Starting phenix.real_space_refine on Thu Jul 2 18:51:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q15_18060/07_2026/8q15_18060.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q15_18060/07_2026/8q15_18060.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/8q15_18060/07_2026/8q15_18060.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q15_18060/07_2026/8q15_18060.map" model { file = "/net/cci-nas-00/data/ceres_data/8q15_18060/07_2026/8q15_18060.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q15_18060/07_2026/8q15_18060.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= 0.005 sd= 0.074 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 238 5.49 5 S 10 5.16 5 C 5670 2.51 5 N 1885 2.21 5 O 2364 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 10167 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 639 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 3, 'TRANS': 80} Chain: "B" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 639 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 3, 'TRANS': 80} Chain: "C" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 688 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 3, 'TRANS': 84} Chain: "D" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 688 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 3, 'TRANS': 84} Chain: "E" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 590 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "F" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 792 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "G" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 630 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "H" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "I" Number of atoms: 2455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 2455 Classifications: {'DNA': 119} Link IDs: {'rna3p': 118} Chain: "J" Number of atoms: 2424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 2424 Classifications: {'DNA': 119} Link IDs: {'rna3p': 118} Time building chain proxies: 1.92, per 1000 atoms: 0.19 Number of scatterers: 10167 At special positions: 0 Unit cell: (78.516, 114.866, 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 10 16.00 P 238 15.00 O 2364 8.00 N 1885 7.00 C 5670 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: 0.76 Conformation dependent library (CDL) restraints added in 226.6 milliseconds 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1252 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 8 sheets defined 78.2% alpha, 2.4% beta 118 base pairs and 198 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 28 through 39 Processing helix chain 'A' and resid 48 through 75 removed outlier: 3.529A pdb=" N ASP A 74 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN A 75 " --> pdb=" O ALA A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 92 Processing helix chain 'A' and resid 92 through 99 Processing helix chain 'B' and resid 28 through 39 Processing helix chain 'B' and resid 47 through 75 removed outlier: 4.256A pdb=" N VAL B 51 " --> pdb=" O ALA B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 92 removed outlier: 3.563A pdb=" N ASP B 92 " --> pdb=" O ALA B 88 " (cutoff:3.500A) 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 114 Processing helix chain 'C' and resid 119 through 131 Processing helix chain 'C' and resid 132 through 152 removed outlier: 3.517A pdb=" N ALA C 136 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 78 Processing helix chain 'D' and resid 84 through 114 Processing helix chain 'D' and resid 119 through 131 Processing helix chain 'D' and resid 133 through 152 Processing helix chain 'E' and resid 64 through 80 removed outlier: 3.992A pdb=" N ASP E 78 " --> pdb=" O GLU E 74 " (cutoff:3.500A) removed outlier: 4.133A 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 removed outlier: 4.015A pdb=" N LEU E 127 " --> pdb=" O LYS E 123 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG E 132 " --> pdb=" O ALA E 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 58 Processing helix chain 'F' and resid 64 through 80 removed outlier: 4.179A pdb=" N ASP F 78 " --> pdb=" O GLU F 74 " (cutoff:3.500A) removed outlier: 4.280A 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 133 removed outlier: 3.617A pdb=" N LEU F 127 " --> pdb=" O LYS F 123 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG F 132 " --> pdb=" O ALA F 128 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 30 Processing helix chain 'G' and resid 31 through 42 Processing helix chain 'G' and resid 50 