Starting phenix.real_space_refine on Fri Oct 10 23:16:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q15_18060/10_2025/8q15_18060.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q15_18060/10_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_18060/10_2025/8q15_18060.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q15_18060/10_2025/8q15_18060.map" model { file = "/net/cci-nas-00/data/ceres_data/8q15_18060/10_2025/8q15_18060.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q15_18060/10_2025/8q15_18060.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.074 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 238 5.49 5 S 10 5.16 5 C 5670 2.51 5 N 1885 2.21 5 O 2364 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/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: 2.34, per 1000 atoms: 0.23 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: 0.86 Conformation dependent library (CDL) restraints added in 234.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 1.43 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: 1.71 Time building geometry restraints manager: 1.12 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.690 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.670 Find NCS groups from input model: 0.090 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.990 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren 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 covalent geometry : bond 0.00309 (10831) covalent geometry : angle 0.52081 (15642) hydrogen bonds : bond 0.10813 ( 690) hydrogen bonds : angle 3.72222 ( 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 : 0.244 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: 0.1523 time to fit residues: 24.8337 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 : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain G residue 47 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 0.2980 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 C 124 GLN D 76 GLN ** 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 = 0.192873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.126907 restraints weight = 12541.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.130450 restraints weight = 8042.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.131329 restraints weight = 5556.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.131846 restraints weight = 5212.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.132421 restraints weight = 4922.763| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.1349 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= 0.148 Angle : 0.528 5.448 15642 Z= 0.318 Chirality : 0.032 0.125 1787 Planarity : 0.004 0.033 1151 Dihedral : 30.492 170.850 3328 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.63 % Allowed : 10.16 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.27 (0.33), residues: 655 helix: 2.92 (0.22), residues: 507 sheet: None (None), residues: 0 loop : -0.67 (0.48), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 128 TYR 0.008 0.001 TYR B 59 PHE 0.010 0.001 PHE F 68 HIS 0.003 0.001 HIS C 78 Details of bonding type rmsd covalent geometry : bond 0.00320 (10831) covalent geometry : angle 0.52786 (15642) hydrogen bonds : bond 0.05743 ( 690) hydrogen bonds : angle 2.99136 ( 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: 9 poor density : 90 time to evaluate : 0.290 Fit side-chains REVERT: B 97 ARG cc_start: 0.8120 (mtp85) cc_final: 0.7811 (ttp-110) REVERT: F 42 PHE cc_start: 0.6339 (m-80) cc_final: 0.6011 (m-10) REVERT: F 82 ASP cc_start: 0.7403 (t70) cc_final: 0.6936 (t0) outliers start: 9 outliers final: 7 residues processed: 94 average time/residue: 0.1344 time to fit residues: 16.3858 Evaluate side-chains 82 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.306 ------------------------------------------------------------------------------- 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 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 50 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 5.9990 chunk 76 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 53 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 chunk 62 optimal weight: 20.0000 chunk 43 optimal weight: 4.9990 chunk 64 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.190557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.123146 restraints weight = 12402.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.124884 restraints weight = 9497.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.125178 restraints weight = 7868.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.126079 restraints weight = 7373.