Starting phenix.real_space_refine on Sun Jun 8 17:02:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q15_18060/06_2025/8q15_18060.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q15_18060/06_2025/8q15_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_18060/06_2025/8q15_18060.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q15_18060/06_2025/8q15_18060.map" model { file = "/net/cci-nas-00/data/ceres_data/8q15_18060/06_2025/8q15_18060.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q15_18060/06_2025/8q15_18060.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 6.88, per 1000 atoms: 0.68 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: 2.68 Conformation dependent library (CDL) restraints added in 614.8 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: 5.44 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: 4.48 Time building geometry restraints manager: 3.14 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 20 " pdb=" O3' DG I 20 " ideal model delta sigma weight residual 1.422 1.464 -0.042 3.00e-02 1.11e+03 1.94e+00 bond pdb=" C2 DC J -20 " pdb=" O2 DC J -20 " ideal model delta sigma weight residual 1.237 1.216 0.021 2.00e-02 2.50e+03 1.09e+00 bond pdb=" CA ILE G 30 " pdb=" CB ILE G 30 " ideal model delta sigma weight residual 1.540 1.526 0.014 1.36e-02 5.41e+03 1.07e+00 bond pdb=" N PRO B 28 " pdb=" CA PRO B 28 " ideal model delta sigma weight residual 1.469 1.481 -0.012 1.28e-02 6.10e+03 9.05e-01 bond pdb=" C3' DG I 64 " pdb=" C2' DG I 64 " ideal model delta sigma weight residual 1.525 1.543 -0.018 2.00e-02 2.50e+03 8.02e-01 ... (remaining 10826 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.09: 14851 1.09 - 2.17: 640 2.17 - 3.26: 139 3.26 - 4.34: 8 4.34 - 5.43: 4 Bond angle restraints: 15642 Sorted by residual: angle pdb=" C4' DC J -20 " pdb=" O4' DC J -20 " pdb=" C1' DC J -20 " ideal model delta sigma weight residual 109.70 106.26 3.44 1.50e+00 4.44e-01 5.27e+00 angle pdb=" C3' DC I 49 " pdb=" C2' DC I 49 " pdb=" C1' DC I 49 " ideal model delta sigma weight residual 101.60 104.78 -3.18 1.50e+00 4.44e-01 4.49e+00 angle pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DG I 21 " ideal model delta sigma weight residual 120.20 123.33 -3.13 1.50e+00 4.44e-01 4.36e+00 angle pdb=" N ILE G 30 " pdb=" CA ILE G 30 " pdb=" C ILE G 30 " ideal model delta sigma weight residual 109.34 105.29 4.05 2.08e+00 2.31e-01 3.79e+00 angle pdb=" C3' DC I 1 " pdb=" C2' DC I 1 " pdb=" C1' DC I 1 " ideal model delta sigma weight residual 101.60 104.50 -2.90 1.50e+00 4.44e-01 3.74e+00 ... (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 - 0.026: 1159 0.026 - 0.052: 457 0.052 - 0.078: 120 0.078 - 0.104: 33 0.104 - 0.130: 18 Chirality restraints: 1787 Sorted by residual: chirality pdb=" C1' DC J -20 " pdb=" O4' DC J -20 " pdb=" C2' DC J -20 " pdb=" N1 DC J -20 " both_signs ideal model delta sigma weight residual False 2.47 2.34 0.13 2.00e-01 2.50e+01 4.23e-01 chirality pdb=" CA ILE H 47 " pdb=" N ILE H 47 " pdb=" C ILE H 47 " pdb=" CB ILE H 47 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.77e-01 chirality pdb=" CA ILE H 30 " pdb=" N ILE H 30 " pdb=" C ILE H 30 " pdb=" CB ILE H 30 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.54e-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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 299.370 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: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 30.470 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.050 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 333.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 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 : 0.003 0.042 10831 Z= 0.147 Angle : 0.521 5.426 15642 Z= 0.320 Chirality : 0.032 0.130 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.003 0.001 HIS G 76 PHE 0.009 0.001 PHE D 99 TYR 0.009 0.001 TYR B 59 ARG 0.003 0.000 ARG G 93 Details of bonding type rmsd hydrogen bonds : bond 0.10813 ( 690) hydrogen bonds : angle 3.72222 ( 1741) covalent geometry : bond 0.00309 (10831) covalent geometry : angle 0.52081 (15642) *********************** 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 : 0.888 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: 0.5414 time to fit residues: 89.4690 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 : 1.257 ------------------------------------------------------------------------------- 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 70 optimal weight: 7.9990 chunk 63 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 76 optimal weight: 6.