through 77 removed outlier: 3.940A pdb=" N GLU G 54 " --> pdb=" O LEU G 50 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASP G 69 " --> pdb=" O ASN G 65 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA G 77 " --> pdb=" O TYR G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 94 removed outlier: 3.544A pdb=" N VAL G 87 " --> pdb=" O THR G 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 26 through 30 Processing helix chain 'H' and resid 31 through 43 Processing helix chain 'H' and resid 50 through 77 removed outlier: 3.903A pdb=" N GLU H 54 " --> pdb=" O LEU H 50 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP H 69 " --> pdb=" O ASN H 65 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA H 77 " --> pdb=" O TYR H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 94 removed outlier: 3.534A pdb=" N VAL H 87 " --> pdb=" O THR H 83 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 45 removed outlier: 6.939A pdb=" N ARG A 44 " --> pdb=" O ILE C 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 'B' and resid 44 through 45 removed outlier: 7.055A pdb=" N ARG B 44 " --> pdb=" O ILE D 118 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 79 through 80 removed outlier: 3.631A pdb=" N ILE B 80 " --> pdb=" O GLY D 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 84 through 85 removed outlier: 6.826A pdb=" N ARG E 84 " --> pdb=" O VAL G 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 119 through 120 Processing sheet with id=AA7, first strand: chain 'F' and resid 84 through 85 removed outlier: 6.670A pdb=" N ARG F 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 'F' and resid 119 through 120 385 hydrogen bonds defined for protein. 1143 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 305 hydrogen bonds 598 hydrogen bond angles 0 basepair planarities 118 basepair parallelities 198 stacking parallelities Total time for adding SS restraints: 1.66 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1730 1.33 - 1.45: 3588 1.45 - 1.57: 5021 1.57 - 1.68: 474 1.68 - 1.80: 18 Bond restraints: 10831 Sorted by residual: bond pdb=" C3' DG I 64 " pdb=" C2' DG I 64 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.13e+01 bond pdb=" C3' DC I 30 " pdb=" C2' DC I 30 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.08e+01 bond pdb=" C3' DG I 29 " pdb=" C2' DG I 29 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.07e+01 bond pdb=" C3' DC J 22 " pdb=" C2' DC J 22 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.06e+01 bond pdb=" C3' DC J -32 " pdb=" C2' DC J -32 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 ... (remaining 10826 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.09: 13955 1.09 - 2.17: 1292 2.17 - 3.26: 372 3.26 - 4.34: 18 4.34 - 5.43: 5 Bond angle restraints: 15642 Sorted by residual: angle pdb=" O4' DT I 22 " pdb=" C4' DT I 22 " pdb=" C3' DT I 22 " ideal model delta sigma weight residual 106.00 103.17 2.83 6.00e-01 2.78e+00 2.23e+01 angle pdb=" O4' DC J -20 " pdb=" C1' DC J -20 " pdb=" N1 DC J -20 " ideal model delta sigma weight residual 108.00 111.11 -3.11 7.00e-01 2.04e+00 1.97e+01 angle pdb=" N3 DT I -23 " pdb=" C4 DT I -23 " pdb=" O4 DT I -23 " ideal model delta sigma weight residual 119.90 122.56 -2.66 6.00e-01 2.78e+00 1.96e+01 angle pdb=" N3 DT I 54 " pdb=" C4 DT I 54 " pdb=" O4 DT I 54 " ideal model delta sigma weight residual 119.90 122.55 -2.65 6.00e-01 2.78e+00 1.94e+01 angle pdb=" N3 DT I -24 " pdb=" C4 DT I -24 " pdb=" O4 DT I -24 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.90e+01 ... (remaining 15637 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.59: 4749 33.59 - 67.18: 1109 67.18 - 100.77: 21 100.77 - 134.36: 0 134.36 - 167.95: 1 Dihedral angle restraints: 5880 sinusoidal: 3942 harmonic: 1938 Sorted by residual: 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 52.05 167.95 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" N GLU F 95 " pdb=" CA GLU F 95 " pdb=" CB GLU F 95 " pdb=" CG GLU F 95 " ideal model delta sinusoidal sigma weight residual -180.00 -121.76 -58.24 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" CA ARG D 128 " pdb=" CB ARG D 128 " pdb=" CG ARG D 128 " pdb=" CD ARG D 128 " ideal model delta sinusoidal sigma weight residual -60.00 -117.04 57.04 3 1.50e+01 4.44e-03 9.42e+00 ... (remaining 5877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 917 0.027 - 0.055: 526 0.055 - 0.082: 226 0.082 - 0.109: 102 0.109 - 0.137: 16 Chirality restraints: 1787 Sorted by residual: chirality pdb=" C3' DG I 50 " pdb=" C4' DG I 50 " pdb=" O3' DG I 50 " pdb=" C2' DG