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.126089 restraints weight = 6828.611| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 10831 Z= 0.295 Angle : 0.646 6.326 15642 Z= 0.375 Chirality : 0.038 0.148 1787 Planarity : 0.005 0.043 1151 Dihedral : 30.795 171.319 3326 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.63 % Allowed : 10.34 % Favored : 86.03 % 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 aren not related in a simple way. whole: 2.26 (0.32), residues: 655 helix: 2.25 (0.22), residues: 510 sheet: None (None), residues: 0 loop : -1.35 (0.49), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 111 TYR 0.014 0.002 TYR F 100 PHE 0.020 0.002 PHE C 94 HIS 0.005 0.001 HIS H 76 Details of bonding type rmsd covalent geometry : bond 0.00702 (10831) covalent geometry : angle 0.64552 (15642) hydrogen bonds : bond 0.06669 ( 690) hydrogen bonds : angle 3.51542 ( 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 103 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 83 time to evaluate : 0.282 Fit side-chains REVERT: D 117 THR cc_start: 0.8616 (p) cc_final: 0.8397 (p) outliers start: 20 outliers final: 17 residues processed: 93 average time/residue: 0.1497 time to fit residues: 18.1360 Evaluate side-chains 90 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.286 ------------------------------------------------------------------------------- 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 126 SER Chi-restraints excluded: chain C residue 147 VAL 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 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 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: 0.9980 chunk 16 optimal weight: 0.8980 chunk 67 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 70 optimal weight: 7.9990 chunk 61 optimal weight: 0.9980 chunk 65 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 75 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 76 GLN F 40 HIS 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 = 0.4290 r_free = 0.4290 target = 0.191102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.125544 restraints weight = 12818.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.128745 restraints weight = 8926.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.129931 restraints weight = 6376.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.130432 restraints weight = 6063.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.130467 restraints weight = 5697.035| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10831 Z= 0.149 Angle : 0.528 5.405 15642 Z= 0.318 Chirality : 0.033 0.126 1787 Planarity : 0.004 0.056 1151 Dihedral : 30.538 173.428 3323 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.54 % Allowed : 14.16 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.08 (0.32), residues: 655 helix: 2.83 (0.22), residues: 507 sheet: None (None), residues: 0 loop : -0.94 (0.49), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 111 TYR 0.011 0.001 TYR C 112 PHE 0.012 0.001 PHE F 68 HIS 0.006 0.001 HIS C 78 Details of bonding type rmsd covalent geometry : bond 0.00323 (10831) covalent geometry : angle 0.52832 (15642) hydrogen bonds : bond 0.05623 ( 690) hydrogen bonds : angle 2.94796 ( 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 101 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.286 Fit side-chains REVERT: C 67 LYS cc_start: 0.8000 (mttt) cc_final: 0.7488 (tttp) REVERT: C 72 LYS cc_start: 0.7907 (mttt) cc_final: 0.7698 (mmtm) REVERT: C 101 LYS cc_start: 0.8588 (mttt) cc_final: 0.8342 (mttm) REVERT: C 145 LYS cc_start: 0.8411 (tttt) cc_final: 0.7928 (mtpt) REVERT: D 117 THR cc_start: 0.8577 (p) cc_final: 0.8368 (p) REVERT: F 82 ASP cc_start: 0.7502 (t0) cc_final: 0.7037 (t0) REVERT: G 45 LYS cc_start: 0.7911 (tmtt) cc_final: 0.7628 (mtmm) outliers start: 14 outliers final: 11 residues processed: 93 average time/residue: 0.1602 time to fit residues: 19.1581 Evaluate side-chains 91 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 VAL 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 62 optimal weight: 20.0000 chunk 7 optimal weight: 10.0000 chunk 5 optimal weight: 20.0000 chunk 81 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 79 optimal weight: 6.9990 chunk 70 optimal weight: 7.9990 chunk 60 optimal weight: 0.0570 chunk 17 optimal weight: 7.9990 overall best weight: 2.3704 ------------------------------------------------------------------------------- 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 ** 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 = 0.4291 r_free = 0.4291 target = 0.192026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.125179 restraints weight = 12279.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.127516 restraints weight = 9426.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.128468 restraints weight = 7215.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.128961 restraints weight = 6927.