Starting phenix.real_space_refine on Wed Aug 5 12:06:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q15_18060/08_2026/8q15_18060.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q15_18060/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8q15_18060/08_2026/8q15_18060.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q15_18060/08_2026/8q15_18060.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8q15_18060/08_2026/8q15_18060.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q15_18060/08_2026/8q15_18060.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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-2.2rc3-6140/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: 1.69, per 1000 atoms: 0.17 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: 0.84 Conformation dependent library (CDL) restraints added in 234.6 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: 1.09 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: 1.48 Time building geometry restraints manager: 1.11 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: 13903 1.09 - 2.17: 1340 2.17 - 3.26: 375 3.26 - 4.34: 19 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: 2.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.910 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.030 ------------------------------------------------------------------------------- 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= 0.509 Angle : 0.704 5.426 15642 Z= 0.642 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 0.70361 / 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 : 0.256 Fit side-chains REVERT: F 82 ASP cc_start: 0.6616 (t70) cc_final: 0.6385 (t0) outliers start: 7 outliers final: 2 residues processed: 132 average time/residue: 0.1463 time to fit residues: 24.3289 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 : 0.210 ------------------------------------------------------------------------------- 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: 0.8980 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: 1.9990 chunk 38 optimal weight: 0.8980 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 D 76 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.193017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.128284 restraints weight = 12540.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.130911 restraints weight = 8585.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.131207 restraints weight = 6736.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.132091 restraints weight = 6255.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.132142 restraints weight = 5822.033| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10831 Z= 0.147 Angle : 0.593 7.125 15642 Z= 0.361 Chirality : 0.041 0.235 1787 Planarity : 0.004 0.038 1151 Dihedral : 30.698 170.747 3328 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.81 % Allowed : 10.16 % Favored : 88.02 % 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: 3.15 (0.32), residues: 655 helix: 2.85 (0.22), residues: 507 sheet: None (None), residues: 0 loop : -0.79 (0.47), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 93 TYR 0.010 0.001 TYR H 89 PHE 0.010 0.001 PHE F 68 HIS 0.002 0.001 HIS F 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.15 (10831) covalent geometry : angle 0.59342 / 0.36 (15642) hydrogen bonds : bond 0.06642 / 4.23 ( 690) hydrogen bonds : angle 3.17817 / 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 99 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.259 Fit side-chains revert: symmetry clash REVERT: C 91 MET cc_start: 0.6974 (mmm) cc_final: 0.6504 (mmm) REVERT: F 42 PHE cc_start: 0.6294 (m-80) cc_final: 0.5944 (m-10) REVERT: F 82 ASP cc_start: 0.7444 (t70) cc_final: 0.6974 (t0) outliers start: 10 outliers final: 7 residues processed: 92 average time/residue: 0.1223 time to fit residues: 15.1453 Evaluate side-chains 86 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.154 ------------------------------------------------------------------------------- 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: 3.9990 chunk 76 optimal weight: 20.0000 chunk 74 optimal weight: 50.0000 chunk 53 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 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: 0.7980 overall best weight: 2.6986 ------------------------------------------------------------------------------- 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 = 0.4296 r_free = 0.4296 target = 0.192495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.126295 restraints weight = 12331.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.127320 restraints weight = 9487.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.128042 restraints weight = 8628.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.128710 restraints weight = 7767.