I 50 " both_signs ideal model delta sigma weight residual False -2.73 -2.59 -0.14 2.00e-01 2.50e+01 4.67e-01 chirality pdb=" C3' DG I 20 " pdb=" C4' DG I 20 " pdb=" O3' DG I 20 " pdb=" C2' DG I 20 " both_signs ideal model delta sigma weight residual False -2.73 -2.60 -0.13 2.00e-01 2.50e+01 4.31e-01 chirality pdb=" C3' DC I 24 " pdb=" C4' DC I 24 " pdb=" O3' DC I 24 " pdb=" C2' DC I 24 " both_signs ideal model delta sigma weight residual False -2.73 -2.60 -0.13 2.00e-01 2.50e+01 4.15e-01 ... (remaining 1784 not shown) Planarity restraints: 1151 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC J -20 " 0.003 2.00e-02 2.50e+03 2.41e-02 1.31e+01 pdb=" N1 DC J -20 " -0.013 2.00e-02 2.50e+03 pdb=" C2 DC J -20 " 0.060 2.00e-02 2.50e+03 pdb=" O2 DC J -20 " -0.035 2.00e-02 2.50e+03 pdb=" N3 DC J -20 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DC J -20 " 0.010 2.00e-02 2.50e+03 pdb=" N4 DC J -20 " -0.010 2.00e-02 2.50e+03 pdb=" C5 DC J -20 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DC J -20 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC J -50 " -0.011 2.00e-02 2.50e+03 1.90e-02 8.16e+00 pdb=" N1 DC J -50 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DC J -50 " 0.048 2.00e-02 2.50e+03 pdb=" O2 DC J -50 " -0.023 2.00e-02 2.50e+03 pdb=" N3 DC J -50 " -0.006 2.00e-02 2.50e+03 pdb=" C4 DC J -50 " 0.010 2.00e-02 2.50e+03 pdb=" N4 DC J -50 " -0.015 2.00e-02 2.50e+03 pdb=" C5 DC J -50 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DC J -50 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 21 " -0.005 2.00e-02 2.50e+03 1.40e-02 5.88e+00 pdb=" N9 DG I 21 " 0.015 2.00e-02 2.50e+03 pdb=" C8 DG I 21 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DG I 21 " -0.000 2.00e-02 2.50e+03 pdb=" C5 DG I 21 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DG I 21 " -0.016 2.00e-02 2.50e+03 pdb=" O6 DG I 21 " 0.013 2.00e-02 2.50e+03 pdb=" N1 DG I 21 " 0.005 2.00e-02 2.50e+03 pdb=" C2 DG I 21 " -0.033 2.00e-02 2.50e+03 pdb=" N2 DG I 21 " 0.023 2.00e-02 2.50e+03 pdb=" N3 DG I 21 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DG I 21 " -0.000 2.00e-02 2.50e+03 ... (remaining 1148 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 455 2.71 - 3.26: 9102 3.26 - 3.80: 19396 3.80 - 4.35: 23269 4.35 - 4.90: 33894 Nonbonded interactions: 86116 Sorted by model distance: nonbonded pdb=" N2 DG I -10 " pdb=" O2 DC J 10 " model vdw 2.160 2.496 nonbonded pdb=" N2 DG I -5 " pdb=" O2 DC J 5 " model vdw 2.201 2.496 nonbonded pdb=" OH TYR E 100 " pdb=" OE1 GLU E 134 " model vdw 2.298 3.040 nonbonded pdb=" N1 DG I -5 " pdb=" N3 DC J 5 " model vdw 2.314 2.560 nonbonded pdb=" N2 DG I -21 " pdb=" O2 DC J 21 " model vdw 2.319 2.496 ... (remaining 86111 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' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = (chain 'G' and resid 26 through 103) 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: 1.900 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: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 9.840 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: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 10831 Z= 0.508 Angle : 0.696 5.426 15642 Z= 0.636 Chirality : 0.042 0.137 1787 Planarity : 0.004 0.037 1151 Dihedral : 26.645 167.955 4628 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.27 % Allowed : 2.36 % Favored : 96.37 % 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: 2.99 (0.33), residues: 655 helix: 2.77 (0.23), residues: 500 sheet: None (None), residues: 0 loop : -0.81 (0.46), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 93 TYR 0.009 0.001 TYR B 59 PHE 0.009 0.001 PHE D 99 HIS 0.003 0.001 HIS G 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.51 (10831) covalent geometry : angle 0.69641 / 0.64 (15642) hydrogen bonds : bond 0.10813 / 6.96 ( 690) hydrogen bonds : angle 3.72222 / 2.73 ( 1741) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 126 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: F 82 ASP cc_start: 0.6616 (t70) cc_final: 0.6387 (t0) outliers start: 7 outliers final: 2 residues processed: 132 average time/residue: 0.1535 time to fit residues: 25.2844 Evaluate side-chains 83 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 81 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain G residue 47 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 0.3980 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 50.0000 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 50.