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.129656 restraints weight = 6556.167| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 10831 Z= 0.222 Angle : 0.587 6.698 15642 Z= 0.345 Chirality : 0.035 0.141 1787 Planarity : 0.005 0.056 1151 Dihedral : 30.655 173.771 3323 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.45 % Allowed : 14.16 % 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 aren not related in a simple way. whole: 2.61 (0.32), residues: 655 helix: 2.56 (0.22), residues: 508 sheet: None (None), residues: 0 loop : -1.41 (0.48), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 111 TYR 0.012 0.002 TYR C 112 PHE 0.014 0.001 PHE C 94 HIS 0.003 0.001 HIS H 76 Details of bonding type rmsd covalent geometry : bond 0.00518 (10831) covalent geometry : angle 0.58723 (15642) hydrogen bonds : bond 0.06186 ( 690) hydrogen bonds : angle 3.26130 ( 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 102 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.271 Fit side-chains REVERT: C 67 LYS cc_start: 0.8158 (mttt) cc_final: 0.7815 (tttm) REVERT: C 101 LYS cc_start: 0.8695 (mttt) cc_final: 0.8463 (mttm) REVERT: C 145 LYS cc_start: 0.8512 (tttt) cc_final: 0.8121 (mtpt) REVERT: C 149 LYS cc_start: 0.8395 (tttt) cc_final: 0.8130 (ttpp) REVERT: D 117 THR cc_start: 0.8560 (p) cc_final: 0.8323 (p) outliers start: 19 outliers final: 19 residues processed: 92 average time/residue: 0.1376 time to fit residues: 16.6141 Evaluate side-chains 100 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL 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 84 SER Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain 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 74 THR Chi-restraints excluded: chain H residue 93 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 38 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 chunk 50 optimal weight: 0.2980 chunk 62 optimal weight: 20.0000 chunk 33 optimal weight: 0.6980 chunk 67 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.4323 r_free = 0.4323 target = 0.195036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.128595 restraints weight = 12295.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.131403 restraints weight = 8912.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.132416 restraints weight = 6793.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.132949 restraints weight = 6228.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.132965 restraints weight = 5788.073| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10831 Z= 0.149 Angle : 0.527 5.667 15642 Z= 0.317 Chirality : 0.032 0.126 1787 Planarity : 0.004 0.040 1151 Dihedral : 30.480 175.447 3323 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.27 % Allowed : 15.06 % 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 aren not related in a simple way. whole: 3.22 (0.33), residues: 655 helix: 2.98 (0.22), residues: 505 sheet: None (None), residues: 0 loop : -1.05 (0.48), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 97 TYR 0.014 0.001 TYR C 112 PHE 0.013 0.001 PHE F 68 HIS 0.005 0.001 HIS C 78 Details of bonding type rmsd covalent geometry : bond 0.00326 (10831) covalent geometry : angle 0.52681 (15642) hydrogen bonds : bond 0.05585 ( 690) hydrogen bonds : angle 2.88993 ( 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 101 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.234 Fit side-chains REVERT: C 67 LYS cc_start: 0.7995 (mttt) cc_final: 0.7685 (tttm) REVERT: C 101 LYS cc_start: 0.8643 (mttt) cc_final: 0.8394 (mttm) REVERT: C 145 LYS cc_start: 0.8443 (tttt) cc_final: 0.8018 (mtpt) REVERT: D 81 ILE cc_start: 0.8615 (OUTLIER) cc_final: 0.8393 (mp) REVERT: D 117 THR cc_start: 0.8537 (p) cc_final: 0.8312 (p) REVERT: F 82 ASP cc_start: 0.7366 (t0) cc_final: 0.6956 (t0) outliers start: 18 outliers final: 14 residues processed: 91 average time/residue: 0.1375 time to fit residues: 16.3190 Evaluate side-chains 93 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.268 ------------------------------------------------------------------------------- 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 122 GLU Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain 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 83 THR Chi-restraints excluded: chain H residue 93 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 42 optimal weight: 0.5980 chunk 75 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 73 optimal weight: 30.0000 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.194184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.127404 restraints weight = 12158.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.130284 restraints weight = 8944.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.131188 restraints weight = 6781.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.131695 restraints weight = 6266.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.131676 restraints weight = 5876.061| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.2450 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= 0.173 Angle : 0.543 7.828 15642 Z= 0.324 Chirality : 0.033 0.133 1787 Planarity : 0.004 0.063 1151 Dihedral : 30.500 175.499 3323 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 4.17 % Allowed : 14.88 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.12 (0.33), residues: 655 helix: 2.92 (0.22), residues: 505 sheet: None (None), residues: 0 loop : -1.14 (0.47), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 111 TYR 0.017 0.002 TYR C 112 PHE 0.012 0.001 PHE H 101 HIS 0.002 0.001 HIS H 76 Details of bonding type rmsd covalent geometry : bond 0.00391 (10831) covalent