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.128818 restraints weight = 6923.462| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 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 0.053 10831 Z= 0.223 Angle : 0.663 6.571 15642 Z= 0.384 Chirality : 0.044 0.247 1787 Planarity : 0.005 0.047 1151 Dihedral : 30.962 171.745 3328 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.45 % Allowed : 10.89 % Favored : 85.66 % 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: 2.44 (0.32), residues: 655 helix: 2.34 (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 0.008 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 0.00484 / 0.22 (10831) covalent geometry : angle 0.66260 / 0.38 (15642) hydrogen bonds : bond 0.07001 / 4.53 ( 690) hydrogen bonds : angle 3.46227 / 2.56 ( 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 98 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: F 42 PHE cc_start: 0.6536 (m-80) cc_final: 0.6241 (m-10) outliers start: 19 outliers final: 17 residues processed: 87 average time/residue: 0.1282 time to fit residues: 14.7417 Evaluate side-chains 91 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.245 ------------------------------------------------------------------------------- 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 C residue 147 VAL Chi-restraints excluded: chain D residue 117 THR 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 Chi-restraints excluded: chain H residue 93 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 38 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 67 optimal weight: 20.0000 chunk 19 optimal weight: 0.6980 chunk 70 optimal weight: 20.0000 chunk 61 optimal weight: 0.0970 chunk 65 optimal weight: 20.0000 chunk 45 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 75 optimal weight: 30.0000 chunk 64 optimal weight: 30.0000 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 = 0.4329 r_free = 0.4329 target = 0.196164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.128750 restraints weight = 12330.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.132480 restraints weight = 8516.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.133475 restraints weight = 5828.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.134131 restraints weight = 5254.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.134347 restraints weight = 5183.142| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 10831 Z= 0.132 Angle : 0.571 6.906 15642 Z= 0.344 Chirality : 0.041 0.238 1787 Planarity : 0.004 0.081 1151 Dihedral : 30.885 173.416 3326 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.36 % Allowed : 12.89 % Favored : 84.75 % 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: 3.18 (0.33), residues: 655 helix: 2.86 (0.22), residues: 507 sheet: None (None), residues: 0 loop : -0.76 (0.49), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 111 TYR 0.033 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 0.00206 / 0.13 (10831) covalent geometry : angle 0.57070 / 0.34 (15642) hydrogen bonds : bond 0.06323 / 4.04 ( 690) hydrogen bonds : angle 3.04917 / 2.26 ( 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 94 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.271 Fit side-chains revert: symmetry clash REVERT: F 42 PHE cc_start: 0.6464 (m-80) cc_final: 0.6121 (m-10) REVERT: F 82 ASP cc_start: 0.7358 (t0) cc_final: 0.6927 (t0) outliers start: 13 outliers final: 11 residues processed: 84 average time/residue: 0.1216 time to fit residues: 13.7668 Evaluate side-chains 86 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.314 ------------------------------------------------------------------------------- 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: 0.6980 chunk 5 optimal weight: 0.9980 chunk 81 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 79 optimal weight: 20.0000 chunk 70 optimal weight: 20.0000 chunk 60 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 76 GLN D 76 GLN G 26 ASN H 26 ASN ** H 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.191190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.124371 restraints weight = 12683.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.128502 restraints weight = 8028.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.129747 restraints weight = 5584.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.129770 restraints weight = 5087.