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 76 GLN C 113 ASN C 124 GLN ** G 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.192962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.128298 restraints weight = 12491.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.131042 restraints weight = 8213.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.131997 restraints weight = 6390.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.132574 restraints weight = 5951.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.132596 restraints weight = 5518.505| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10831 Z= 0.147 Angle : 0.589 6.766 15642 Z= 0.359 Chirality : 0.041 0.218 1787 Planarity : 0.005 0.040 1151 Dihedral : 30.771 171.536 3328 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.63 % Allowed : 10.16 % Favored : 88.20 % 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 (0.32), residues: 655 helix: 2.85 (0.22), residues: 507 sheet: None (None), residues: 0 loop : -0.84 (0.46), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 93 TYR 0.012 0.001 TYR H 89 PHE 0.010 0.001 PHE F 68 HIS 0.002 0.001 HIS E 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.15 (10831) covalent geometry : angle 0.58871 / 0.36 (15642) hydrogen bonds : bond 0.06641 / 4.23 ( 690) hydrogen bonds : angle 3.17729 / 2.35 ( 1741) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.258 Fit side-chains revert: symmetry clash REVERT: C 91 MET cc_start: 0.6967 (mmm) cc_final: 0.6511 (mmm) REVERT: F 42 PHE cc_start: 0.6331 (m-80) cc_final: 0.5977 (m-10) REVERT: F 82 ASP cc_start: 0.7383 (t70) cc_final: 0.6928 (t0) REVERT: H 93 ARG cc_start: 0.8450 (mtp-110) cc_final: 0.8048 (ttm-80) outliers start: 9 outliers final: 7 residues processed: 91 average time/residue: 0.1152 time to fit residues: 13.8973 Evaluate side-chains 83 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain H residue 50 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 1.9990 chunk 76 optimal weight: 20.0000 chunk 74 optimal weight: 50.0000 chunk 53 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 62 optimal weight: 50.0000 chunk 43 optimal weight: 5.9990 chunk 64 optimal weight: 20.0000 chunk 29 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 84 HIS C 76 GLN ** H 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 94 GLN ** 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 = 0.4298 r_free = 0.4298 target = 0.192780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.125867 restraints weight = 12318.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.127399 restraints weight = 9085.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.127698 restraints weight = 7645.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.128651 restraints weight = 7233.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.128711 restraints weight = 6668.119| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 10831 Z= 0.218 Angle : 0.644 6.229 15642 Z= 0.378 Chirality : 0.043 0.226 1787 Planarity : 0.005 0.053 1151 Dihedral : 31.025 172.405 3328 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.09 % Allowed : 11.07 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.51 (0.32), residues: 655 helix: 2.39 (0.22), residues: 508 sheet: None (None), residues: 0 loop : -1.07 (0.49), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 111 TYR 0.019 0.002 TYR C 112 PHE 0.014 0.002 PHE C 94 HIS 0.004 0.001 HIS H 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.22 (10831) covalent geometry : angle 0.64373 / 0.38 (15642) hydrogen bonds : bond 0.06942 / 4.49 ( 690) hydrogen bonds : angle 3.42780 / 2.54 ( 1741) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: B 37 LYS cc_start: 0.8710 (mttm) cc_final: 0.8460 (mttm) REVERT: F 42 PHE cc_start: 0.6510 (m-80) cc_final: 0.6209 (m-10) outliers start: 17 outliers final: 14 residues processed: 89 average time/residue: 0.1322 time to fit residues: 15.3243 Evaluate side-chains 89 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 83 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 38 optimal weight: 0.0970 chunk 16 optimal weight: 0.9980 chunk 67 optimal weight: 20.0000 chunk 19 optimal weight: 0.9980 chunk 70 optimal weight: 20.0000 chunk 61 optimal weight: 0.6980 chunk 65 optimal weight: 20.0000 chunk 45 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 75 optimal weight: 20.0000 chunk 64 optimal weight: 20.0000 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 76 GLN D 76 GLN ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 26 ASN ** H 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.191212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.125312 restraints weight = 12848.