Starting phenix.real_space_refine on Fri Sep 11 21:02:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6esf_3947/09_2026/6esf_3947.cif Found real_map, /net/cci-nas-00/data/ceres_data/6esf_3947/09_2026/6esf_3947.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6esf_3947/09_2026/6esf_3947.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6esf_3947/09_2026/6esf_3947.map" model { file = "/net/cci-nas-00/data/ceres_data/6esf_3947/09_2026/6esf_3947.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6esf_3947/09_2026/6esf_3947.cif" } resolution = 3.7 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= 0.001 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 294 5.49 5 S 12 5.16 5 C 6680 2.51 5 N 2275 2.21 5 O 2830 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12091 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 811 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 678 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "C" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 804 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "D" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 807 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 683 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "G" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 811 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Time building chain proxies: 2.24, per 1000 atoms: 0.19 Number of scatterers: 12091 At special positions: 0 Unit cell: (82.96, 121.04, 114.24, 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 12 16.00 P 294 15.00 O 2830 8.00 N 2275 7.00 C 6680 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: 0.74 Conformation dependent library (CDL) restraints added in 321.3 milliseconds 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1430 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 8 sheets defined 68.9% alpha, 2.4% beta 142 base pairs and 246 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 4.087A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 113 Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.546A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.663A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.606A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR B 72 " --> pdb=" O ASP B 68 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.681A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 46 through 72 Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.546A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 79 Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.746A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 120 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 113 removed outlier: 3.600A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.549A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.697A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 75 removed outlier: 3.697A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N HIS F 75 " --> pdb=" O THR F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.863A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 46 through 72 Processing helix chain 'G' and resid 79 through 88 Processing helix chain 'G' and resid 90 through 97 removed outlier: 3.518A pdb=" N ASN G 94 " --> pdb=" O ASP G 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 removed outlier: 4.309A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 120 removed outlier: 3.603A pdb=" N HIS H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA H 107 " --> pdb=" O LEU H 103 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA2, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.061A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.677A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 101 Processing sheet with id=AA5, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.780A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.766A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 77 through 78 374 hydrogen bonds defined for protein. 1116 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 363 hydrogen bonds 722 hydrogen bond angles 0 basepair planarities 142 basepair parallelities 246 stacking parallelities Total time for adding SS restraints: 2.10 Time building geometry restraints manager: 1.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1923 1.33 - 1.45: 4420 1.45 - 1.56: 5955 1.56 - 1.68: 586 1.68 - 1.80: 22 Bond restraints: 12906 Sorted by residual: bond pdb=" C3' DC J 6 " pdb=" O3' DC J 6 " ideal model delta sigma weight residual 1.435 1.376 0.059 1.30e-02 5.92e+03 2.07e+01 bond pdb=" C1' DC J -73 " pdb=" N1 DC J -73 " ideal model delta sigma weight residual 1.468 1.529 -0.061 1.40e-02 5.10e+03 1.92e+01 bond pdb=" N7 DA I 28 " pdb=" C5 DA I 28 " ideal model delta sigma weight residual 1.388 1.366 0.022 6.00e-03 2.78e+04 1.34e+01 bond pdb=" N7 DA J -33 " pdb=" C5 DA J -33 " ideal model delta sigma weight residual 1.388 1.366 0.022 6.00e-03 2.78e+04 1.29e+01 bond pdb=" C3' DC J -38 " pdb=" O3' DC J -38 " ideal model delta sigma weight residual 1.435 1.389 0.046 1.30e-02 5.92e+03 1.24e+01 ... (remaining 12901 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 16769 1.83 - 3.66: 1761 3.66 - 5.49: 135 5.49 - 7.32: 22 7.32 - 9.14: 5 Bond angle restraints: 18692 Sorted by residual: angle pdb=" O4' DA I 42 " pdb=" C1' DA I 42 " pdb=" N9 DA I 42 " ideal model delta sigma weight residual 108.00 111.63 -3.63 