Starting phenix.real_space_refine on Fri Jul 3 01:34:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q16_18061/07_2026/8q16_18061.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q16_18061/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8q16_18061/07_2026/8q16_18061.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q16_18061/07_2026/8q16_18061.map" model { file = "/net/cci-nas-00/data/ceres_data/8q16_18061/07_2026/8q16_18061.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q16_18061/07_2026/8q16_18061.cif" } 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): 0.01s 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: 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: 2.32, per 1000 atoms: 0.20 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: 0.89 Conformation dependent library (CDL) restraints added in 214.1 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: 1.55 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: 2.12 Time building geometry restraints manager: 1.21 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: 16176 1.11 - 2.22: 1655 2.22 - 3.33: 400 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: 3.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.680 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.710 ------------------------------------------------------------------------------- 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 : 0.722 5.553 18252 Z= 0.646 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 0.72174 / 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 : 0.282 Fit side-chains REVERT: A 25 LEU cc_start: 0.8403 (mt) cc_final: 0.7918 (mt) REVERT: A 26 GLN cc_start: 0.8150 (mm-40) cc_final: 0.7809 (mm110) REVERT: B 77 LYS cc_start: 0.8733 (mmtt) cc_final: 0.8476 (ttmm) REVERT: B 106 SER cc_start: 0.9147 (m) cc_final: 0.8764 (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: 0.7671 (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: 0.2086 time to fit residues: 30.4157 Evaluate side-chains 81 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 80 time to evaluate : 0.272 ------------------------------------------------------------------------------- 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: 50.0000 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: 0.7980 chunk 45 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3935 r_free = 0.3935 target = 0.155670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.102414 restraints weight = 15587.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.104759 restraints weight = 10431.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.106271 restraints weight = 8252.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.107073 restraints weight = 7293.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.107598 restraints weight = 6842.364| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.0971 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= 0.156 Angle : 0.588 7.027 18252 Z= 0.363 Chirality : 0.041 0.216 2087 Planarity : 0.004 0.042 1280 Dihedral : 30.365 178.172 4011 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 6.90 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: 2.91 (0.31), residues: 716 helix: 2.78 (0.22), residues: 537 sheet: None (None), residues: 0 loop : -0.89 (0.40), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 129 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 0.00268 / 0.16 (12583) covalent geometry : angle 0.58814 / 0.36 (18252) hydrogen bonds : bond 0.05839 / 4.09 ( 782) hydrogen bonds : angle 3.03533 / 2.24 ( 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 89 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 82 time to evaluate : 0.238 Fit side-chains REVERT: A 25 LEU cc_start: 0.8321 (mt) cc_final: 0.8074 (mp) REVERT: A 26 GLN cc_start: 0.7974 (mm-40) cc_final: 0.7623 (mm110) REVERT: A 76 LYS cc_start: 0.8987 (tppt) cc_final: 0.8660 (mttp) REVERT: B 106 SER cc_start: 0.8990 (m) cc_final: 0.8753 (t) REVERT: B 112 ASN cc_start: 0.8219 (t0) cc_final: 0.8016 (p0) REVERT: D 88 MET cc_start: 0.8262 (tpp) cc_final: 0.7564 (tpp) REVERT: F 53 ARG cc_start: 0.8219 (ttm-80) cc_final: 0.7926 (mtt90) outliers start: 7 outliers final: 6 residues processed: 85 average time/residue: 0.1709 time to fit residues: 18.4803 Evaluate side-chains 81 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 0.263 ------------------------------------------------------------------------------- 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: 1.9990 chunk 46 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 9 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 chunk 84 optimal weight: 20.0000 chunk 20 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 76 GLN D 124 GLN ** G 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.155279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.101909 restraints weight = 15780.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.104252 restraints weight = 10553.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.105774 restraints weight = 8352.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.106648 restraints weight = 7373.