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.128787 restraints weight = 8391.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.129840 restraints weight = 5791.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.130274 restraints weight = 5414.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.130655 restraints weight = 5128.601| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10831 Z= 0.135 Angle : 0.559 6.565 15642 Z= 0.340 Chirality : 0.040 0.216 1787 Planarity : 0.005 0.086 1151 Dihedral : 30.964 174.070 3326 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.36 % Allowed : 13.79 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.20 (0.33), residues: 655 helix: 2.89 (0.22), residues: 507 sheet: None (None), residues: 0 loop : -0.78 (0.49), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 111 TYR 0.030 0.002 TYR C 112 PHE 0.013 0.001 PHE F 68 HIS 0.002 0.001 HIS C 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.14 (10831) covalent geometry : angle 0.55888 / 0.34 (15642) hydrogen bonds : bond 0.06310 / 4.03 ( 690) hydrogen bonds : angle 3.03426 / 2.25 ( 1741) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.189 Fit side-chains REVERT: B 37 LYS cc_start: 0.8693 (mttm) cc_final: 0.8485 (mttm) REVERT: F 42 PHE cc_start: 0.6408 (m-80) cc_final: 0.6057 (m-10) REVERT: F 82 ASP cc_start: 0.7474 (t0) cc_final: 0.7026 (t0) REVERT: H 93 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.8110 (ttm-80) outliers start: 13 outliers final: 10 residues processed: 87 average time/residue: 0.1126 time to fit residues: 13.0813 Evaluate side-chains 89 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 93 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 62 optimal weight: 50.0000 chunk 7 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 55 optimal weight: 0.6980 chunk 16 optimal weight: 7.9990 chunk 12 optimal weight: 0.9990 chunk 79 optimal weight: 20.0000 chunk 70 optimal weight: 20.0000 chunk 60 optimal weight: 0.0980 chunk 17 optimal weight: 4.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 76 GLN ** C 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 GLN ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 94 GLN ** 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 = 0.4303 r_free = 0.4303 target = 0.193379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.125554 restraints weight = 12228.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.129098 restraints weight = 8774.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.130075 restraints weight = 6030.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.130101 restraints weight = 5779.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.130255 restraints weight = 5407.039| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10831 Z= 0.192 Angle : 0.600 6.503 15642 Z= 0.355 Chirality : 0.041 0.224 1787 Planarity : 0.005 0.061 1151 Dihedral : 31.062 173.989 3323 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.27 % Allowed : 13.61 % Favored : 83.12 % 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: 2.75 (0.33), residues: 655 helix: 2.60 (0.22), residues: 510 sheet: None (None), residues: 0 loop : -1.17 (0.48), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 111 TYR 0.025 0.002 TYR C 112 PHE 0.012 0.001 PHE F 68 HIS 0.003 0.001 HIS G 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.19 (10831) covalent geometry : angle 0.59975 / 0.35 (15642) hydrogen bonds : bond 0.06600 / 4.25 ( 690) hydrogen bonds : angle 3.23090 / 2.39 ( 1741) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 0.207 Fit side-chains REVERT: B 37 LYS cc_start: 0.8716 (mttm) cc_final: 0.8515 (mttm) REVERT: F 42 PHE cc_start: 0.6541 (m-80) cc_final: 0.6214 (m-10) outliers start: 18 outliers final: 17 residues processed: 89 average time/residue: 0.1086 time to fit residues: 13.0341 Evaluate side-chains 92 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 93 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 38 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 53 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 63 optimal weight: 40.0000 chunk 50 optimal weight: 1.9990 chunk 62 optimal weight: 50.0000 chunk 33 optimal weight: 1.9990 chunk 67 optimal weight: 20.0000 chunk 22 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 76 GLN ** C 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 26 ASN ** H 94 GLN ** 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 = 0.4308 r_free = 0.4308 target = 0.193726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.126196 restraints weight = 12277.