7.00e-01 2.04e+00 2.69e+01 angle pdb=" O4' DT I -57 " pdb=" C1' DT I -57 " pdb=" N1 DT I -57 " ideal model delta sigma weight residual 108.00 111.47 -3.47 7.00e-01 2.04e+00 2.46e+01 angle pdb=" N3 DT I -24 " pdb=" C4 DT I -24 " pdb=" O4 DT I -24 " ideal model delta sigma weight residual 119.90 122.84 -2.94 6.00e-01 2.78e+00 2.41e+01 angle pdb=" O5' DA I 28 " pdb=" C5' DA I 28 " pdb=" C4' DA I 28 " ideal model delta sigma weight residual 109.40 113.31 -3.91 8.00e-01 1.56e+00 2.39e+01 angle pdb=" O4' DT J 38 " pdb=" C1' DT J 38 " pdb=" N1 DT J 38 " ideal model delta sigma weight residual 108.00 111.39 -3.39 7.00e-01 2.04e+00 2.35e+01 ... (remaining 18687 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.90: 5499 35.90 - 71.80: 1480 71.80 - 107.69: 27 107.69 - 143.59: 1 143.59 - 179.49: 1 Dihedral angle restraints: 7008 sinusoidal: 4794 harmonic: 2214 Sorted by residual: dihedral pdb=" CA LEU E 60 " pdb=" C LEU E 60 " pdb=" N LEU E 61 " pdb=" CA LEU E 61 " ideal model delta harmonic sigma weight residual -180.00 -155.84 -24.16 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA TYR H 34 " pdb=" C TYR H 34 " pdb=" N ALA H 35 " pdb=" CA ALA H 35 " ideal model delta harmonic sigma weight residual 180.00 -155.97 -24.03 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA ILE A 62 " pdb=" C ILE A 62 " pdb=" N ARG A 63 " pdb=" CA ARG A 63 " ideal model delta harmonic sigma weight residual 180.00 -156.16 -23.84 0 5.00e+00 4.00e-02 2.27e+01 ... (remaining 7005 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1407 0.053 - 0.106: 597 0.106 - 0.158: 111 0.158 - 0.211: 13 0.211 - 0.264: 2 Chirality restraints: 2130 Sorted by residual: chirality pdb=" CG LEU G 34 " pdb=" CB LEU G 34 " pdb=" CD1 LEU G 34 " pdb=" CD2 LEU G 34 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" C3' DC I 52 " pdb=" C4' DC I 52 " pdb=" O3' DC I 52 " pdb=" C2' DC I 52 " both_signs ideal model delta sigma weight residual False -2.73 -2.52 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CG LEU C 34 " pdb=" CB LEU C 34 " pdb=" CD1 LEU C 34 " pdb=" CD2 LEU C 34 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 2127 not shown) Planarity restraints: 1345 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 99 " -0.042 5.00e-02 4.00e+02 6.33e-02 6.42e+00 pdb=" N PRO D 100 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO D 100 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 100 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 67 " 0.033 2.00e-02 2.50e+03 1.59e-02 6.32e+00 pdb=" N1 DT I 67 " -0.034 2.00e-02 2.50e+03 pdb=" C2 DT I 67 " -0.001 2.00e-02 2.50e+03 pdb=" O2 DT I 67 " -0.007 2.00e-02 2.50e+03 pdb=" N3 DT I 67 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DT I 67 " 0.009 2.00e-02 2.50e+03 pdb=" O4 DT I 67 " 0.009 2.00e-02 2.50e+03 pdb=" C5 DT I 67 " 0.001 2.00e-02 2.50e+03 pdb=" C7 DT I 67 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DT I 67 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 26 " -0.035 2.00e-02 2.50e+03 1.46e-02 5.86e+00 pdb=" N9 DA I 26 " 0.021 2.00e-02 2.50e+03 pdb=" C8 DA I 26 " 0.017 2.00e-02 2.50e+03 pdb=" N7 DA I 26 " -0.000 2.00e-02 2.50e+03 pdb=" C5 DA I 26 " -0.007 2.00e-02 2.50e+03 pdb=" C6 DA I 26 " -0.003 2.00e-02 2.50e+03 pdb=" N6 DA I 26 " -0.012 2.00e-02 2.50e+03 pdb=" N1 DA I 26 " -0.000 2.00e-02 2.50e+03 pdb=" C2 DA I 26 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DA I 26 " 0.011 2.00e-02 2.50e+03 pdb=" C4 DA I 26 " 0.005 2.00e-02 2.50e+03 ... (remaining 1342 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2465 2.78 - 3.31: 10427 3.31 - 3.84: 25095 3.84 - 4.37: 27796 4.37 - 4.90: 38509 Nonbonded interactions: 104292 Sorted by model distance: nonbonded pdb=" N2 DG I 73 " pdb=" O2 DC J -73 " model vdw 2.249 3.120 nonbonded pdb=" OH TYR A 99 " pdb=" OE2 GLU A 133 " model vdw 2.275 3.040 nonbonded pdb=" OH TYR C 39 " pdb=" OE1 GLU D 68 " model vdw 2.282 3.040 nonbonded pdb=" OG1 THR H 87 " pdb=" OE1 GLU H 90 " model vdw 2.293 3.040 nonbonded pdb=" O VAL H 115 " pdb=" OG1 THR H 119 " model vdw 2.299 3.040 ... (remaining 104287 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 37 and (name N or name CA or name C or name O or name CB \ )) or resid 38 through 134)) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 18 through 101) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 16 through 119) } ncs_group { reference = chain 'D' 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: 0.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.340 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 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 : 0.009 0.070 12906 Z= 0.728 Angle : 1.102 9.144 18692 Z= 0.879 Chirality : 0.056 0.264 2130 Planarity : 0.007 0.063 1345 Dihedral : 28.705 179.491 5578 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.94 % Allowed : 3.13 % Favored : 95.