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.131540 restraints weight = 4913.737| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10831 Z= 0.135 Angle : 0.564 6.958 15642 Z= 0.338 Chirality : 0.040 0.236 1787 Planarity : 0.004 0.059 1151 Dihedral : 30.920 173.963 3323 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.09 % Allowed : 12.89 % Favored : 84.03 % 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: 3.26 (0.33), residues: 655 helix: 2.94 (0.22), residues: 507 sheet: None (None), residues: 0 loop : -0.81 (0.48), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 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 E 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.14 (10831) covalent geometry : angle 0.56440 / 0.34 (15642) hydrogen bonds : bond 0.06262 / 4.00 ( 690) hydrogen bonds : angle 3.00942 / 2.23 ( 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 95 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: F 42 PHE cc_start: 0.6395 (m-80) cc_final: 0.6034 (m-10) REVERT: F 82 ASP cc_start: 0.7470 (t0) cc_final: 0.7029 (t0) REVERT: G 45 LYS cc_start: 0.7727 (tmtt) cc_final: 0.7457 (mtmt) outliers start: 17 outliers final: 14 residues processed: 84 average time/residue: 0.1126 time to fit residues: 12.7035 Evaluate side-chains 88 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.260 ------------------------------------------------------------------------------- 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 84 SER Chi-restraints excluded: chain C residue 122 GLU 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 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: 1.9990 chunk 55 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 63 optimal weight: 50.0000 chunk 50 optimal weight: 0.6980 chunk 62 optimal weight: 50.0000 chunk 33 optimal weight: 0.7980 chunk 67 optimal weight: 20.0000 chunk 22 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.195899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.128700 restraints weight = 12254.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.133197 restraints weight = 8566.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.133898 restraints weight = 5795.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.134161 restraints weight = 5203.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.134359 restraints weight = 5041.754| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.1928 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= 0.141 Angle : 0.568 7.141 15642 Z= 0.338 Chirality : 0.040 0.236 1787 Planarity : 0.004 0.054 1151 Dihedral : 30.942 174.628 3323 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.72 % Allowed : 14.88 % Favored : 82.40 % 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: 3.31 (0.33), residues: 655 helix: 2.96 (0.22), residues: 507 sheet: None (None), residues: 0 loop : -0.74 (0.48), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 128 TYR 0.027 0.002 TYR C 112 PHE 0.012 0.001 PHE F 68 HIS 0.004 0.001 HIS C 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.14 (10831) covalent geometry : angle 0.56793 / 0.34 (15642) hydrogen bonds : bond 0.06236 / 3.99 ( 690) hydrogen bonds : angle 2.99765 / 2.21 ( 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 98 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.154 Fit side-chains REVERT: C 101 LYS cc_start: 0.8646 (mttt) cc_final: 0.8399 (mttm) REVERT: C 145 LYS cc_start: 0.8425 (tttt) cc_final: 0.7998 (mtpt) REVERT: F 42 PHE cc_start: 0.6542 (m-80) cc_final: 0.6165 (m-10) REVERT: F 82 ASP cc_start: 0.7341 (t0) cc_final: 0.6927 (t0) outliers start: 15 outliers final: 15 residues processed: 89 average time/residue: 0.0986 time to fit residues: 11.7738 Evaluate side-chains 94 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.155 ------------------------------------------------------------------------------- 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 84 SER Chi-restraints excluded: chain C residue 122 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 0.9980 chunk 79 optimal weight: 20.0000 chunk 39 optimal weight: 6.9990 chunk 11 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 74 optimal weight: 50.0000 chunk 17 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 75 optimal weight: 30.0000 chunk 30 optimal weight: 0.8980 chunk 73 optimal weight: 50.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.196699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.129777 restraints weight = 12102.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.134108 restraints weight = 8494.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.134829 restraints weight = 5800.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.135098 restraints weight = 5178.