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 HIS 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.189230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.122805 restraints weight = 12499.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.126835 restraints weight = 8466.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.127489 restraints weight = 5731.224| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10831 Z= 0.190 Angle : 0.568 5.639 15642 Z= 0.337 Chirality : 0.034 0.128 1787 Planarity : 0.004 0.035 1151 Dihedral : 30.594 170.692 3328 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.72 % Allowed : 9.62 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.85 (0.33), residues: 655 helix: 2.63 (0.22), residues: 508 sheet: None (None), residues: 0 loop : -0.90 (0.49), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 78 PHE 0.011 0.001 PHE C 94 TYR 0.010 0.001 TYR H 52 ARG 0.005 0.001 ARG D 128 Details of bonding type rmsd hydrogen bonds : bond 0.06076 ( 690) hydrogen bonds : angle 3.19810 ( 1741) covalent geometry : bond 0.00437 (10831) covalent geometry : angle 0.56819 (15642) *********************** 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 103 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.776 Fit side-chains REVERT: F 42 PHE cc_start: 0.6396 (m-80) cc_final: 0.6069 (m-10) outliers start: 15 outliers final: 12 residues processed: 95 average time/residue: 0.2900 time to fit residues: 36.2894 Evaluate side-chains 90 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.655 ------------------------------------------------------------------------------- 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 90 ARG Chi-restraints excluded: chain B residue 102 VAL 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 113 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 52 optimal weight: 0.7980 chunk 62 optimal weight: 20.0000 chunk 60 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 59 optimal weight: 0.7980 chunk 71 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.192121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.126516 restraints weight = 12768.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.130317 restraints weight = 8504.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.131894 restraints weight = 5844.707| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10831 Z= 0.147 Angle : 0.519 5.435 15642 Z= 0.312 Chirality : 0.032 0.125 1787 Planarity : 0.004 0.034 1151 Dihedral : 30.487 172.764 3326 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.18 % Allowed : 12.52 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.34 (0.33), residues: 655 helix: 2.98 (0.22), residues: 507 sheet: None (None), residues: 0 loop : -0.73 (0.49), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 78 PHE 0.011 0.001 PHE F 68 TYR 0.009 0.001 TYR C 112 ARG 0.006 0.000 ARG D 128 Details of bonding type rmsd hydrogen bonds : bond 0.05557 ( 690) hydrogen bonds : angle 2.90893 ( 1741) covalent geometry : bond 0.00322 (10831) covalent geometry : angle 0.51853 (15642) *********************** 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 101 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.686 Fit side-chains REVERT: B 96 SER cc_start: 0.8596 (t) cc_final: 0.8188 (p) REVERT: C 67 LYS cc_start: 0.7813 (mttt) cc_final: 0.7288 (tttp) REVERT: C 101 LYS cc_start: 0.8579 (mttt) cc_final: 0.8365 (mttm) REVERT: C 145 LYS cc_start: 0.8395 (tttt) cc_final: 0.7935 (mtpt) REVERT: F 42 PHE cc_start: 0.6454 (m-80) cc_final: 0.6080 (m-10) REVERT: F 82 ASP cc_start: 0.7403 (t0) cc_final: 0.6962 (t0) REVERT: G 45 LYS cc_start: 0.7856 (tmtt) cc_final: 0.7648 (mtmm) REVERT: G 85 MET cc_start: 0.8316 (mmm) cc_final: 0.8085 (mmm) outliers start: 12 outliers final: 10 residues processed: 96 average time/residue: 0.3317 time to fit residues: 40.1300 Evaluate side-chains 91 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain B residue 90 ARG Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 97 THR 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 57 optimal weight: 0.0970 chunk 21 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 64 optimal weight: 10.0000 chunk 79 optimal weight: 7.9990 chunk 67 optimal weight: 6.9990 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 76 GLN ** C 113 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 = 0.4294 r_free = 0.4294 target = 0.192107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.124609 restraints weight = 12310.