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.25 (0.23), residues: 746 helix: -2.79 (0.15), residues: 510 sheet: None (None), residues: 0 loop : -2.41 (0.36), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 129 TYR 0.016 0.003 TYR C 50 PHE 0.033 0.004 PHE C 25 HIS 0.014 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00883 / 0.73 (12906) covalent geometry : angle 1.10205 / 0.88 (18692) hydrogen bonds : bond 0.10461 / 6.98 ( 737) hydrogen bonds : angle 6.86556 / 4.72 ( 1838) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 282 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.7714 (mmtp) cc_final: 0.7459 (mttm) REVERT: A 123 ASP cc_start: 0.7701 (m-30) cc_final: 0.7454 (m-30) REVERT: C 33 LEU cc_start: 0.8327 (mt) cc_final: 0.7742 (tp) REVERT: C 76 THR cc_start: 0.8924 (p) cc_final: 0.8428 (t) REVERT: D 31 LYS cc_start: 0.7801 (mttt) cc_final: 0.7413 (pttm) REVERT: E 74 ILE cc_start: 0.8944 (mt) cc_final: 0.8636 (mt) REVERT: E 123 ASP cc_start: 0.7765 (m-30) cc_final: 0.7223 (m-30) REVERT: G 33 LEU cc_start: 0.8240 (mt) cc_final: 0.7814 (tp) REVERT: G 34 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8666 (mt) REVERT: G 84 GLN cc_start: 0.8332 (tp40) cc_final: 0.8089 (tp-100) REVERT: G 95 LYS cc_start: 0.8352 (ttmt) cc_final: 0.7804 (tppt) REVERT: H 31 LYS cc_start: 0.8535 (tptp) cc_final: 0.8094 (ttpt) REVERT: H 48 ASP cc_start: 0.8133 (m-30) cc_final: 0.7675 (p0) REVERT: H 90 GLU cc_start: 0.7876 (mp0) cc_final: 0.7654 (mp0) REVERT: H 117 LYS cc_start: 0.8643 (tttm) cc_final: 0.8381 (tttt) outliers start: 6 outliers final: 1 residues processed: 286 average time/residue: 0.1324 time to fit residues: 51.4224 Evaluate side-chains 169 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 167 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 51 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 0.0070 chunk 45 optimal weight: 0.7980 overall best weight: 0.9602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS A 68 GLN A 85 GLN A 108 ASN C 24 GLN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.095297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.080199 restraints weight = 43783.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.081958 restraints weight = 22000.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.083133 restraints weight = 14214.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.083862 restraints weight = 10945.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.084265 restraints weight = 9461.737| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12906 Z= 0.165 Angle : 0.776 12.082 18692 Z= 0.441 Chirality : 0.051 0.234 2130 Planarity : 0.006 0.067 1345 Dihedral : 32.787 177.603 4065 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.13 % Allowed : 16.30 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.27), residues: 746 helix: -0.62 (0.20), residues: 528 sheet: None (None), residues: 0 loop : -2.16 (0.41), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 89 TYR 0.020 0.002 TYR C 39 PHE 0.013 0.002 PHE D 67 HIS 0.008 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.17 (12906) covalent geometry : angle 0.77620 / 0.44 (18692) hydrogen bonds : bond 0.06153 / 4.07 ( 737) hydrogen bonds : angle 4.07368 / 2.82 ( 1838) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 207 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8115 (mm) cc_final: 0.7761 (mm) REVERT: A 94 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7663 (mm-30) REVERT: A 106 ASP cc_start: 0.7255 (t70) cc_final: 0.6889 (m-30) REVERT: A 107 THR cc_start: 0.8782 (t) cc_final: 0.8576 (t) REVERT: A 123 ASP cc_start: 0.7755 (m-30) cc_final: 0.7444 (m-30) REVERT: C 25 PHE cc_start: 0.8875 (OUTLIER) cc_final: 0.8623 (m-80) REVERT: C 33 LEU cc_start: 0.8026 (mt) cc_final: 0.7706 (tp) REVERT: C 57 TYR cc_start: 0.8732 (t80) cc_final: 0.8293 (t80) REVERT: C 64 GLU cc_start: 0.7686 (tm-30) cc_final: 0.7240 (tm-30) REVERT: C 76 THR cc_start: 0.8852 (p) cc_final: 0.8407 (t) REVERT: C 100 VAL cc_start: 0.9111 (p) cc_final: 0.8665 (m) REVERT: D 31 LYS cc_start: 0.7622 (mttt) cc_final: 0.7210 (pttt) REVERT: D 43 LYS cc_start: 0.7348 (OUTLIER) cc_final: 0.6819 (mtmt) REVERT: D 90 GLU cc_start: 0.8324 (mp0) cc_final: 0.8083 (mp0) REVERT: D 117 LYS cc_start: 0.8170 (tttt) cc_final: 0.7958 (tttt) REVERT: E 50 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7638 (mm-30) REVERT: E 123 ASP cc_start: 0.7946 (m-30) cc_final: 0.7031 (m-30) REVERT: G 85 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7670 (mt) REVERT: H 31 LYS cc_start: 0.8274 (tptp) cc_final: 0.7881 (ttpt) outliers start: 20 outliers final: 10 residues processed: 218 average time/residue: 0.0990 time to fit residues: 31.8643 Evaluate side-chains 186 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 173 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain F residue 18 HIS Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 103 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 2 optimal weight: 5.9990 chunk 50 optimal weight: 0.3980 chunk 37 optimal weight: 1.9990 chunk 90 optimal weight: 30.0000 chunk 47 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 chunk 46 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 77 optimal weight: 30.0000 chunk 74 optimal weight: 40.0000 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 108 ASN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN G 68 ASN ** H 46 HIS ** 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 = 0.3748 r_free = 0.3748 target = 0.095093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.079606 restraints weight = 43932.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.081341 restraints weight = 22497.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.082497 restraints weight = 14711.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.083200 restraints weight = 11416.