cc_final: 0.7551 (tp30) REVERT: D 88 MET cc_start: 0.8315 (tpp) cc_final: 0.7485 (tpp) REVERT: H 94 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7290 (mp10) outliers start: 14 outliers final: 9 residues processed: 85 average time/residue: 0.1405 time to fit residues: 15.4955 Evaluate side-chains 85 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 94 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 66 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 84 optimal weight: 20.0000 chunk 26 optimal weight: 0.9980 chunk 97 optimal weight: 50.0000 chunk 4 optimal weight: 0.9980 chunk 74 optimal weight: 20.0000 chunk 18 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.155967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.102789 restraints weight = 15712.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.105095 restraints weight = 10419.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.106515 restraints weight = 8273.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.107457 restraints weight = 7323.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.107881 restraints weight = 6863.275| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 12583 Z= 0.141 Angle : 0.563 5.657 18252 Z= 0.340 Chirality : 0.039 0.239 2087 Planarity : 0.004 0.036 1280 Dihedral : 30.567 177.873 4009 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.00 % Allowed : 13.50 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.16 (0.30), residues: 716 helix: 3.01 (0.21), residues: 537 sheet: None (None), residues: 0 loop : -0.98 (0.39), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 129 TYR 0.009 0.001 TYR B 59 PHE 0.009 0.001 PHE E 42 HIS 0.003 0.001 HIS F 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.14 (12583) covalent geometry : angle 0.56283 / 0.34 (18252) hydrogen bonds : bond 0.04929 / 3.49 ( 782) hydrogen bonds : angle 2.69019 / 1.98 ( 1948) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.284 Fit side-chains REVERT: A 26 GLN cc_start: 0.7810 (mm-40) cc_final: 0.7511 (mm-40) REVERT: B 106 SER cc_start: 0.8996 (m) cc_final: 0.8777 (t) REVERT: C 75 LYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8756 (mmtm) REVERT: C 100 GLU cc_start: 0.7743 (tp30) cc_final: 0.7534 (tp30) REVERT: D 88 MET cc_start: 0.8238 (tpp) cc_final: 0.7548 (tpp) REVERT: H 94 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.7321 (mp10) outliers start: 12 outliers final: 8 residues processed: 82 average time/residue: 0.1320 time to fit residues: 13.9576 Evaluate side-chains 83 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 94 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 74 optimal weight: 20.0000 chunk 91 optimal weight: 10.0000 chunk 84 optimal weight: 20.0000 chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 89 optimal weight: 10.0000 chunk 28 optimal weight: 0.9980 chunk 72 optimal weight: 30.0000 chunk 82 optimal weight: 20.0000 chunk 52 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.153204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.101011 restraints weight = 15769.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.102321 restraints weight = 10660.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.102784 restraints weight = 8546.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.102971 restraints weight = 8584.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.103114 restraints weight = 8091.085| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12583 Z= 0.204 Angle : 0.628 5.800 18252 Z= 0.363 Chirality : 0.042 0.240 2087 Planarity : 0.005 0.040 1280 Dihedral : 30.757 178.492 4009 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.33 % Allowed : 14.50 % Favored : 83.17 % 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: 2.71 (0.30), residues: 716 helix: 2.69 (0.21), residues: 538 sheet: None (None), residues: 0 loop : -1.20 (0.40), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 53 TYR 0.008 0.001 TYR B 59 PHE 0.011 0.001 PHE C 94 HIS 0.004 0.001 HIS H 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.20 (12583) covalent geometry : angle 0.62761 / 0.36 (18252) hydrogen bonds : bond 0.05507 / 3.84 ( 782) hydrogen bonds : angle 2.92222 / 2.16 ( 1948) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.185 Fit side-chains REVERT: C 75 LYS cc_start: 0.9082 (OUTLIER) cc_final: 0.8840 (mmtp) REVERT: C 100 GLU cc_start: 0.7755 (tp30) cc_final: 0.7544 (tp30) REVERT: H 94 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.7291 (mp10) outliers start: 14 outliers final: 7 residues processed: 89 average time/residue: 0.1342 time to fit residues: 15.5349 Evaluate side-chains 84 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 94 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 95 optimal weight: 20.0000 chunk 75 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 80 optimal weight: 10.0000 chunk 81 optimal weight: 20.0000 chunk 44 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 82 optimal weight: 20.0000 chunk 16 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 124 GLN E 69 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.152110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.099873 restraints weight = 15767.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.101239 restraints weight = 10680.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.101612 restraints weight = 8582.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.101816 restraints weight = 8658.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.101952 restraints weight = 8197.589| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 12583 Z= 0.222 Angle : 0.656 5.950 18252 Z= 0.375 Chirality : 0.043 0.242 2087 Planarity : 0.005 0.047 1280 Dihedral : 30.892 178.580 4009 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.00 % Allowed : 15.33 % Favored : 82.67 % 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: 2.36 (0.30), residues: 716 helix: 2.48 (0.21), residues: 538 sheet: None (None), residues: 0 loop : -1.49 (0.40), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 53 TYR 0.010 0.002 TYR D 66 PHE 0.010 0.001 PHE C 94 HIS 0.004 0.001 HIS H 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.22 (12583) covalent geometry : angle 0.65607 / 0.38 (18252) hydrogen bonds : bond 0.05694 / 3.97 ( 782) hydrogen bonds : angle 3.01892 / 2.24 ( 1948) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.203 Fit side-chains REVERT: C 75 LYS cc_start: 0.9116 (OUTLIER) cc_final: 0.8542 (mppt) REVERT: H 94 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7344 (mp10) outliers start: 12 outliers final: 10 residues processed: 90 average time/residue: 0.1287 time to fit residues: 15.0909 Evaluate side-chains 91 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 94 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 65 optimal weight: 0.0980 chunk 64 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 77 optimal weight: 9.9990 chunk 95 optimal weight: 20.0000 chunk 68 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 89 optimal weight: 20.0000 chunk 96 optimal weight: 20.0000 chunk 70 optimal weight: 50.