Starting phenix.real_space_refine on Thu Aug 6 16:39:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dwl_47254/08_2026/9dwl_47254.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dwl_47254/08_2026/9dwl_47254.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dwl_47254/08_2026/9dwl_47254.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dwl_47254/08_2026/9dwl_47254.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dwl_47254/08_2026/9dwl_47254.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dwl_47254/08_2026/9dwl_47254.map" } resolution = 3.9 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= 0.000 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5748 atoms to isotropic. 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 293 5.49 5 S 10 5.16 5 C 6554 2.51 5 N 2217 2.21 5 O 2803 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-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11877 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 800 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 821 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 800 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 784 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "H" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 699 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "I" Number of atoms: 2587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 2587 Classifications: {'DNA': 127} Link IDs: {'rna3p': 126} Chain: "J" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "K" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 386 Classifications: {'DNA': 19} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 18} Time building chain proxies: 2.01, per 1000 atoms: 0.17 Number of scatterers: 11877 At special positions: 0 Unit cell: (79.54, 120.28, 123.19, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 P 293 15.00 O 2803 8.00 N 2217 7.00 C 6554 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: 0.70 Conformation dependent library (CDL) restraints added in 320.0 milliseconds 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1384 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 8 sheets defined 73.7% alpha, 2.4% beta 143 base pairs and 250 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'A' and resid 44 through 49 Processing helix chain 'A' and resid 50 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.892A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.724A pdb=" N HIS A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ALA A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.570A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.714A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.530A pdb=" N ILE B 34 " --> pdb=" O THR B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.118A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.584A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.521A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.516A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 4.011A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 124 removed outlier: 3.843A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N HIS D 109 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA D 110 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS D 120 " --> pdb=" O LYS D 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 removed outlier: 3.749A pdb=" N ARG E 49 " --> pdb=" O THR E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.921A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.549A pdb=" N ALA E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.749A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.504A 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 76 removed outlier: 4.121A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.639A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.853A 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 37 removed outlier: 3.747A pdb=" N VAL G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 72 Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 removed outlier: 3.612A pdb=" N VAL H 41 " --> pdb=" O TYR H 37 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR H 42 " --> pdb=" O SER H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.594A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.627A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 124 removed outlier: 3.878A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N HIS H 109 " --> pdb=" O GLU H 105 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER H 124 " --> pdb=" O LYS H 120 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.440A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.449A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.776A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.278A 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: 7.559A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (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 78 371 hydrogen bonds defined for protein. 