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.083612 restraints weight = 9915.588| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12906 Z= 0.160 Angle : 0.713 10.401 18692 Z= 0.408 Chirality : 0.047 0.215 2130 Planarity : 0.005 0.060 1345 Dihedral : 32.627 178.999 4065 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 5.02 % Allowed : 17.55 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.30), residues: 746 helix: 0.45 (0.21), residues: 528 sheet: None (None), residues: 0 loop : -1.84 (0.42), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 89 TYR 0.021 0.002 TYR B 88 PHE 0.011 0.001 PHE H 67 HIS 0.009 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.16 (12906) covalent geometry : angle 0.71282 / 0.41 (18692) hydrogen bonds : bond 0.05701 / 3.77 ( 737) hydrogen bonds : angle 3.56414 / 2.49 ( 1838) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 176 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.7310 (OUTLIER) cc_final: 0.6697 (m-30) REVERT: A 123 ASP cc_start: 0.7848 (m-30) cc_final: 0.7505 (m-30) REVERT: C 33 LEU cc_start: 0.8204 (mt) cc_final: 0.7824 (tp) REVERT: C 76 THR cc_start: 0.8852 (p) cc_final: 0.8446 (t) REVERT: C 95 LYS cc_start: 0.8733 (tppt) cc_final: 0.8520 (tptt) REVERT: C 100 VAL cc_start: 0.9125 (OUTLIER) cc_final: 0.8675 (m) REVERT: D 31 LYS cc_start: 0.7552 (mttt) cc_final: 0.7245 (pttt) REVERT: E 123 ASP cc_start: 0.8118 (m-30) cc_final: 0.7135 (m-30) REVERT: G 68 ASN cc_start: 0.8309 (t0) cc_final: 0.7641 (t0) REVERT: H 31 LYS cc_start: 0.8264 (tptp) cc_final: 0.7840 (ttpt) REVERT: H 48 ASP cc_start: 0.7505 (p0) cc_final: 0.7118 (p0) REVERT: H 110 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7559 (mm-30) REVERT: H 117 LYS cc_start: 0.8562 (tttt) cc_final: 0.8243 (tttt) outliers start: 32 outliers final: 20 residues processed: 199 average time/residue: 0.0939 time to fit residues: 27.8439 Evaluate side-chains 181 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 159 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain F residue 18 HIS Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 103 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 75 optimal weight: 30.0000 chunk 21 optimal weight: 0.7980 chunk 79 optimal weight: 30.0000 chunk 53 optimal weight: 6.9990 chunk 89 optimal weight: 20.0000 chunk 78 optimal weight: 30.0000 chunk 40 optimal weight: 9.9990 chunk 96 optimal weight: 30.0000 chunk 92 optimal weight: 30.0000 chunk 14 optimal weight: 2.9990 chunk 34 optimal weight: 0.0270 overall best weight: 4.1644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.093106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.077370 restraints weight = 44064.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.079020 restraints weight = 23044.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.080107 restraints weight = 15381.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.080751 restraints weight = 12153.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.081147 restraints weight = 10667.257| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12906 Z= 0.234 Angle : 0.771 9.046 18692 Z= 0.434 Chirality : 0.048 0.224 2130 Planarity : 0.006 0.051 1345 Dihedral : 32.567 178.147 4065 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 6.58 % Allowed : 18.65 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.31), residues: 746 helix: 0.70 (0.22), residues: 529 sheet: None (None), residues: 0 loop : -1.66 (0.45), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 116 TYR 0.034 0.002 TYR B 88 PHE 0.012 0.002 PHE F 100 HIS 0.008 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.23 (12906) covalent geometry : angle 0.77146 / 0.43 (18692) hydrogen bonds : bond 0.06278 / 4.11 ( 737) hydrogen bonds : angle 3.71814 / 2.63 ( 1838) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 159 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.7119 (t70) cc_final: 0.6863 (m-30) REVERT: A 123 ASP cc_start: 0.7849 (m-30) cc_final: 0.7546 (m-30) REVERT: B 74 GLU cc_start: 0.7874 (tp30) cc_final: 0.7287 (tp30) REVERT: C 33 LEU cc_start: 0.8398 (mt) cc_final: 0.7931 (tp) REVERT: C 64 GLU cc_start: 0.7684 (tm-30) cc_final: 0.7360 (tm-30) REVERT: C 76 THR cc_start: 0.8840 (p) cc_final: 0.8402 (t) REVERT: D 31 LYS cc_start: 0.7762 (mttt) cc_final: 0.7347 (pttt) REVERT: D 117 LYS cc_start: 0.8170 (tttt) cc_final: 0.7968 (tttt) REVERT: E 123 ASP cc_start: 0.8054 (m-30) cc_final: 0.7153 (m-30) REVERT: G 68 ASN cc_start: 0.8546 (t0) cc_final: 0.7997 (t0) REVERT: H 31 LYS cc_start: 0.8280 (tptp) cc_final: 0.7795 (ttpt) REVERT: H 34 TYR cc_start: 0.8418 (m-80) cc_final: 0.7837 (m-10) REVERT: H 48 ASP cc_start: 0.7730 (p0) cc_final: 0.7213 (p0) REVERT: H 58 ILE cc_start: 0.9103 (OUTLIER) cc_final: 0.8827 (tt) REVERT: H 110 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7535 (mm-30) REVERT: H 117 LYS cc_start: 0.8567 (tttt) cc_final: 0.8279 (tttt) outliers start: 42 outliers final: 32 residues processed: 188 average time/residue: 0.0969 time to fit residues: 26.9245 Evaluate side-chains 181 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 148 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 41 TYR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 18 HIS Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 103 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 24 optimal weight: 0.9980 chunk 94 optimal weight: 20.0000 chunk 81 optimal weight: 30.0000 chunk 89 optimal weight: 20.0000 chunk 61 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 chunk 78 optimal weight: 30.0000 chunk 10 optimal weight: 1.9990 chunk 45 optimal weight: 0.0570 chunk 23 optimal weight: 0.8980 chunk 70 optimal weight: 7.9990 overall best weight: 1.3902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN G 38 ASN ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.094940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.079215 restraints weight = 43904.