geometry : angle 0.54301 (15642) hydrogen bonds : bond 0.05710 ( 690) hydrogen bonds : angle 2.98257 ( 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 102 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 79 time to evaluate : 0.241 Fit side-chains REVERT: C 67 LYS cc_start: 0.8118 (mttt) cc_final: 0.7773 (tttm) REVERT: C 101 LYS cc_start: 0.8647 (mttt) cc_final: 0.8381 (mttm) REVERT: C 145 LYS cc_start: 0.8440 (tttt) cc_final: 0.8036 (mtpt) REVERT: D 81 ILE cc_start: 0.8619 (OUTLIER) cc_final: 0.8391 (mp) REVERT: F 82 ASP cc_start: 0.7375 (t0) cc_final: 0.6979 (t0) outliers start: 23 outliers final: 20 residues processed: 88 average time/residue: 0.1117 time to fit residues: 13.2493 Evaluate side-chains 99 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 0.238 ------------------------------------------------------------------------------- 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 D residue 81 ILE Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 7 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 50 optimal weight: 0.0970 chunk 75 optimal weight: 10.0000 chunk 35 optimal weight: 0.9980 chunk 73 optimal weight: 30.0000 chunk 63 optimal weight: 10.0000 chunk 41 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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** ** G 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 26 ASN ** H 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.196173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.129637 restraints weight = 12167.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.133221 restraints weight = 8698.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.134348 restraints weight = 5919.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.134862 restraints weight = 5203.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.135166 restraints weight = 5133.761| |-----------------------------------------------------------------------------| r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.2644 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= 0.143 Angle : 0.517 5.310 15642 Z= 0.312 Chirality : 0.032 0.169 1787 Planarity : 0.004 0.049 1151 Dihedral : 30.443 177.263 3323 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.72 % Allowed : 17.06 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.44 (0.33), residues: 655 helix: 3.11 (0.22), residues: 505 sheet: None (None), residues: 0 loop : -0.86 (0.48), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 97 TYR 0.025 0.002 TYR C 112 PHE 0.012 0.001 PHE F 68 HIS 0.004 0.001 HIS G 76 Details of bonding type rmsd covalent geometry : bond 0.00311 (10831) covalent geometry : angle 0.51725 (15642) hydrogen bonds : bond 0.05482 ( 690) hydrogen bonds : angle 2.80635 ( 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 101 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.269 Fit side-chains REVERT: C 67 LYS cc_start: 0.8125 (mttt) cc_final: 0.7752 (tttm) REVERT: C 145 LYS cc_start: 0.8395 (tttt) cc_final: 0.7973 (mtpt) REVERT: D 81 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8339 (mp) REVERT: F 82 ASP cc_start: 0.7346 (t0) cc_final: 0.6946 (t0) outliers start: 15 outliers final: 13 residues processed: 91 average time/residue: 0.1359 time to fit residues: 16.1977 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 : 0.208 ------------------------------------------------------------------------------- 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 84 SER Chi-restraints excluded: chain C residue 122 GLU 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 62 LEU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain H residue 93 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 34 optimal weight: 0.9990 chunk 55 optimal weight: 0.1980 chunk 46 optimal weight: 0.9990 chunk 73 optimal weight: 30.0000 chunk 43 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 41 optimal weight: 4.9990 overall best weight: 1.4388 ------------------------------------------------------------------------------- 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 = 0.4321 r_free = 0.4321 target = 0.194501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.127728 restraints weight = 12259.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.131452 restraints weight = 8789.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.132347 restraints weight = 5998.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.132829 restraints weight = 5394.