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 69 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.154273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.101160 restraints weight = 15621.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.103152 restraints weight = 10633.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.104512 restraints weight = 8640.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.105073 restraints weight = 7713.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.105073 restraints weight = 7310.673| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12583 Z= 0.151 Angle : 0.584 5.672 18252 Z= 0.347 Chirality : 0.040 0.240 2087 Planarity : 0.004 0.032 1280 Dihedral : 30.750 178.053 4009 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.67 % Allowed : 16.33 % Favored : 82.00 % 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: 2.77 (0.31), residues: 716 helix: 2.77 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -1.27 (0.40), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 129 TYR 0.008 0.001 TYR F 55 PHE 0.008 0.001 PHE E 42 HIS 0.003 0.001 HIS F 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.15 (12583) covalent geometry : angle 0.58416 / 0.35 (18252) hydrogen bonds : bond 0.05068 / 3.57 ( 782) hydrogen bonds : angle 2.77574 / 2.05 ( 1948) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.181 Fit side-chains REVERT: A 75 ASN cc_start: 0.8608 (m-40) cc_final: 0.7986 (t0) REVERT: C 75 LYS cc_start: 0.9061 (OUTLIER) cc_final: 0.8815 (mmtm) REVERT: H 94 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7319 (mp10) outliers start: 10 outliers final: 8 residues processed: 82 average time/residue: 0.1440 time to fit residues: 15.0899 Evaluate side-chains 83 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 94 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 40 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 47 optimal weight: 0.0980 chunk 43 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 80 optimal weight: 10.0000 chunk 25 optimal weight: 0.0570 chunk 65 optimal weight: 2.9990 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 28 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.156786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.103891 restraints weight = 15840.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.106228 restraints weight = 10496.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.107776 restraints weight = 8308.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.108559 restraints weight = 7315.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.109186 restraints weight = 6863.321| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 12583 Z= 0.129 Angle : 0.570 15.010 18252 Z= 0.339 Chirality : 0.038 0.239 2087 Planarity : 0.004 0.031 1280 Dihedral : 30.610 177.653 4009 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.00 % Allowed : 17.33 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.22 (0.31), residues: 716 helix: 3.06 (0.21), residues: 537 sheet: None (None), residues: 0 loop : -0.97 (0.40), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 129 TYR 0.010 0.001 TYR B 59 PHE 0.009 0.001 PHE F 68 HIS 0.004 0.001 HIS F 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.13 (12583) covalent geometry : angle 0.56966 / 0.34 (18252) hydrogen bonds : bond 0.04690 / 3.33 ( 782) hydrogen bonds : angle 2.58358 / 1.90 ( 1948) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 80 time to evaluate : 0.262 Fit side-chains REVERT: A 75 ASN cc_start: 0.8583 (m-40) cc_final: 0.8015 (t0) REVERT: C 75 LYS cc_start: 0.9041 (OUTLIER) cc_final: 0.8749 (mmtm) REVERT: G 93 ARG cc_start: 0.8749 (mmm-85) cc_final: 0.8511 (mmm160) outliers start: 6 outliers final: 4 residues processed: 84 average time/residue: 0.1385 time to fit residues: 15.2013 Evaluate side-chains 78 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain H residue 50 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 58 optimal weight: 3.9990 chunk 84 optimal weight: 20.0000 chunk 33 optimal weight: 0.7980 chunk 13 optimal weight: 0.0970 chunk 7 optimal weight: 0.2980 chunk 38 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 81 optimal weight: 20.0000 chunk 6 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.155949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.102811 restraints weight = 15757.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.105125 restraints weight = 10522.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.106624 restraints weight = 8373.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.107230 restraints weight = 7403.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.107962 restraints weight = 6983.765| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 12583 Z= 0.136 Angle : 0.566 11.706 18252 Z= 0.337 Chirality : 0.038 0.240 2087 Planarity : 0.004 0.035 1280 Dihedral : 30.644 177.812 4009 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.00 % Allowed : 17.50 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.19 (0.31), residues: 716 helix: 3.05 (0.21), residues: 537 sheet: None (None), residues: 0 loop : -1.01 (0.40), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 129 TYR 0.009 0.001 TYR B 59 PHE 0.008 0.001 PHE E 42 HIS 0.003 0.001 HIS F 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.14 (12583) covalent geometry : angle 0.56636 / 0.34 (18252) hydrogen bonds : bond 0.04760 / 3.37 ( 782) hydrogen bonds : angle 2.61905 / 1.93 ( 1948) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1440.92 seconds wall clock time: 25 minutes 28.04 seconds (1528.04 seconds total)