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.080930 restraints weight = 22646.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.082083 restraints weight = 14977.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.082759 restraints weight = 11706.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.083039 restraints weight = 10221.181| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12906 Z= 0.152 Angle : 0.688 10.697 18692 Z= 0.394 Chirality : 0.045 0.215 2130 Planarity : 0.005 0.054 1345 Dihedral : 32.467 177.298 4065 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 5.49 % Allowed : 22.10 % Favored : 72.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.31), residues: 746 helix: 1.15 (0.22), residues: 521 sheet: None (None), residues: 0 loop : -1.43 (0.45), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 63 TYR 0.028 0.002 TYR B 88 PHE 0.007 0.001 PHE D 67 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.15 (12906) covalent geometry : angle 0.68787 / 0.39 (18692) hydrogen bonds : bond 0.05274 / 3.51 ( 737) hydrogen bonds : angle 3.35761 / 2.38 ( 1838) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 168 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.7747 (m-30) cc_final: 0.7243 (m-30) REVERT: B 74 GLU cc_start: 0.7941 (tp30) cc_final: 0.7364 (tp30) REVERT: C 33 LEU cc_start: 0.8337 (mt) cc_final: 0.7995 (tp) REVERT: C 64 GLU cc_start: 0.7709 (tm-30) cc_final: 0.7471 (tm-30) REVERT: C 76 THR cc_start: 0.8798 (p) cc_final: 0.8439 (t) REVERT: C 100 VAL cc_start: 0.9079 (p) cc_final: 0.8627 (m) REVERT: D 31 LYS cc_start: 0.7627 (mttt) cc_final: 0.7241 (pttt) REVERT: D 43 LYS cc_start: 0.7344 (mtpt) cc_final: 0.7013 (mtmt) REVERT: D 59 MET cc_start: 0.8219 (tpp) cc_final: 0.7679 (tpp) REVERT: D 117 LYS cc_start: 0.8172 (tttt) cc_final: 0.7924 (tttt) REVERT: E 123 ASP cc_start: 0.7986 (m-30) cc_final: 0.7320 (m-30) REVERT: F 25 ASN cc_start: 0.8001 (OUTLIER) cc_final: 0.7726 (m-40) REVERT: G 64 GLU cc_start: 0.7705 (tm-30) cc_final: 0.7499 (tm-30) REVERT: G 68 ASN cc_start: 0.8463 (t0) cc_final: 0.7709 (t0) REVERT: H 31 LYS cc_start: 0.8234 (tptp) cc_final: 0.7823 (ttpt) REVERT: H 34 TYR cc_start: 0.8342 (m-80) cc_final: 0.7823 (m-10) REVERT: H 48 ASP cc_start: 0.7768 (p0) cc_final: 0.7243 (p0) REVERT: H 59 MET cc_start: 0.8345 (tpp) cc_final: 0.7921 (tpp) REVERT: H 110 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7515 (mm-30) REVERT: H 117 LYS cc_start: 0.8573 (tttt) cc_final: 0.8302 (ttpt) outliers start: 35 outliers final: 24 residues processed: 192 average time/residue: 0.0961 time to fit residues: 27.2469 Evaluate side-chains 183 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 158 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 18 HIS Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 103 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 15 optimal weight: 0.0010 chunk 14 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 88 optimal weight: 30.0000 chunk 84 optimal weight: 30.0000 chunk 19 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 48 optimal weight: 0.6980 overall best weight: 0.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.095408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.079857 restraints weight = 44118.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.081567 restraints weight = 22854.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.082692 restraints weight = 15146.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.083383 restraints weight = 11902.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.083746 restraints weight = 10389.149| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12906 Z= 0.142 Angle : 0.674 10.490 18692 Z= 0.385 Chirality : 0.044 0.212 2130 Planarity : 0.005 0.057 1345 Dihedral : 32.372 176.518 4065 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 4.70 % Allowed : 23.67 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.31), residues: 746 helix: 1.36 (0.22), residues: 521 sheet: None (None), residues: 0 loop : -1.34 (0.46), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 23 TYR 0.018 0.001 TYR G 39 PHE 0.007 0.001 PHE D 67 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.14 (12906) covalent geometry : angle 0.67385 / 0.39 (18692) hydrogen bonds : bond 0.05037 / 3.35 ( 737) hydrogen bonds : angle 3.21692 / 2.28 ( 1838) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 169 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 SER cc_start: 0.8226 (p) cc_final: 0.7929 (p) REVERT: A 108 ASN cc_start: 0.8507 (t0) cc_final: 0.8275 (t0) REVERT: A 123 ASP cc_start: 0.7696 (m-30) cc_final: 0.7217 (m-30) REVERT: B 25 ASN cc_start: 0.7714 (OUTLIER) cc_final: 0.7399 (m-40) REVERT: B 74 GLU cc_start: 0.7884 (tp30) cc_final: 0.7258 (tp30) REVERT: C 33 LEU cc_start: 0.8293 (mt) cc_final: 0.7962 (tp) REVERT: C 64 GLU cc_start: 0.7655 (tm-30) cc_final: 0.7389 (tm-30) REVERT: C 76 THR cc_start: 0.8759 (p) cc_final: 0.8419 (t) REVERT: C 100 VAL cc_start: 0.9082 (p) cc_final: 0.8652 (m) REVERT: D 31 LYS cc_start: 0.7647 (mttt) cc_final: 0.7226 (pttt) REVERT: D 43 LYS cc_start: 0.7352 (mtpt) cc_final: 