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.106942 restraints weight = 6900.833| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12583 Z= 0.153 Angle : 0.571 6.118 18252 Z= 0.349 Chirality : 0.040 0.218 2087 Planarity : 0.004 0.033 1280 Dihedral : 30.543 177.828 4011 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.17 % Allowed : 10.00 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.96 (0.31), residues: 716 helix: 2.82 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -0.92 (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 0.00281 / 0.15 (12583) covalent geometry : angle 0.57076 / 0.35 (18252) hydrogen bonds : bond 0.05300 / 3.75 ( 782) hydrogen bonds : angle 2.85740 / 2.10 ( 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 94 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.289 Fit side-chains REVERT: A 25 LEU cc_start: 0.8289 (mt) cc_final: 0.8088 (mp) REVERT: A 26 GLN cc_start: 0.7995 (mm-40) cc_final: 0.7633 (mm110) REVERT: B 106 SER cc_start: 0.9018 (m) cc_final: 0.8778 (t) REVERT: C 113 ASN cc_start: 0.8708 (m-40) cc_final: 0.8473 (m110) REVERT: D 88 MET cc_start: 0.8289 (tpp) cc_final: 0.7491 (tpp) REVERT: H 94 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7188 (mp10) outliers start: 13 outliers final: 8 residues processed: 87 average time/residue: 0.1728 time to fit residues: 19.2567 Evaluate side-chains 87 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.280 ------------------------------------------------------------------------------- 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 81 ILE 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: 0.6980 chunk 44 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 75 optimal weight: 9.9990 chunk 22 optimal weight: 0.8980 chunk 79 optimal weight: 10.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3946 r_free = 0.3946 target = 0.156476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.103183 restraints weight = 15701.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.105564 restraints weight = 10420.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.107127 restraints weight = 8252.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.107984 restraints weight = 7279.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.107984 restraints weight = 6805.820| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1442 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= 0.140 Angle : 0.550 5.783 18252 Z= 0.339 Chirality : 0.039 0.221 2087 Planarity : 0.004 0.033 1280 Dihedral : 30.562 177.525 4009 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.17 % Allowed : 11.33 % Favored : 86.50 % 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: 3.14 (0.31), residues: 716 helix: 2.95 (0.21), residues: 538 sheet: None (None), residues: 0 loop : -0.86 (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 0.00240 / 0.14 (12583) covalent geometry : angle 0.55042 / 0.34 (18252) hydrogen bonds : bond 0.05013 / 3.55 ( 782) hydrogen bonds : angle 2.71754 / 2.00 ( 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: 13 poor density : 81 time to evaluate : 0.221 Fit side-chains REVERT: A 26 GLN cc_start: 0.7978 (mm-40) cc_final: 0.7632 (mm110) REVERT: B 106 SER cc_start: 0.9014 (m) cc_final: 0.8757 (t) REVERT: C 100 GLU cc_start: 0.7747 (tp30) cc_final: 0.7525 (tp30) REVERT: D 88 MET cc_start: 0.8242 (tpp) cc_final: 0.7506 (tpp) REVERT: F 53 ARG cc_start: 0.8367 (ttm-80) cc_final: 0.7898 (mtt90) REVERT: H 94 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.7193 (mp10) outliers start: 13 outliers final: 8 residues processed: 88 average time/residue: 0.1473 time to fit residues: 16.6706 Evaluate side-chains 85 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 113 ILE 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: 3.9990 chunk 75 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 9 optimal weight: 9.9990 chunk 73 optimal weight: 20.0000 chunk 63 optimal weight: 0.0870 chunk 31 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 72 optimal weight: 30.0000 chunk 91 optimal weight: 10.0000 overall best weight: 2.0962 ------------------------------------------------------------------------------- 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 = 0.3906 r_free = 0.3906 target = 0.152891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.100172 restraints weight = 15794.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.101997 restraints weight = 10639.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.102445 restraints weight = 8392.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.102637 restraints weight = 8194.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.102785 restraints weight = 7756.234| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 12583 Z= 0.213 Angle : 0.630 5.757 18252 Z= 0.368 Chirality : 0.042 0.222 2087 Planarity : 0.005 0.037 1280 Dihedral : 30.777 178.206 4009 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.50 % Allowed : 13.83 % Favored : 84.67 % 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: 2.59 (0.30), residues: 716 helix: 2.62 (0.21), residues: 537 sheet: None (None), residues: 0 loop : -1.23 (0.39), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 129 TYR 0.009 0.001 TYR B 59 PHE 0.012 0.001 PHE C 94 HIS 0.004 0.001 HIS H 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.21 (12583) covalent geometry : angle 0.62988 / 0.37 (18252) hydrogen bonds : bond 0.05613 / 3.91 ( 782) hydrogen bonds : angle 2.98084 / 2.20 ( 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 87 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.222 Fit side-chains REVERT: A 26 GLN cc_start: 0.7974 (mm-40) cc_final: 0.7591 (mm110) REVERT: B 106 SER cc_start: 0.9095 (m) cc_final: 0.8886 (t) REVERT: H 94 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7296 (mp10) outliers start: 9 outliers final: 7 residues processed: 83 average time/residue: 0.1496 time to fit residues: 16.0736 Evaluate side-chains 85 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.213 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 8 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 84 optimal weight: 20.0000 chunk 26 optimal weight: 0.9990 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: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3935 r_free = 0.3935 target = 0.155517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.101914 restraints weight = 15682.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.104223 restraints weight = 10496.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.105754 restraints weight = 8352.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.106371 restraints weight = 7374.