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.135459 restraints weight = 5019.172| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10831 Z= 0.132 Angle : 0.555 7.135 15642 Z= 0.333 Chirality : 0.039 0.231 1787 Planarity : 0.004 0.047 1151 Dihedral : 30.938 175.308 3323 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.90 % Allowed : 15.25 % Favored : 81.85 % 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: 3.41 (0.33), residues: 655 helix: 3.02 (0.22), residues: 507 sheet: None (None), residues: 0 loop : -0.64 (0.49), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 128 TYR 0.018 0.001 TYR C 112 PHE 0.012 0.001 PHE F 68 HIS 0.004 0.001 HIS C 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.13 (10831) covalent geometry : angle 0.55543 / 0.33 (15642) hydrogen bonds : bond 0.06196 / 3.97 ( 690) hydrogen bonds : angle 2.93140 / 2.16 ( 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 99 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.155 Fit side-chains REVERT: C 101 LYS cc_start: 0.8622 (mttt) cc_final: 0.8376 (mttm) REVERT: C 145 LYS cc_start: 0.8399 (tttt) cc_final: 0.7967 (mtpt) REVERT: F 42 PHE cc_start: 0.6547 (m-80) cc_final: 0.6141 (m-10) REVERT: F 82 ASP cc_start: 0.7385 (t0) cc_final: 0.6963 (t0) REVERT: G 45 LYS cc_start: 0.7683 (tmtt) cc_final: 0.7480 (mtmt) outliers start: 16 outliers final: 15 residues processed: 91 average time/residue: 0.1066 time to fit residues: 12.9855 Evaluate side-chains 96 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.172 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 7 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 75 optimal weight: 30.0000 chunk 35 optimal weight: 0.9990 chunk 73 optimal weight: 50.0000 chunk 63 optimal weight: 50.0000 chunk 41 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 76 HIS ** 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 = 0.4337 r_free = 0.4337 target = 0.196396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.129044 restraints weight = 12104.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.132790 restraints weight = 8483.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.133944 restraints weight = 5754.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.133939 restraints weight = 5375.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.134346 restraints weight = 5100.611| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10831 Z= 0.136 Angle : 0.559 7.846 15642 Z= 0.333 Chirality : 0.039 0.228 1787 Planarity : 0.004 0.043 1151 Dihedral : 30.947 175.811 3323 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.90 % Allowed : 15.61 % Favored : 81.49 % 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: 3.44 (0.33), residues: 655 helix: 3.03 (0.22), residues: 507 sheet: None (None), residues: 0 loop : -0.57 (0.48), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 128 TYR 0.012 0.001 TYR C 112 PHE 0.010 0.001 PHE H 101 HIS 0.003 0.001 HIS C 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.14 (10831) covalent geometry : angle 0.55878 / 0.33 (15642) hydrogen bonds : bond 0.06182 / 3.96 ( 690) hydrogen bonds : angle 2.93716 / 2.17 ( 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 99 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.156 Fit side-chains REVERT: C 101 LYS cc_start: 0.8630 (mttt) cc_final: 0.8386 (mttm) REVERT: C 145 LYS cc_start: 0.8412 (tttt) cc_final: 0.8007 (mtpt) REVERT: F 82 ASP cc_start: 0.7330 (t0) cc_final: 0.6927 (t0) outliers start: 16 outliers final: 16 residues processed: 90 average time/residue: 0.1113 time to fit residues: 13.4611 Evaluate side-chains 97 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.231 ------------------------------------------------------------------------------- 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 34 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 73 optimal weight: 50.0000 chunk 43 optimal weight: 0.5980 chunk 83 optimal weight: 30.0000 chunk 48 optimal weight: 0.0570 chunk 3 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 70 optimal weight: 20.0000 chunk 41 optimal weight: 4.9990 overall best weight: 0.8902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 26 ASN ** 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 = 0.4341 r_free = 0.4341 target = 0.196828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.129769 restraints weight = 12202.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.133212 restraints weight = 8562.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.134420 restraints weight = 5889.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.134475 restraints weight = 5446.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.134863 restraints weight = 5308.500| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10831 Z= 0.132 Angle : 0.549 7.204 15642 Z= 0.329 Chirality : 0.039 0.224 1787 Planarity : 0.004 0.040 1151 Dihedral : 30.933 176.573 3323 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.72 % Allowed : 15.97 % Favored : 81.31 % 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: 3.49 (0.32), residues: 655 helix: 3.07 (0.22), residues: 507 sheet: None (None), residues: 0 loop : -0.57 (0.47), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 128 TYR 0.020 0.001 TYR C 112 PHE 0.010 0.001 PHE F 68 HIS 0.003 0.001 HIS C 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.13 (10831) covalent geometry : angle 0.54914 / 0.33 (15642) hydrogen bonds : bond 0.06157 / 3.95 ( 690) hydrogen