0.7111 (mtmt) REVERT: D 59 MET cc_start: 0.8230 (tpp) cc_final: 0.7656 (tpp) REVERT: D 117 LYS cc_start: 0.8220 (tttt) cc_final: 0.7617 (ttpt) REVERT: E 82 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8426 (mt) REVERT: E 122 LYS cc_start: 0.8057 (ptpt) cc_final: 0.7783 (ptmt) REVERT: E 123 ASP cc_start: 0.8012 (m-30) cc_final: 0.7359 (m-30) REVERT: G 61 GLU cc_start: 0.7831 (tp30) cc_final: 0.7558 (tp30) REVERT: G 68 ASN cc_start: 0.8425 (t0) cc_final: 0.7676 (t0) REVERT: G 92 GLU cc_start: 0.6996 (pt0) cc_final: 0.6784 (pt0) REVERT: H 31 LYS cc_start: 0.8264 (tptp) cc_final: 0.7865 (ttpt) REVERT: H 34 TYR cc_start: 0.8274 (m-80) cc_final: 0.7739 (m-10) REVERT: H 48 ASP cc_start: 0.7645 (p0) cc_final: 0.7039 (p0) REVERT: H 59 MET cc_start: 0.8186 (tpp) cc_final: 0.7854 (tpp) REVERT: H 110 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7510 (mm-30) REVERT: H 117 LYS cc_start: 0.8492 (tttt) cc_final: 0.8213 (ttpt) outliers start: 30 outliers final: 23 residues processed: 188 average time/residue: 0.0965 time to fit residues: 26.8094 Evaluate side-chains 182 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 157 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 18 HIS Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 103 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 59 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 74 optimal weight: 30.0000 chunk 42 optimal weight: 2.9990 chunk 73 optimal weight: 30.0000 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN G 38 ASN ** H 46 HIS ** 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 = 0.3752 r_free = 0.3752 target = 0.095573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.080135 restraints weight = 43715.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.081808 restraints weight = 22709.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.082948 restraints weight = 15138.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.083637 restraints weight = 11891.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.084005 restraints weight = 10384.206| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12906 Z= 0.142 Angle : 0.673 10.381 18692 Z= 0.384 Chirality : 0.044 0.210 2130 Planarity : 0.005 0.056 1345 Dihedral : 32.293 176.375 4063 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 5.17 % Allowed : 24.14 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.31), residues: 746 helix: 1.48 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -1.31 (0.46), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 30 TYR 0.017 0.001 TYR G 39 PHE 0.007 0.001 PHE E 104 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.14 (12906) covalent geometry : angle 0.67325 / 0.38 (18692) hydrogen bonds : bond 0.04882 / 3.26 ( 737) hydrogen bonds : angle 3.14423 / 2.23 ( 1838) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 164 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 SER cc_start: 0.8194 (p) cc_final: 0.7898 (p) REVERT: A 108 ASN cc_start: 0.8480 (t0) cc_final: 0.8167 (t0) REVERT: A 123 ASP cc_start: 0.7713 (m-30) cc_final: 0.7206 (m-30) REVERT: B 74 GLU cc_start: 0.7897 (tp30) cc_final: 0.7218 (tp30) REVERT: C 33 LEU cc_start: 0.8283 (mt) cc_final: 0.7954 (tp) REVERT: C 56 GLU cc_start: 0.8285 (tt0) cc_final: 0.7604 (tm-30) REVERT: C 64 GLU cc_start: 0.7657 (tm-30) cc_final: 0.7368 (tm-30) REVERT: C 100 VAL cc_start: 0.9053 (p) cc_final: 0.8594 (m) REVERT: D 31 LYS cc_start: 0.7637 (mttt) cc_final: 0.7152 (ttpt) REVERT: D 43 LYS cc_start: 0.7343 (mtpt) cc_final: 0.7122 (mtmt) REVERT: D 59 MET cc_start: 0.8238 (tpp) cc_final: 0.7635 (tpp) REVERT: E 123 ASP cc_start: 0.8001 (m-30) cc_final: 0.7138 (m-30) REVERT: F 49 LEU cc_start: 0.8640 (mp) cc_final: 0.8411 (mm) REVERT: G 68 ASN cc_start: 0.8464 (t0) cc_final: 0.7796 (t0) REVERT: H 31 LYS cc_start: 0.8180 (tptp) cc_final: 0.7801 (ttpt) REVERT: H 34 TYR cc_start: 0.8264 (m-80) cc_final: 0.7723 (m-10) REVERT: H 48 ASP cc_start: 0.7663 (p0) cc_final: 0.7055 (p0) REVERT: H 59 MET cc_start: 0.8204 (tpp) cc_final: 0.7864 (tpp) REVERT: H 110 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7477 (mm-30) REVERT: H 117 LYS cc_start: 0.8472 (tttt) cc_final: 0.8170 (ttpt) outliers start: 33 outliers final: 24 residues processed: 187 average time/residue: 0.0954 time to fit residues: 26.3924 Evaluate side-chains 178 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 154 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 18 HIS Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 103 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 59 optimal weight: 0.7980 chunk 35 optimal weight: 8.9990 chunk 94 optimal weight: 20.0000 chunk 99 optimal weight: 30.0000 chunk 8 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 78 optimal weight: 30.0000 chunk 48 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 9 optimal weight: 0.0070 overall best weight: 2.1604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN ** H 46 HIS ** 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 = 0.3739 r_free = 0.3739 target = 0.094959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.079097 restraints weight = 43691.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.080815 restraints weight = 22884.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.081943 restraints weight = 15253.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.082625 restraints weight = 11980.