1101 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 367 hydrogen bonds 734 hydrogen bond angles 0 basepair planarities 143 basepair parallelities 250 stacking parallelities Total time for adding SS restraints: 2.06 Time building geometry restraints manager: 1.06 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: 2297 1.33 - 1.45: 4201 1.45 - 1.57: 5583 1.57 - 1.69: 584 1.69 - 1.81: 20 Bond restraints: 12685 Sorted by residual: bond pdb=" P DT K 129 " pdb=" OP3 DT K 129 " ideal model delta sigma weight residual 1.480 1.594 -0.114 2.00e-02 2.50e+03 3.23e+01 bond pdb=" C3' DT J 15 " pdb=" C2' DT J 15 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.10e+01 bond pdb=" C3' DG J 95 " pdb=" C2' DG J 95 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.86e+00 bond pdb=" C3' DG I 21 " pdb=" C2' DG I 21 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.69e+00 bond pdb=" C3' DG J 39 " pdb=" O3' DG J 39 " ideal model delta sigma weight residual 1.435 1.395 0.040 1.30e-02 5.92e+03 9.60e+00 ... (remaining 12680 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 16933 1.60 - 3.20: 1329 3.20 - 4.80: 94 4.80 - 6.40: 24 6.40 - 8.00: 10 Bond angle restraints: 18390 Sorted by residual: angle pdb=" O4' DC I 111 " pdb=" C4' DC I 111 " pdb=" C3' DC I 111 " ideal model delta sigma weight residual 106.00 103.06 2.94 6.00e-01 2.78e+00 2.39e+01 angle pdb=" C TYR F 88 " pdb=" CA TYR F 88 " pdb=" CB TYR F 88 " ideal model delta sigma weight residual 110.79 103.07 7.72 1.66e+00 3.63e-01 2.16e+01 angle pdb=" N3 DT I 32 " pdb=" C4 DT I 32 " pdb=" O4 DT I 32 " ideal model delta sigma weight residual 119.90 122.68 -2.78 6.00e-01 2.78e+00 2.14e+01 angle pdb=" N3 DT J 51 " pdb=" C4 DT J 51 " pdb=" O4 DT J 51 " ideal model delta sigma weight residual 119.90 122.64 -2.74 6.00e-01 2.78e+00 2.09e+01 angle pdb=" N GLU B 63 " pdb=" CA GLU B 63 " pdb=" CB GLU B 63 " ideal model delta sigma weight residual 110.28 117.36 -7.08 1.55e+00 4.16e-01 2.08e+01 ... (remaining 18385 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.36: 5130 28.36 - 56.72: 1556 56.72 - 85.08: 167 85.08 - 113.44: 4 113.44 - 141.80: 4 Dihedral angle restraints: 6861 sinusoidal: 4713 harmonic: 2148 Sorted by residual: dihedral pdb=" CD ARG B 92 " pdb=" NE ARG B 92 " pdb=" CZ ARG B 92 " pdb=" NH1 ARG B 92 " ideal model delta sinusoidal sigma weight residual 0.00 41.78 -41.78 1 1.00e+01 1.00e-02 2.44e+01 dihedral pdb=" N ARG A 40 " pdb=" C ARG A 40 " pdb=" CA ARG A 40 " pdb=" CB ARG A 40 " ideal model delta harmonic sigma weight residual 122.80 111.76 11.04 0 2.50e+00 1.60e-01 1.95e+01 dihedral pdb=" CD ARG C 71 " pdb=" NE ARG C 71 " pdb=" CZ ARG C 71 " pdb=" NH1 ARG C 71 " ideal model delta sinusoidal sigma weight residual 0.00 35.46 -35.46 1 1.00e+01 1.00e-02 1.78e+01 ... (remaining 6858 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.129: 2063 0.129 - 0.259: 30 0.259 - 0.388: 2 0.388 - 0.518: 0 0.518 - 0.647: 1 Chirality restraints: 2096 Sorted by residual: chirality pdb=" P DA I 1 " pdb=" OP1 DA I 1 " pdb=" OP2 DA I 1 " pdb=" O5' DA I 1 " both_signs ideal model delta sigma weight residual True 2.34 -2.98 -0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" CA ARG A 40 " pdb=" N ARG A 40 " pdb=" C ARG A 40 " pdb=" CB ARG A 40 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" CA PRO A 38 " pdb=" N PRO A 38 " pdb=" C PRO A 38 " pdb=" CB PRO A 38 " both_signs ideal model delta sigma weight residual False 2.72 2.37 0.35 2.00e-01 2.50e+01 3.11e+00 ... (remaining 2093 not shown) Planarity restraints: 1312 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 92 " 0.753 9.50e-02 1.11e+02 3.38e-01 6.97e+01 pdb=" NE ARG B 92 " -0.042 2.00e-02 2.50e+03 pdb=" CZ ARG B 92 " -0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG B 92 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG B 92 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 71 " -0.634 9.50e-02 1.11e+02 2.84e-01 4.93e+01 pdb=" NE ARG C 71 " 0.038 2.00e-02 2.50e+03 pdb=" CZ ARG C 71 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG C 71 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 71 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 