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.127726 restraints weight = 9116.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.128677 restraints weight = 6627.600| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10831 Z= 0.226 Angle : 0.590 6.304 15642 Z= 0.346 Chirality : 0.035 0.141 1787 Planarity : 0.005 0.038 1151 Dihedral : 30.684 173.132 3323 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.99 % Allowed : 11.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.63 (0.32), residues: 655 helix: 2.56 (0.22), residues: 508 sheet: None (None), residues: 0 loop : -1.36 (0.48), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 76 PHE 0.015 0.002 PHE C 94 TYR 0.013 0.002 TYR D 66 ARG 0.007 0.001 ARG D 128 Details of bonding type rmsd hydrogen bonds : bond 0.06207 ( 690) hydrogen bonds : angle 3.26713 ( 1741) covalent geometry : bond 0.00529 (10831) covalent geometry : angle 0.58991 (15642) *********************** 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 107 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 0.793 Fit side-chains REVERT: C 67 LYS cc_start: 0.8086 (mttt) cc_final: 0.7689 (tttp) REVERT: C 101 LYS cc_start: 0.8689 (mttt) cc_final: 0.8452 (mttm) REVERT: C 145 LYS cc_start: 0.8494 (tttt) cc_final: 0.8085 (mtpt) REVERT: D 117 THR cc_start: 0.8593 (p) cc_final: 0.8381 (p) outliers start: 22 outliers final: 17 residues processed: 95 average time/residue: 0.3153 time to fit residues: 38.7699 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 : 0.782 ------------------------------------------------------------------------------- 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 126 SER 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 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 83 THR 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 13 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 82 optimal weight: 8.9990 chunk 66 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 83 optimal weight: 10.0000 chunk 27 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 40 HIS 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 = 0.4316 r_free = 0.4316 target = 0.194373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.127381 restraints weight = 12212.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.130500 restraints weight = 8890.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.131452 restraints weight = 6463.918| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10831 Z= 0.163 Angle : 0.537 5.864 15642 Z= 0.321 Chirality : 0.033 0.130 1787 Planarity : 0.004 0.068 1151 Dihedral : 30.559 174.428 3323 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.09 % Allowed : 14.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.03 (0.32), residues: 655 helix: 2.80 (0.22), residues: 508 sheet: None (None), residues: 0 loop : -1.00 (0.47), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 78 PHE 0.012 0.001 PHE F 68 TYR 0.010 0.001 TYR C 112 ARG 0.008 0.000 ARG D 111 Details of bonding type rmsd hydrogen bonds : bond 0.05687 ( 690) hydrogen bonds : angle 2.99012 ( 1741) covalent geometry : bond 0.00365 (10831) covalent geometry : angle 0.53697 (15642) *********************** 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 101 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.717 Fit side-chains REVERT: C 67 LYS cc_start: 0.7914 (mttt) cc_final: 0.7571 (tttp) REVERT: C 101 LYS cc_start: 0.8651 (mttt) cc_final: 0.8402 (mttm) REVERT: C 145 LYS cc_start: 0.8456 (tttt) cc_final: 0.8056 (mtpt) REVERT: D 81 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.8387 (mp) REVERT: D 117 THR cc_start: 0.8544 (p) cc_final: 0.8323 (p) REVERT: F 82 ASP cc_start: 0.7340 (t0) cc_final: 0.6928 (t0) REVERT: G 45 LYS cc_start: 0.7851 (tmtt) cc_final: 0.7627 (mtmm) outliers start: 17 outliers final: 13 residues processed: 91 average time/residue: 0.2912 time to fit residues: 35.0559 Evaluate side-chains 94 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.725 ------------------------------------------------------------------------------- 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 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 81 THR 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 74 THR Chi-restraints excluded: chain H residue 83 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.194476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.127523 restraints weight = 12236.