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.107106 restraints weight = 6957.548| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12583 Z= 0.143 Angle : 0.555 5.557 18252 Z= 0.339 Chirality : 0.039 0.220 2087 Planarity : 0.004 0.029 1280 Dihedral : 30.675 177.570 4009 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.17 % Allowed : 13.83 % Favored : 84.00 % 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: 2.97 (0.30), residues: 716 helix: 2.89 (0.21), residues: 537 sheet: None (None), residues: 0 loop : -1.13 (0.39), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 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 0.00255 / 0.14 (12583) covalent geometry : angle 0.55546 / 0.34 (18252) hydrogen bonds : bond 0.05008 / 3.54 ( 782) hydrogen bonds : angle 2.72811 / 2.01 ( 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 91 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.241 Fit side-chains REVERT: H 94 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.7311 (mp10) outliers start: 13 outliers final: 7 residues processed: 88 average time/residue: 0.1582 time to fit residues: 18.0650 Evaluate side-chains 81 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.341 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- 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: 0.6980 chunk 21 optimal weight: 0.9980 chunk 89 optimal weight: 10.0000 chunk 28 optimal weight: 0.9990 chunk 72 optimal weight: 30.0000 chunk 82 optimal weight: 20.0000 chunk 52 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.3925 r_free = 0.3925 target = 0.154680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.100922 restraints weight = 15721.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.103240 restraints weight = 10650.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.104771 restraints weight = 8483.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.105527 restraints weight = 7480.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.106054 restraints weight = 7037.514| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1733 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= 0.161 Angle : 0.578 5.720 18252 Z= 0.345 Chirality : 0.040 0.222 2087 Planarity : 0.004 0.041 1280 Dihedral : 30.740 177.832 4009 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.00 % Allowed : 15.50 % Favored : 82.50 % 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: 2.90 (0.30), residues: 716 helix: 2.85 (0.21), residues: 537 sheet: None (None), residues: 0 loop : -1.14 (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 0.009 0.001 PHE E 42 HIS 0.003 0.001 HIS H 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.16 (12583) covalent geometry : angle 0.57750 / 0.35 (18252) hydrogen bonds : bond 0.05134 / 3.60 ( 782) hydrogen bonds : angle 2.78354 / 2.06 ( 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 84 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.277 Fit side-chains REVERT: C 119 THR cc_start: 0.8804 (OUTLIER) cc_final: 0.8597 (t) REVERT: H 94 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.7289 (mp10) outliers start: 12 outliers final: 9 residues processed: 80 average time/residue: 0.1401 time to fit residues: 14.5874 Evaluate side-chains 81 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.236 ------------------------------------------------------------------------------- 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 119 THR 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 83 THR 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: 3.9990 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: 0.2980 chunk 82 optimal weight: 20.0000 chunk 16 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- 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 = 0.3904 r_free = 0.3904 target = 0.152857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.099757 restraints weight = 15764.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.102313 restraints weight = 10901.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.102912 restraints weight = 8170.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.103106 restraints weight = 7837.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.103138 restraints weight = 7556.666| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1816 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= 0.201 Angle : 0.614 5.644 18252 Z= 0.359 Chirality : 0.041 0.223 2087 Planarity : 0.004 0.032 1280 Dihedral : 30.859 178.102 4009 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.17 % Allowed : 15.67 % Favored : 82.17 % 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: 2.66 (0.31), residues: 716 helix: 2.66 (0.21), residues: 539 sheet: None (None), residues: 0 loop : -1.24 (0.40), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 129 TYR 0.009 0.001 TYR B 59 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 0.00436 / 0.20 (12583) covalent geometry : angle 0.61387 / 0.36 (18252) hydrogen bonds : bond 0.05475 / 3.82 ( 782) hydrogen bonds : angle 2.90305 / 2.15 ( 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 90 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.289 Fit side-chains REVERT: D 88 MET cc_start: 0.8424 (mmm) cc_final: 0.7990 (tpp) REVERT: H 94 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7276 (mp10) outliers start: 13 outliers final: 10 residues processed: 85 average time/residue: 0.1475 time to fit residues: 16.2050 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 : 0.277 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 64 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 1 optimal weight: 0.0050 chunk 77 optimal weight: 10.0000 chunk 95 optimal weight: 20.0000 chunk 68 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 89 optimal weight: 10.0000 chunk 96 optimal weight: 20.0000 chunk 70 optimal weight: 50.0000 overall best weight: 0.9196 ------------------------------------------------------------------------------- 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 = 0.3928 r_free = 0.3928 target = 0.155200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.101855 restraints weight = 15633.