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.082974 restraints weight = 10480.158| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12906 Z= 0.161 Angle : 0.684 9.700 18692 Z= 0.388 Chirality : 0.044 0.205 2130 Planarity : 0.005 0.055 1345 Dihedral : 32.211 176.278 4063 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 4.86 % Allowed : 24.14 % Favored : 71.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.31), residues: 746 helix: 1.47 (0.22), residues: 530 sheet: None (None), residues: 0 loop : -1.40 (0.45), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 63 TYR 0.016 0.002 TYR G 39 PHE 0.008 0.001 PHE D 67 HIS 0.009 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.16 (12906) covalent geometry : angle 0.68426 / 0.39 (18692) hydrogen bonds : bond 0.05095 / 3.38 ( 737) hydrogen bonds : angle 3.20967 / 2.29 ( 1838) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 150 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 SER cc_start: 0.8019 (p) cc_final: 0.7699 (p) REVERT: A 108 ASN cc_start: 0.8547 (t0) cc_final: 0.8268 (t0) REVERT: A 123 ASP cc_start: 0.7767 (m-30) cc_final: 0.7264 (m-30) REVERT: B 29 ILE cc_start: 0.8690 (OUTLIER) cc_final: 0.8423 (mp) REVERT: B 74 GLU cc_start: 0.8006 (tp30) cc_final: 0.7300 (tp30) REVERT: C 33 LEU cc_start: 0.8390 (mt) cc_final: 0.8043 (tp) REVERT: C 64 GLU cc_start: 0.7740 (tm-30) cc_final: 0.7460 (tm-30) REVERT: D 31 LYS cc_start: 0.7437 (mttt) cc_final: 0.7057 (ttpt) REVERT: D 43 LYS cc_start: 0.7297 (mtpt) cc_final: 0.7078 (mtmt) REVERT: D 59 MET cc_start: 0.8325 (tpp) cc_final: 0.7869 (tpp) REVERT: D 117 LYS cc_start: 0.8232 (tttt) cc_final: 0.7827 (tmmt) REVERT: E 82 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8501 (mt) REVERT: E 123 ASP cc_start: 0.7772 (m-30) cc_final: 0.7187 (m-30) REVERT: G 68 ASN cc_start: 0.8457 (t0) cc_final: 0.7704 (t0) REVERT: H 31 LYS cc_start: 0.8156 (tptp) cc_final: 0.7739 (ttpt) REVERT: H 34 TYR cc_start: 0.8370 (m-80) cc_final: 0.7816 (m-10) REVERT: H 48 ASP cc_start: 0.7728 (p0) cc_final: 0.7114 (p0) REVERT: H 59 MET cc_start: 0.8422 (tpp) cc_final: 0.7997 (tpp) REVERT: H 110 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7498 (mm-30) REVERT: H 117 LYS cc_start: 0.8514 (tttt) cc_final: 0.8195 (ttpt) outliers start: 31 outliers final: 26 residues processed: 171 average time/residue: 0.0949 time to fit residues: 24.4716 Evaluate side-chains 171 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 143 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 18 HIS Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 103 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 30 optimal weight: 1.9990 chunk 36 optimal weight: 0.0570 chunk 16 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 88 optimal weight: 30.0000 chunk 83 optimal weight: 30.0000 chunk 72 optimal weight: 40.0000 chunk 84 optimal weight: 30.0000 chunk 94 optimal weight: 20.0000 chunk 50 optimal weight: 0.4980 overall best weight: 1.9104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN ** H 46 HIS ** 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 = 0.3741 r_free = 0.3741 target = 0.095116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.079395 restraints weight = 43462.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.081091 restraints weight = 22796.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.082208 restraints weight = 15225.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.082897 restraints weight = 11969.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.083282 restraints weight = 10459.519| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 12906 Z= 0.157 Angle : 0.683 9.946 18692 Z= 0.387 Chirality : 0.044 0.206 2130 Planarity : 0.005 0.054 1345 Dihedral : 32.165 176.232 4063 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 5.02 % Allowed : 24.29 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.31), residues: 746 helix: 1.54 (0.22), residues: 528 sheet: None (None), residues: 0 loop : -1.38 (0.45), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 35 TYR 0.016 0.001 TYR G 39 PHE 0.008 0.001 PHE D 67 HIS 0.009 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.16 (12906) covalent geometry : angle 0.68265 / 0.39 (18692) hydrogen bonds : bond 0.04942 / 3.30 ( 737) hydrogen bonds : angle 3.15676 / 2.26 ( 1838) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 146 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 SER cc_start: 0.7982 (p) cc_final: 0.7657 (p) REVERT: A 108 ASN cc_start: 0.8535 (t0) cc_final: 0.8232 (t0) REVERT: A 123 ASP cc_start: 0.7745 (m-30) cc_final: 0.7211 (m-30) REVERT: B 29 ILE cc_start: 0.8547 (OUTLIER) cc_final: 0.8225 (mp) REVERT: B 74 GLU cc_start: 0.8020 (tp30) cc_final: 0.7291 (tp30) REVERT: C 33 LEU cc_start: 0.8379 (mt) cc_final: 0.8042 (tp) REVERT: C 64 GLU cc_start: 0.7741 (tm-30) cc_final: 0.7457 (tm-30) REVERT: D 31 LYS cc_start: 0.7421 (mttt) cc_final: 0.7043 (ttpt) REVERT: D 59 MET cc_start: 0.8275 (tpp) cc_final: 0.7829 (tpp) REVERT: E 123 ASP cc_start: 0.7775 (m-30) cc_final: 0.7193 (m-30) REVERT: F 18 HIS cc_start: 0.4854 (OUTLIER) cc_final: 0.3825 (p-80) REVERT: F 49 LEU cc_start: 0.8666 (mp) cc_final: 0.8350 (mm) REVERT: G 68 ASN cc_start: 0.8419 (t0) cc_final: 0.7681 (t0) REVERT: H 31 LYS cc_start: 0.8157 (tptp) cc_final: 0.7739 (ttpt) REVERT: H 34 TYR cc_start: 0.8350 (m-80) cc_final: 0.7797 (m-10) REVERT: H 48 ASP cc_start: 0.7709 (p0) cc_final: 0.7115 (p0) REVERT: H 59 MET cc_start: 0.8390 (tpp) cc_final: 