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.130137 restraints weight = 8804.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.131064 restraints weight = 6034.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.131300 restraints weight = 5371.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.131536 restraints weight = 5224.078| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10831 Z= 0.170 Angle : 0.585 6.758 15642 Z= 0.348 Chirality : 0.041 0.220 1787 Planarity : 0.004 0.057 1151 Dihedral : 31.077 174.636 3323 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.63 % Allowed : 14.34 % Favored : 82.03 % 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: 2.85 (0.33), residues: 655 helix: 2.65 (0.22), residues: 508 sheet: None (None), residues: 0 loop : -0.99 (0.48), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 128 TYR 0.027 0.002 TYR C 112 PHE 0.012 0.001 PHE F 68 HIS 0.002 0.001 HIS C 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.17 (10831) covalent geometry : angle 0.58484 / 0.35 (15642) hydrogen bonds : bond 0.06477 / 4.17 ( 690) hydrogen bonds : angle 3.15736 / 2.33 ( 1741) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 77 time to evaluate : 0.154 Fit side-chains REVERT: B 37 LYS cc_start: 0.8731 (mttm) cc_final: 0.8523 (mttm) REVERT: D 81 ILE cc_start: 0.8597 (OUTLIER) cc_final: 0.8356 (mp) REVERT: D 117 THR cc_start: 0.8491 (p) cc_final: 0.8255 (p) REVERT: F 42 PHE cc_start: 0.6534 (m-80) cc_final: 0.6187 (m-10) REVERT: F 82 ASP cc_start: 0.7333 (t0) cc_final: 0.6943 (t0) REVERT: G 45 LYS cc_start: 0.7743 (tmtt) cc_final: 0.7535 (mtmt) outliers start: 20 outliers final: 19 residues processed: 86 average time/residue: 0.1114 time to fit residues: 12.8624 Evaluate side-chains 95 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 75 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 93 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 0.6980 chunk 79 optimal weight: 20.0000 chunk 39 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 74 optimal weight: 50.0000 chunk 17 optimal weight: 7.9990 chunk 42 optimal weight: 0.9990 chunk 75 optimal weight: 20.0000 chunk 30 optimal weight: 0.7980 chunk 73 optimal weight: 50.0000 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 76 GLN ** C 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 26 ASN ** H 94 GLN ** 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 = 0.4312 r_free = 0.4312 target = 0.194209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.126604 restraints weight = 12109.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.130648 restraints weight = 8694.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.131427 restraints weight = 5911.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.131560 restraints weight = 5321.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.133508 restraints weight = 5244.153| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10831 Z= 0.159 Angle : 0.573 6.646 15642 Z= 0.342 Chirality : 0.040 0.215 1787 Planarity : 0.004 0.051 1151 Dihedral : 31.092 175.197 3323 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 4.54 % Allowed : 14.34 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.94 (0.33), residues: 655 helix: 2.71 (0.22), residues: 508 sheet: None (None), residues: 0 loop : -0.94 (0.49), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 128 TYR 0.029 0.002 TYR C 112 PHE 0.012 0.001 PHE F 68 HIS 0.003 0.001 HIS C 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.16 (10831) covalent geometry : angle 0.57330 / 0.34 (15642) hydrogen bonds : bond 0.06410 / 4.12 ( 690) hydrogen bonds : angle 3.11990 / 2.30 ( 1741) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 80 time to evaluate : 0.224 Fit side-chains REVERT: A 34 ARG cc_start: 0.8364 (mtp-110) cc_final: 0.7988 (mtp180) REVERT: B 37 LYS cc_start: 0.8746 (mttm) cc_final: 0.8533 (mttm) REVERT: D 81 ILE cc_start: 0.8640 (OUTLIER) cc_final: 0.8419 (mp) REVERT: F 42 PHE cc_start: 0.6533 (m-80) cc_final: 0.6130 (m-10) REVERT: F 82 ASP cc_start: 0.7341 (t0) cc_final: 0.6937 (t0) outliers start: 25 outliers final: 22 residues processed: 93 average time/residue: 0.1089 time to fit residues: 13.7236 Evaluate side-chains 100 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 77 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 93 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 7 optimal weight: 8.9990 chunk 29 optimal weight: 0.4980 chunk 50 optimal weight: 3.9990 chunk 75 optimal weight: 30.0000 chunk 35 optimal weight: 0.6980 chunk 73 optimal weight: 50.0000 chunk 63 optimal weight: 40.0000 chunk 41 optimal weight: 0.8980 chunk 22 optimal weight: 0.0000 chunk 27 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 76 GLN ** C 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.196668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.129954 restraints weight = 12159.