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.104127 restraints weight = 10482.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.105595 restraints weight = 8366.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.106413 restraints weight = 7416.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.106901 restraints weight = 6959.462| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12583 Z= 0.142 Angle : 0.557 5.708 18252 Z= 0.338 Chirality : 0.039 0.220 2087 Planarity : 0.004 0.029 1280 Dihedral : 30.731 177.516 4009 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.50 % Allowed : 16.33 % Favored : 82.17 % 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: 3.02 (0.31), residues: 716 helix: 2.92 (0.21), residues: 537 sheet: None (None), residues: 0 loop : -1.05 (0.40), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 129 TYR 0.008 0.001 TYR B 59 PHE 0.008 0.001 PHE E 42 HIS 0.004 0.001 HIS F 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.14 (12583) covalent geometry : angle 0.55716 / 0.34 (18252) hydrogen bonds : bond 0.04902 / 3.47 ( 782) hydrogen bonds : angle 2.69915 / 1.99 ( 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 89 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.259 Fit side-chains REVERT: A 75 ASN cc_start: 0.8605 (m-40) cc_final: 0.7980 (t0) REVERT: D 88 MET cc_start: 0.8413 (mmm) cc_final: 0.7894 (tpp) REVERT: H 94 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7310 (mp10) outliers start: 9 outliers final: 8 residues processed: 85 average time/residue: 0.1374 time to fit residues: 14.9794 Evaluate side-chains 87 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.292 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 40 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 1 optimal weight: 0.0470 chunk 42 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 80 optimal weight: 10.0000 chunk 25 optimal weight: 0.0170 chunk 65 optimal weight: 2.9990 overall best weight: 0.5516 ------------------------------------------------------------------------------- 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 = 0.3948 r_free = 0.3948 target = 0.156762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.103751 restraints weight = 15837.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.106109 restraints weight = 10496.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.107655 restraints weight = 8274.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.108527 restraints weight = 7271.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.108959 restraints weight = 6802.289| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2043 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= 0.129 Angle : 0.541 5.682 18252 Z= 0.331 Chirality : 0.038 0.221 2087 Planarity : 0.004 0.031 1280 Dihedral : 30.675 177.408 4009 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.33 % Allowed : 16.83 % Favored : 81.83 % 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: 3.25 (0.30), residues: 716 helix: 3.09 (0.21), residues: 536 sheet: None (None), residues: 0 loop : -0.97 (0.39), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 111 TYR 0.010 0.001 TYR B 59 PHE 0.008 0.001 PHE E 42 HIS 0.004 0.001 HIS F 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.13 (12583) covalent geometry : angle 0.54109 / 0.33 (18252) hydrogen bonds : bond 0.04709 / 3.34 ( 782) hydrogen bonds : angle 2.57889 / 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 87 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.291 Fit side-chains REVERT: A 75 ASN cc_start: 0.8547 (m-40) cc_final: 0.7998 (t0) REVERT: G 93 ARG cc_start: 0.8782 (mmm-85) cc_final: 0.8487 (mmm160) REVERT: H 94 GLN cc_start: 0.7873 (OUTLIER) cc_final: 0.7306 (mp10) outliers start: 8 outliers final: 7 residues processed: 83 average time/residue: 0.1579 time to fit residues: 16.9280 Evaluate side-chains 82 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.178 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 58 optimal weight: 0.4980 chunk 84 optimal weight: 20.0000 chunk 33 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 81 optimal weight: 20.0000 chunk 6 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 18 optimal weight: 0.0980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3951 r_free = 0.3951 target = 0.156950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.103924 restraints weight = 15737.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.106284 restraints weight = 10414.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.107760 restraints weight = 8245.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.108727 restraints weight = 7256.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.109146 restraints weight = 6806.215| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2137 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= 0.129 Angle : 0.539 7.223 18252 Z= 0.329 Chirality : 0.038 0.221 2087 Planarity : 0.004 0.057 1280 Dihedral : 30.667 177.300 4009 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.17 % Allowed : 17.50 % Favored : 81.33 % 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: 3.25 (0.30), residues: 716 helix: 3.09 (0.21), residues: 536 sheet: None (None), residues: 0 loop : -0.95 (0.39), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 128 TYR 0.010 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 0.00217 / 0.13 (12583) covalent geometry : angle 0.53915 / 0.33 (18252) hydrogen bonds : bond 0.04670 / 3.31 ( 782) hydrogen bonds : angle 2.58631 / 1.90 ( 1948) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1652.15 seconds wall clock time: 29 minutes 11.97 seconds (1751.97 seconds total)