0.7970 (tpp) REVERT: H 110 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7479 (mm-30) REVERT: H 117 LYS cc_start: 0.8412 (tttt) cc_final: 0.8081 (ttpt) outliers start: 32 outliers final: 24 residues processed: 169 average time/residue: 0.0933 time to fit residues: 23.7335 Evaluate side-chains 169 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 143 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain F residue 18 HIS Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 103 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 47 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 82 optimal weight: 30.0000 chunk 5 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 59 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 chunk 63 optimal weight: 0.0970 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN ** H 46 HIS ** 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 = 0.3744 r_free = 0.3744 target = 0.095265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.079442 restraints weight = 43875.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.081165 restraints weight = 22742.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.082312 restraints weight = 15077.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.082963 restraints weight = 11788.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.083399 restraints weight = 10344.584| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12906 Z= 0.155 Angle : 0.682 9.956 18692 Z= 0.387 Chirality : 0.044 0.205 2130 Planarity : 0.005 0.054 1345 Dihedral : 32.130 176.129 4063 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 4.39 % Allowed : 24.76 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.31), residues: 746 helix: 1.57 (0.22), residues: 530 sheet: None (None), residues: 0 loop : -1.34 (0.45), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 35 TYR 0.013 0.001 TYR G 39 PHE 0.008 0.001 PHE D 67 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.15 (12906) covalent geometry : angle 0.68229 / 0.39 (18692) hydrogen bonds : bond 0.04922 / 3.28 ( 737) hydrogen bonds : angle 3.16425 / 2.28 ( 1838) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 147 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 SER cc_start: 0.7983 (p) cc_final: 0.7659 (p) REVERT: A 108 ASN cc_start: 0.8530 (t0) cc_final: 0.8240 (t0) REVERT: A 123 ASP cc_start: 0.7836 (m-30) cc_final: 0.7316 (m-30) REVERT: B 29 ILE cc_start: 0.8512 (OUTLIER) cc_final: 0.8194 (mp) REVERT: B 74 GLU cc_start: 0.8072 (tp30) cc_final: 0.7309 (tp30) REVERT: C 33 LEU cc_start: 0.8408 (mt) cc_final: 0.8064 (tp) REVERT: C 64 GLU cc_start: 0.7806 (tm-30) cc_final: 0.7506 (tm-30) REVERT: D 31 LYS cc_start: 0.7463 (mttt) cc_final: 0.7076 (pttt) REVERT: D 59 MET cc_start: 0.8297 (tpp) cc_final: 0.7846 (tpp) REVERT: D 117 LYS cc_start: 0.8157 (tttt) cc_final: 0.7673 (ttpt) REVERT: E 123 ASP cc_start: 0.7781 (m-30) cc_final: 0.7166 (m-30) REVERT: F 18 HIS cc_start: 0.4648 (OUTLIER) cc_final: 0.3832 (p-80) REVERT: F 49 LEU cc_start: 0.8673 (mp) cc_final: 0.8348 (mm) REVERT: G 68 ASN cc_start: 0.8440 (t0) cc_final: 0.7679 (t0) REVERT: H 31 LYS cc_start: 0.8136 (tptp) cc_final: 0.7722 (ttpt) REVERT: H 34 TYR cc_start: 0.8386 (m-80) cc_final: 0.7825 (m-10) REVERT: H 48 ASP cc_start: 0.7742 (p0) cc_final: 0.7145 (p0) REVERT: H 59 MET cc_start: 0.8416 (tpp) cc_final: 0.7970 (tpp) REVERT: H 110 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7496 (mm-30) REVERT: H 117 LYS cc_start: 0.8404 (tttt) cc_final: 0.8095 (ttpt) outliers start: 28 outliers final: 23 residues processed: 166 average time/residue: 0.0927 time to fit residues: 23.4750 Evaluate side-chains 169 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain F residue 18 HIS Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 103 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 77 optimal weight: 30.0000 chunk 88 optimal weight: 30.0000 chunk 36 optimal weight: 0.5980 chunk 2 optimal weight: 6.9990 chunk 49 optimal weight: 0.9980 chunk 69 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 18 HIS ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.095622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.079757 restraints weight = 43650.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.081491 restraints weight = 22587.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.082630 restraints weight = 14985.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.083334 restraints weight = 11743.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.083665 restraints weight = 10225.930| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 12906 Z= 0.149 Angle : 0.684 10.057 18692 Z= 0.386 Chirality : 0.043 0.206 2130 Planarity : 0.005 0.054 1345 Dihedral : 32.085 176.091 4063 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 4.39 % Allowed : 24.92 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.32), residues: 746 helix: 1.72 (0.22), residues: 524 sheet: None (None), residues: 0 loop : -1.23 (0.45), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 49 TYR 0.015 0.001 TYR G 39 PHE 0.008 0.001 PHE D 67 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.15 (12906) covalent geometry : angle 0.68359 / 0.39 (18692) hydrogen bonds : bond 0.04822 / 3.21 ( 737) hydrogen bonds : angle 3.11592 / 2.25 ( 1838) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1693.12 seconds wall clock time: 29 minutes 59.68 seconds (1799.68 seconds total)