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.130525 restraints weight = 8946.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.131447 restraints weight = 6537.016| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10831 Z= 0.164 Angle : 0.537 6.437 15642 Z= 0.321 Chirality : 0.033 0.131 1787 Planarity : 0.004 0.060 1151 Dihedral : 30.534 174.956 3323 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.63 % Allowed : 13.97 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.09 (0.32), residues: 655 helix: 2.89 (0.22), residues: 508 sheet: None (None), residues: 0 loop : -1.19 (0.47), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 114 PHE 0.011 0.001 PHE F 68 TYR 0.017 0.002 TYR C 112 ARG 0.007 0.000 ARG D 111 Details of bonding type rmsd hydrogen bonds : bond 0.05673 ( 690) hydrogen bonds : angle 2.96733 ( 1741) covalent geometry : bond 0.00368 (10831) covalent geometry : angle 0.53666 (15642) *********************** 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 104 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.783 Fit side-chains REVERT: C 67 LYS cc_start: 0.8021 (mttt) cc_final: 0.7587 (tttm) REVERT: C 101 LYS cc_start: 0.8657 (mttt) cc_final: 0.8417 (mttm) REVERT: C 145 LYS cc_start: 0.8439 (tttt) cc_final: 0.8041 (mtpt) REVERT: D 81 ILE cc_start: 0.8644 (OUTLIER) cc_final: 0.8427 (mp) REVERT: F 82 ASP cc_start: 0.7372 (t0) cc_final: 0.6949 (t0) REVERT: G 45 LYS cc_start: 0.7856 (tmtt) cc_final: 0.7604 (mtmm) outliers start: 20 outliers final: 16 residues processed: 93 average time/residue: 0.2774 time to fit residues: 34.1946 Evaluate side-chains 97 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.697 ------------------------------------------------------------------------------- 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 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 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 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 63 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 66 optimal weight: 7.9990 chunk 42 optimal weight: 0.7980 chunk 62 optimal weight: 20.0000 chunk 5 optimal weight: 30.0000 chunk 77 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 76 GLN ** C 113 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 = 0.4266 r_free = 0.4266 target = 0.189031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.122547 restraints weight = 12402.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.124044 restraints weight = 9240.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.124245 restraints weight = 8107.038| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 10831 Z= 0.307 Angle : 0.661 9.411 15642 Z= 0.383 Chirality : 0.039 0.150 1787 Planarity : 0.006 0.059 1151 Dihedral : 30.847 174.051 3323 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 4.72 % Allowed : 14.70 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.32), residues: 655 helix: 2.16 (0.22), residues: 506 sheet: None (None), residues: 0 loop : -1.41 (0.48), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 76 PHE 0.021 0.002 PHE C 94 TYR 0.014 0.002 TYR F 100 ARG 0.006 0.001 ARG D 111 Details of bonding type rmsd hydrogen bonds : bond 0.06742 ( 690) hydrogen bonds : angle 3.54508 ( 1741) covalent geometry : bond 0.00729 (10831) covalent geometry : angle 0.66145 (15642) *********************** 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 116 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 90 time to evaluate : 0.609 Fit side-chains revert: symmetry clash REVERT: C 67 LYS cc_start: 0.8062 (mttt) cc_final: 0.7640 (tttm) REVERT: C 145 LYS cc_start: 0.8556 (tttt) cc_final: 0.8137 (mtpt) REVERT: D 81 ILE cc_start: 0.8704 (OUTLIER) cc_final: 0.8455 (mp) outliers start: 26 outliers final: 22 residues processed: 104 average time/residue: 0.2598 time to fit residues: 