63 " -0.489 9.50e-02 1.11e+02 2.19e-01 2.95e+01 pdb=" NE ARG A 63 " 0.029 2.00e-02 2.50e+03 pdb=" CZ ARG A 63 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 63 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 63 " -0.017 2.00e-02 2.50e+03 ... (remaining 1309 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2757 2.82 - 3.34: 10722 3.34 - 3.86: 23122 3.86 - 4.38: 25677 4.38 - 4.90: 35714 Nonbonded interactions: 97992 Sorted by model distance: nonbonded pdb=" NH2 ARG A 40 " pdb=" O3' DT J 83 " model vdw 2.297 3.120 nonbonded pdb=" O ILE C 78 " pdb=" OG SER D 55 " model vdw 2.298 3.040 nonbonded pdb=" NZ LYS E 79 " pdb=" O THR E 80 " model vdw 2.305 3.120 nonbonded pdb=" NH1 ARG G 32 " pdb=" OP2 DG J 30 " model vdw 2.337 3.120 nonbonded pdb=" N THR D 90 " pdb=" OE2 GLU D 93 " model vdw 2.344 3.120 ... (remaining 97987 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 16 through 117) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 35 through 124) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.060 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 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 : 0.007 0.114 12685 Z= 0.573 Angle : 0.869 7.999 18390 Z= 0.724 Chirality : 0.053 0.647 2096 Planarity : 0.015 0.338 1312 Dihedral : 27.704 141.801 5477 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.65 % Allowed : 1.14 % Favored : 98.21 % 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: 1.14 (0.31), residues: 726 helix: 1.69 (0.23), residues: 504 sheet: None (None), residues: 0 loop : -1.47 (0.37), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 92 TYR 0.025 0.002 TYR B 98 PHE 0.022 0.002 PHE E 104 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00661 / 0.57 (12685) covalent geometry : angle 0.86917 / 0.72 (18390) hydrogen bonds : bond 0.11362 / 7.93 ( 738) hydrogen bonds : angle 4.08529 / 2.87 ( 1835) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 196 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.9364 (mm) cc_final: 0.8865 (mm) REVERT: A 61 LEU cc_start: 0.9521 (mp) cc_final: 0.9204 (mp) REVERT: B 35 ARG cc_start: 0.9493 (mtp85) cc_final: 0.8755 (mtm-85) REVERT: C 38 ASN cc_start: 0.8175 (t0) cc_final: 0.7934 (t0) REVERT: C 64 GLU cc_start: 0.9021 (tp30) cc_final: 0.8659 (tp30) REVERT: C 72 ASP cc_start: 0.8727 (m-30) cc_final: 0.8345 (m-30) REVERT: E 90 MET cc_start: 0.9226 (mmm) cc_final: 0.9019 (mmp) REVERT: E 120 MET cc_start: 0.8375 (mpp) cc_final: 0.8164 (mpp) REVERT: F 67 ARG cc_start: 0.9494 (ttm170) cc_final: 0.9241 (ttp-110) REVERT: F 93 GLN cc_start: 0.9080 (mp10) cc_final: 0.8821 (mp10) REVERT: G 75 LYS cc_start: 0.9246 (mmpt) cc_final: 0.9010 (mmmm) REVERT: H 71 GLU cc_start: 0.9234 (tp30) cc_final: 0.8732 (tp30) REVERT: H 87 SER cc_start: 0.9366 (OUTLIER) cc_final: 0.9066 (p) REVERT: H 105 GLU cc_start: 0.8527 (tm-30) cc_final: 0.8216 (tm-30) REVERT: H 106 LEU cc_start: 0.9642 (mt) cc_final: 0.9205 (mt) outliers start: 4 outliers final: 0 residues processed: 200 average time/residue: 0.1063 time to fit residues: 29.3692 Evaluate side-chains 143 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 142 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 87 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 20.0000 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN A 108 ASN E 68 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.061045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.040748 restraints weight = 70449.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.041611 restraints weight = 35934.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.042207 restraints weight = 24346.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.042530 restraints weight = 19777.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.042755 restraints weight = 17872.120| |-----------------------------------------------------------------------------| r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12685 Z= 0.170 Angle : 0.666 9.702 18390 Z= 0.398 Chirality : 0.044 0.260 2096 Planarity : 0.005 0.049 1312 Dihedral : 30.708 143.652 4021 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.08 % Allowed : 13.80 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.31), residues: 726 helix: 1.79 (0.22), residues: 513 sheet: None (None), residues: 0 loop : -1.30 (0.39), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 86 TYR 0.022 0.002 TYR F 88 PHE 0.010 0.001 PHE E 104 HIS 0.005 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.17 (12685) covalent geometry : angle 0.66604 / 0.40 (18390) hydrogen bonds : bond 0.04946 / 3.30 ( 