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.133682 restraints weight = 8593.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.135111 restraints weight = 5862.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.135002 restraints weight = 5388.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.135310 restraints weight = 5117.600| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10831 Z= 0.127 Angle : 0.549 7.622 15642 Z= 0.332 Chirality : 0.039 0.205 1787 Planarity : 0.004 0.041 1151 Dihedral : 31.027 176.136 3323 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.09 % Allowed : 15.97 % Favored : 80.94 % 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: 3.38 (0.33), residues: 655 helix: 3.01 (0.22), residues: 505 sheet: None (None), residues: 0 loop : -0.66 (0.49), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 128 TYR 0.029 0.002 TYR C 112 PHE 0.013 0.001 PHE F 68 HIS 0.003 0.001 HIS C 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.13 (10831) covalent geometry : angle 0.54880 / 0.33 (15642) hydrogen bonds : bond 0.06153 / 3.93 ( 690) hydrogen bonds : angle 2.90251 / 2.14 ( 1741) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 0.211 Fit side-chains REVERT: A 34 ARG cc_start: 0.8302 (mtp-110) cc_final: 0.7987 (mtp-110) REVERT: C 67 LYS cc_start: 0.7950 (mttt) cc_final: 0.7737 (tttp) REVERT: C 101 LYS cc_start: 0.8646 (mttt) cc_final: 0.8401 (mttm) REVERT: C 145 LYS cc_start: 0.8399 (tttt) cc_final: 0.7960 (mtpt) REVERT: D 81 ILE cc_start: 0.8639 (OUTLIER) cc_final: 0.8422 (mp) REVERT: F 82 ASP cc_start: 0.7336 (t0) cc_final: 0.6926 (t0) REVERT: G 94 GLN cc_start: 0.8243 (mm-40) cc_final: 0.7990 (mt0) outliers start: 17 outliers final: 14 residues processed: 96 average time/residue: 0.1219 time to fit residues: 15.0748 Evaluate side-chains 95 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain H residue 93 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 34 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 73 optimal weight: 50.0000 chunk 43 optimal weight: 4.9990 chunk 83 optimal weight: 30.0000 chunk 48 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 70 optimal weight: 20.0000 chunk 41 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 76 GLN ** C 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 26 ASN ** H 94 GLN ** 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 = 0.4332 r_free = 0.4332 target = 0.196169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.129311 restraints weight = 12257.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.132992 restraints weight = 8791.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.132987 restraints weight = 7387.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.133959 restraints weight = 5836.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.134314 restraints weight = 5232.259| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10831 Z= 0.133 Angle : 0.548 6.920 15642 Z= 0.329 Chirality : 0.039 0.205 1787 Planarity : 0.004 0.066 1151 Dihedral : 31.042 176.288 3323 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.90 % Allowed : 16.88 % Favored : 80.22 % 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: 3.39 (0.33), residues: 655 helix: 3.01 (0.22), residues: 507 sheet: None (None), residues: 0 loop : -0.65 (0.49), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 111 TYR 0.024 0.002 TYR C 112 PHE 0.012 0.001 PHE F 68 HIS 0.002 0.001 HIS C 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.13 (10831) covalent geometry : angle 0.54824 / 0.33 (15642) hydrogen bonds : bond 0.06198 / 3.97 ( 690) hydrogen bonds : angle 2.94089 / 2.17 ( 1741) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.236 Fit side-chains REVERT: A 34 ARG cc_start: 0.8319 (mtp-110) cc_final: 0.7995 (mtp-110) REVERT: C 67 LYS cc_start: 0.7969 (mttt) cc_final: 0.7764 (tttp) REVERT: C 101 LYS cc_start: 0.8624 (mttt) cc_final: 0.8388 (mttm) REVERT: C 145 LYS cc_start: 0.8393 (tttt) cc_final: 0.7984 (mtpt) REVERT: D 81 ILE cc_start: 0.8651 (OUTLIER) cc_final: 0.8445 (mp) REVERT: F 82 ASP cc_start: 0.7291 (t0) cc_final: 0.6893 (t0) REVERT: G 45 LYS cc_start: 0.8128 (mtmt) cc_final: 0.7667 (tmtt) outliers start: 16 outliers final: 14 residues processed: 87 average time/residue: 0.1164 time to fit residues: 13.6669 Evaluate side-chains 93 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain H residue 93 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 21 optimal weight: 0.9990 chunk 66 optimal weight: 20.0000 chunk 70 optimal weight: 20.0000 chunk 41 optimal weight: 6.9990 chunk 77 optimal weight: 20.0000 chunk 74 optimal weight: 50.0000 chunk 56 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 75 optimal weight: 20.0000 chunk 22 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 76 GLN ** C 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.193517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.126486 restraints weight = 12130.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.130380 restraints weight = 8587.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.130948 restraints weight = 6005.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.131196 restraints weight = 5608.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.131452 restraints weight = 5426.264| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10831 Z= 0.185 Angle : 0.593 7.291 15642 Z= 0.347 Chirality : 0.040 0.220 1787 Planarity : 0.005 0.066 1151 Dihedral : 31.102 175.414 3323 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.27 % Allowed : 15.97 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.83 (0.32), residues: 655 helix: 2.64 (0.22), residues: 510 sheet: None (None), residues: 0 loop : -1.08 (0.47), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 128 TYR 0.022 0.002 TYR C 112 PHE 0.014 0.002 PHE H 101 HIS 0.004 0.001 HIS C 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.19 (10831) covalent geometry : angle 0.59347 / 0.35 (15642) hydrogen bonds : bond 0.06464 / 4.16 ( 690) hydrogen bonds : angle 3.15012 / 2.32 ( 1741) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 0.261 Fit side-chains REVERT: A 34 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.8057 (mtp-110) REVERT: C 67 LYS cc_start: 0.8000 (mttt) cc_final: 0.7776 (tttp) REVERT: C 101 LYS cc_start: 0.8654 (mttt) cc_final: 0.8431 (mttm) REVERT: C 145 LYS cc_start: 0.8414 (tttt) cc_final: 0.8021 (mtpt) REVERT: D 81 ILE cc_start: 0.8684 (OUTLIER) cc_final: 0.8482 (mp) REVERT: F 82 ASP cc_start: 0.7344 (t0) cc_final: 0.6948 (t0) REVERT: G 45 LYS cc_start: 0.8132 (mtmt) cc_final: 0.7652 (tmtt) outliers start: 18 outliers final: 15 residues processed: 87 average time/residue: 0.1339 time to fit residues: 15.3401 Evaluate side-chains 94 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 77 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain H residue 93 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 57 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 76 optimal weight: 20.0000 chunk 12 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 77 optimal weight: 20.0000 chunk 16 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 70 optimal weight: 20.0000 chunk 36 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 94 GLN ** 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 = 0.4331 r_free = 0.4331 target = 0.195949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.129112 restraints weight = 12108.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.133151 restraints weight = 8384.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.133860 restraints weight = 5736.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.134343 restraints weight = 5236.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.134606 restraints weight = 5110.612| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10831 Z= 0.133 Angle : 0.548 6.749 15642 Z= 0.330 Chirality : 0.039 0.199 1787 Planarity : 0.004 0.060 1151 Dihedral : 31.027 177.368 3323 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.09 % Allowed : 17.24 % Favored : 79.67 % 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: 3.20 (0.33), residues: 655 helix: 2.92 (0.22), residues: 506 sheet: None (None), residues: 0 loop : -0.88 (0.46), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 111 TYR 0.021 0.002 TYR C 112 PHE 0.011 0.001 PHE F 68 HIS 0.004 0.001 HIS C 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.13 (10831) covalent geometry : angle 0.54840 / 0.33 (15642) hydrogen bonds : bond 0.06179 / 3.95 ( 690) hydrogen bonds : angle 2.96256 / 2.19 ( 1741) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1397.00 seconds wall clock time: 24 minutes 51.12 seconds (1491.12 seconds total)