bonds : angle 2.90847 / 2.14 ( 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 99 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.173 Fit side-chains REVERT: C 101 LYS cc_start: 0.8595 (mttt) cc_final: 0.8385 (mttm) REVERT: C 145 LYS cc_start: 0.8386 (tttt) cc_final: 0.8009 (mtpt) REVERT: F 82 ASP cc_start: 0.7290 (t0) cc_final: 0.6907 (t0) REVERT: G 45 LYS cc_start: 0.8130 (mtmt) cc_final: 0.7657 (tmtt) REVERT: H 85 MET cc_start: 0.7794 (tpt) cc_final: 0.7575 (mmm) outliers start: 15 outliers final: 13 residues processed: 91 average time/residue: 0.1032 time to fit residues: 12.5349 Evaluate side-chains 95 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.156 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 21 optimal weight: 0.2980 chunk 66 optimal weight: 20.0000 chunk 70 optimal weight: 20.0000 chunk 41 optimal weight: 0.0170 chunk 77 optimal weight: 20.0000 chunk 74 optimal weight: 50.0000 chunk 56 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 75 optimal weight: 20.0000 chunk 22 optimal weight: 0.8980 overall best weight: 0.8420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4342 r_free = 0.4342 target = 0.197005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.129952 restraints weight = 12037.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.133290 restraints weight = 8492.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.134547 restraints weight = 5912.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.134576 restraints weight = 5444.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.134956 restraints weight = 5322.162| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10831 Z= 0.132 Angle : 0.551 7.213 15642 Z= 0.329 Chirality : 0.039 0.221 1787 Planarity : 0.004 0.063 1151 Dihedral : 30.920 177.167 3323 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.72 % Allowed : 15.61 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.54 (0.32), residues: 655 helix: 3.11 (0.22), residues: 505 sheet: None (None), residues: 0 loop : -0.53 (0.47), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 111 TYR 0.023 0.002 TYR C 112 PHE 0.010 0.001 PHE F 68 HIS 0.004 0.001 HIS C 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.13 (10831) covalent geometry : angle 0.55144 / 0.33 (15642) hydrogen bonds : bond 0.06137 / 3.93 ( 690) hydrogen bonds : angle 2.90399 / 2.14 ( 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 95 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.251 Fit side-chains REVERT: C 101 LYS cc_start: 0.8590 (mttt) cc_final: 0.8386 (mttm) REVERT: C 145 LYS cc_start: 0.8419 (tttt) cc_final: 0.8022 (mtpt) REVERT: F 82 ASP cc_start: 0.7296 (t0) cc_final: 0.6900 (t0) REVERT: G 45 LYS cc_start: 0.8104 (mtmt) cc_final: 0.7639 (tmtt) outliers start: 15 outliers final: 15 residues processed: 87 average time/residue: 0.1063 time to fit residues: 12.5512 Evaluate side-chains 94 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.161 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 57 optimal weight: 0.0870 chunk 11 optimal weight: 0.9980 chunk 76 optimal weight: 20.0000 chunk 12 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 77 optimal weight: 20.0000 chunk 16 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 70 optimal weight: 20.0000 chunk 36 optimal weight: 0.7980 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 26 ASN ** 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 = 0.4351 r_free = 0.4351 target = 0.197871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.131681 restraints weight = 12100.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.135257 restraints weight = 8897.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.135417 restraints weight = 7399.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.136021 restraints weight = 5978.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.136406 restraints weight = 5470.442| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2503 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= 0.127 Angle : 0.545 8.689 15642 Z= 0.326 Chirality : 0.039 0.216 1787 Planarity : 0.004 0.062 1151 Dihedral : 30.896 178.041 3323 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.09 % Allowed : 15.61 % Favored : 81.31 % 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: 3.52 (0.33), residues: 655 helix: 3.09 (0.22), residues: 505 sheet: None (None), residues: 0 loop : -0.52 (0.47), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 111 TYR 0.028 0.002 TYR C 112 PHE 0.010 0.001 PHE F 68 HIS 0.011 0.001 HIS G 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.13 (10831) covalent geometry : angle 0.54515 / 0.33 (15642) hydrogen bonds : bond 0.06097 / 3.90 ( 690) hydrogen bonds : angle 2.87996 / 2.13 ( 1741) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1329.24 seconds wall clock time: 23 minutes 37.08 seconds (1417.08 seconds total)