36.2672 Evaluate side-chains 109 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 0.699 ------------------------------------------------------------------------------- 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 70 ASN Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 102 VAL 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 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 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 83 THR Chi-restraints excluded: chain H residue 93 ARG Chi-restraints excluded: chain H residue 101 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 chunk 77 optimal weight: 7.9990 chunk 47 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 75 optimal weight: 10.0000 chunk 19 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.194916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.129195 restraints weight = 12207.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.132227 restraints weight = 8784.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.133141 restraints weight = 6649.585| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.2689 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= 0.148 Angle : 0.541 7.985 15642 Z= 0.322 Chirality : 0.033 0.198 1787 Planarity : 0.004 0.042 1151 Dihedral : 30.511 176.879 3323 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.90 % Allowed : 17.60 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.07 (0.33), residues: 655 helix: 2.85 (0.22), residues: 505 sheet: None (None), residues: 0 loop : -1.01 (0.49), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS G 76 PHE 0.012 0.001 PHE F 68 TYR 0.015 0.001 TYR C 112 ARG 0.006 0.000 ARG D 111 Details of bonding type rmsd hydrogen bonds : bond 0.05593 ( 690) hydrogen bonds : angle 2.91769 ( 1741) covalent geometry : bond 0.00323 (10831) covalent geometry : angle 0.54082 (15642) *********************** 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 104 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.708 Fit side-chains REVERT: C 67 LYS cc_start: 0.7884 (mttt) cc_final: 0.7509 (tttm) REVERT: C 101 LYS cc_start: 0.8668 (mttt) cc_final: 0.8423 (mttm) REVERT: C 145 LYS cc_start: 0.8494 (tttt) cc_final: 0.8043 (mtpt) REVERT: C 149 LYS cc_start: 0.8674 (tttm) cc_final: 0.8309 (tttm) REVERT: D 81 ILE cc_start: 0.8572 (OUTLIER) cc_final: 0.8344 (mp) outliers start: 16 outliers final: 12 residues processed: 96 average time/residue: 0.2961 time to fit residues: 37.1679 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 : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain D residue 81 ILE 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 74 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 22 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 48 optimal weight: 0.0000 chunk 67 optimal weight: 7.9990 chunk 51 optimal weight: 0.5980 chunk 13 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 overall best weight: 1.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 113 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 = 0.4317 r_free = 0.4317 target = 0.194187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.127472 restraints weight = 12208.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.131416 restraints weight = 8665.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.132244 restraints weight = 5821.921| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10831 Z= 0.164 Angle : 0.543 5.719 15642 Z= 0.323 Chirality : 0.033 0.130 1787 Planarity : 0.004 0.063 1151 Dihedral : 30.566 177.448 3323 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.54 % Allowed : 18.33 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.15 (0.33), residues: 655 helix: 2.91 (0.22), residues: 503 sheet: None (None), residues: 0 loop : -0.95 (0.49), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS G 76 PHE 0.011 0.001 PHE H 101 TYR 0.016 0.002 TYR C 112 ARG 0.006 0.000 ARG D 111 Details of bonding type rmsd hydrogen bonds : bond 0.05666 ( 690) hydrogen bonds : angle 2.96809 ( 1741) covalent geometry : bond 0.00371 (10831) covalent geometry : angle 0.54271 (15642) *********************** 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 98 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.830 Fit side-chains REVERT: C 67 LYS cc_start: 0.7946 (mttt) cc_final: 0.7537 (tttm) REVERT: C 101 LYS cc_start: 0.8646 (mttt) cc_final: 0.8391 (mttm) REVERT: C 145 LYS cc_start: 0.8529 (tttt) cc_final: 0.8045 (mtpt) REVERT: C 149 LYS cc_start: 0.8638 (tttm) cc_final: 0.8288 (tttm) REVERT: D 81 ILE cc_start: 0.8598 (OUTLIER) cc_final: 0.8350 (mp) outliers start: 14 outliers final: 13 residues processed: 90 average time/residue: 0.2965 time to fit residues: 35.9959 Evaluate side-chains 97 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain D residue 81 ILE 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 74 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 76 optimal weight: 7.9990 chunk 2 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 5 optimal weight: 20.0000 chunk 9 optimal weight: 0.0980 chunk 42 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 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 = 0.4333 r_free = 0.4333 target = 0.195690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.129361 restraints weight = 12151.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.133556 restraints weight = 8340.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.134130 restraints weight = 5586.334| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.2923 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= 0.149 Angle : 0.527 5.348 15642 Z= 0.315 Chirality : 0.032 0.130 1787 Planarity : 0.004 0.055 1151 Dihedral : 30.515 179.155 3323 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.90 % Allowed : 17.79 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.32 (0.33), residues: 655 helix: 3.00 (0.22), residues: 504 sheet: None (None), residues: 0 loop : -0.78 (0.50), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 76 PHE 0.012 0.001 PHE F 68 TYR 0.032 0.002 TYR C 112 ARG 0.006 0.000 ARG D 111 Details of bonding type rmsd hydrogen bonds : bond 0.05525 ( 690) hydrogen bonds : angle 2.87143 ( 1741) covalent geometry : bond 0.00328 (10831) covalent geometry : angle 0.52655 (15642) ********************** 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: 16 poor density : 79 time to evaluate : 0.709 Fit side-chains REVERT: C 67 LYS cc_start: 0.7869 (mttt) cc_final: 0.7492 (tttm) REVERT: C 145 LYS cc_start: 0.8527 (tttt) cc_final: 0.8056 (mtpt) REVERT: C 149 LYS cc_start: 0.8636 (tttm) cc_final: 0.8293 (tttm) REVERT: D 81 ILE cc_start: 0.8578 (OUTLIER) cc_final: 0.8336 (mp) outliers start: 16 outliers final: 14 residues processed: 87 average time/residue: 0.2998 time to fit residues: 35.8187 Evaluate side-chains 91 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain D residue 81 ILE 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 F residue 125 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 Chi-restraints excluded: chain H residue 101 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 41 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 76 optimal weight: 7.9990 chunk 33 optimal weight: 0.4980 chunk 53 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 51 optimal weight: 0.5980 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 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 = 0.4328 r_free = 0.4328 target = 0.195215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.128792 restraints weight = 12109.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.131791 restraints weight = 8539.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.132760 restraints weight = 6019.336| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.2984 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= 0.161 Angle : 0.535 8.162 15642 Z= 0.319 Chirality : 0.033 0.132 1787 Planarity : 0.004 0.055 1151 Dihedral : 30.541 179.224 3323 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.72 % Allowed : 18.15 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.23 (0.33), residues: 655 helix: 2.94 (0.22), residues: 506 sheet: None (None), residues: 0 loop : -0.89 (0.50), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 76 PHE 0.011 0.001 PHE H 101 TYR 0.033 0.002 TYR C 112 ARG 0.006 0.000 ARG D 111 Details of bonding type rmsd hydrogen bonds : bond 0.05592 ( 690) hydrogen bonds : angle 2.93136 ( 1741) covalent geometry : bond 0.00362 (10831) covalent geometry : angle 0.53522 (15642) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3668.85 seconds wall clock time: 66 minutes 20.96 seconds (3980.96 seconds total)