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.133156 restraints weight = 5227.699| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10831 Z= 0.173 Angle : 0.543 5.425 15642 Z= 0.322 Chirality : 0.033 0.162 1787 Planarity : 0.004 0.050 1151 Dihedral : 30.482 177.294 3323 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.63 % Allowed : 15.61 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.19 (0.32), residues: 655 helix: 2.94 (0.22), residues: 507 sheet: None (None), residues: 0 loop : -1.02 (0.48), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 97 TYR 0.025 0.002 TYR C 112 PHE 0.012 0.001 PHE H 101 HIS 0.002 0.001 HIS G 76 Details of bonding type rmsd covalent geometry : bond 0.00394 (10831) covalent geometry : angle 0.54311 (15642) hydrogen bonds : bond 0.05674 ( 690) hydrogen bonds : angle 2.95087 ( 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 102 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.247 Fit side-chains REVERT: A 34 ARG cc_start: 0.8126 (ttp-110) cc_final: 0.7715 (ttp-110) REVERT: C 67 LYS cc_start: 0.8137 (mttt) cc_final: 0.7770 (tttm) REVERT: C 145 LYS cc_start: 0.8433 (tttt) cc_final: 0.8015 (mtpt) REVERT: D 81 ILE cc_start: 0.8585 (OUTLIER) cc_final: 0.8364 (mp) outliers start: 20 outliers final: 15 residues processed: 91 average time/residue: 0.1320 time to fit residues: 15.9307 Evaluate side-chains 96 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.300 ------------------------------------------------------------------------------- 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 84 SER Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 93 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 21 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 70 optimal weight: 7.9990 chunk 41 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 56 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 chunk 22 optimal weight: 0.9980 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 = 0.4305 r_free = 0.4305 target = 0.192981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.125586 restraints weight = 12073.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.129111 restraints weight = 8790.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.129839 restraints weight = 6064.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.130477 restraints weight = 5556.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.130554 restraints weight = 5349.387| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 10831 Z= 0.201 Angle : 0.571 6.449 15642 Z= 0.336 Chirality : 0.034 0.170 1787 Planarity : 0.004 0.051 1151 Dihedral : 30.586 177.658 3323 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.63 % Allowed : 15.79 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.84 (0.32), residues: 655 helix: 2.67 (0.22), residues: 508 sheet: None (None), residues: 0 loop : -1.12 (0.48), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 97 TYR 0.020 0.002 TYR C 112 PHE 0.014 0.002 PHE H 101 HIS 0.002 0.001 HIS C 78 Details of bonding type rmsd covalent geometry : bond 0.00465 (10831) covalent geometry : angle 0.57100 (15642) hydrogen bonds : bond 0.05946 ( 690) hydrogen bonds : angle 3.11624 ( 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 100 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.267 Fit side-chains REVERT: C 67 LYS cc_start: 0.8096 (mttt) cc_final: 0.7754 (tttm) REVERT: C 145 LYS cc_start: 0.8522 (tttt) cc_final: 0.8072 (mtpt) REVERT: D 81 ILE cc_start: 0.8626 (OUTLIER) cc_final: 0.8388 (mp) outliers start: 20 outliers final: 17 residues processed: 90 average time/residue: 0.1416 time to fit residues: 16.7138 Evaluate side-chains 97 residues out of total 551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 0.266 ------------------------------------------------------------------------------- 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 84 SER Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 74 THR 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 Chi-restraints excluded: chain H residue 93 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 57 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 76 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 47 optimal weight: 0.4980 chunk 77 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 70 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4337 r_free = 0.4337 target = 0.196139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.129837 restraints weight = 12074.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.133820 restraints weight = 8611.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.134641 restraints weight = 5871.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.135016 restraints weight = 5242.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.135233 restraints weight = 5139.666| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10831 Z= 0.148 Angle : 0.531 6.112 15642 Z= 0.317 Chirality : 0.033 0.173 1787 Planarity : 0.004 0.042 1151 Dihedral : 30.474 179.273 3323 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.90 % Allowed : 16.88 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.32 (0.33), residues: 655 helix: 2.98 (0.22), residues: 506 sheet: None (None), residues: 0 loop : -0.77 (0.49), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 97 TYR 0.023 0.001 TYR C 112 PHE 0.012 0.001 PHE F 68 HIS 0.002 0.001 HIS E 114 Details of bonding type rmsd covalent geometry : bond 0.00324 (10831) covalent geometry : angle 0.53051 (15642) hydrogen bonds : bond 0.05543 ( 690) hydrogen bonds : angle 2.86764 ( 1741) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1506.52 seconds wall clock time: 26 minutes 40.74 seconds (1600.74 seconds total)