738) hydrogen bonds : angle 3.21979 / 2.25 ( 1835) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 154 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8790 (mt-10) cc_final: 0.8543 (pt0) REVERT: A 56 LYS cc_start: 0.9540 (ptpt) cc_final: 0.9308 (tptt) REVERT: A 59 GLU cc_start: 0.7775 (tm-30) cc_final: 0.7537 (tm-30) REVERT: A 60 LEU cc_start: 0.9166 (mm) cc_final: 0.8638 (mm) REVERT: A 61 LEU cc_start: 0.9493 (mp) cc_final: 0.9095 (mp) REVERT: A 120 MET cc_start: 0.8721 (mmm) cc_final: 0.8465 (mmm) REVERT: B 35 ARG cc_start: 0.9502 (mtp85) cc_final: 0.8846 (mtm-85) REVERT: B 98 TYR cc_start: 0.8994 (m-80) cc_final: 0.8752 (m-80) REVERT: C 38 ASN cc_start: 0.8162 (t0) cc_final: 0.7881 (t0) REVERT: C 64 GLU cc_start: 0.9015 (tp30) cc_final: 0.8677 (tp30) REVERT: D 71 GLU cc_start: 0.9113 (tt0) cc_final: 0.8831 (tm-30) REVERT: E 59 GLU cc_start: 0.8366 (mp0) cc_final: 0.8155 (mp0) REVERT: E 60 LEU cc_start: 0.9368 (tp) cc_final: 0.9009 (tt) REVERT: E 93 GLN cc_start: 0.9406 (mm110) cc_final: 0.9131 (mm110) REVERT: F 37 LEU cc_start: 0.9603 (OUTLIER) cc_final: 0.9393 (mm) REVERT: F 67 ARG cc_start: 0.9449 (ttm170) cc_final: 0.8970 (mtm-85) REVERT: F 84 MET cc_start: 0.8852 (mmm) cc_final: 0.8492 (mmm) REVERT: F 93 GLN cc_start: 0.8956 (mp10) cc_final: 0.8463 (mp10) REVERT: G 35 ARG cc_start: 0.8445 (ttp-170) cc_final: 0.7851 (ttp-170) REVERT: G 75 LYS cc_start: 0.9175 (mmpt) cc_final: 0.8947 (mmmm) REVERT: H 105 GLU cc_start: 0.8548 (tm-30) cc_final: 0.8141 (tm-30) REVERT: H 106 LEU cc_start: 0.9660 (mt) cc_final: 0.9141 (mt) outliers start: 19 outliers final: 13 residues processed: 163 average time/residue: 0.1049 time to fit residues: 24.0584 Evaluate side-chains 152 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 138 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 87 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 75 optimal weight: 30.0000 chunk 90 optimal weight: 20.0000 chunk 49 optimal weight: 1.9990 chunk 84 optimal weight: 50.0000 chunk 0 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 60 optimal weight: 9.9990 chunk 91 optimal weight: 20.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.059951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.040561 restraints weight = 70150.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.041476 restraints weight = 35651.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.042101 restraints weight = 23817.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.042458 restraints weight = 19072.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.042649 restraints weight = 16966.006| |-----------------------------------------------------------------------------| r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12685 Z= 0.187 Angle : 0.645 7.584 18390 Z= 0.386 Chirality : 0.043 0.262 2096 Planarity : 0.004 0.049 1312 Dihedral : 30.725 143.021 4021 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.41 % Allowed : 16.07 % Favored : 80.52 % 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: 1.54 (0.31), residues: 726 helix: 1.89 (0.23), residues: 516 sheet: None (None), residues: 0 loop : -1.21 (0.40), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 20 TYR 0.022 0.002 TYR B 88 PHE 0.005 0.001 PHE A 78 HIS 0.008 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.19 (12685) covalent geometry : angle 0.64516 / 0.39 (18390) hydrogen bonds : bond 0.05009 / 3.37 ( 738) hydrogen bonds : angle 3.13642 / 2.18 ( 1835) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.9205 (mm) cc_final: 0.8888 (mm) REVERT: A 61 LEU cc_start: 0.9504 (mp) cc_final: 0.9119 (mp) REVERT: A 90 MET cc_start: 0.9295 (mmp) cc_final: 0.9032 (mmp) REVERT: B 35 ARG cc_start: 0.9493 (mtp85) cc_final: 0.8728 (mtm-85) REVERT: B 63 GLU cc_start: 0.8954 (OUTLIER) cc_final: 0.8588 (pm20) REVERT: B 98 TYR cc_start: 0.9105 (m-80) cc_final: 0.8799 (m-80) REVERT: C 38 ASN cc_start: 0.8237 (t0) cc_final: 0.7942 (t0) REVERT: C 64 GLU cc_start: 0.9006 (tp30) cc_final: 0.8663 (tp30) REVERT: C 71 ARG cc_start: 0.9073 (ttp80) cc_final: 0.8776 (ttp80) REVERT: D 71 GLU cc_start: 0.9145 (tt0) cc_final: 0.8868 (tm-30) REVERT: E 59 GLU cc_start: 0.8467 (mp0) cc_final: 0.8222 (mp0) REVERT: E 60 LEU cc_start: 0.9390 (tp) cc_final: 0.8944 (tt) REVERT: F 37 LEU cc_start: 0.9584 (OUTLIER) cc_final: 0.9322 (mm) REVERT: F 67 ARG cc_start: 0.9453 (ttm110) cc_final: 0.8902 (mtm-85) REVERT: F 84 MET cc_start: 0.8909 (mmm) cc_final: 0.8334 (mmm) REVERT: F 93 GLN cc_start: 0.8955 (mp10) cc_final: 0.8726 (mp10) REVERT: G 35 ARG cc_start: 0.8453 (ttp-170) cc_final: 0.7852 (ttp-170) REVERT: G 41 GLU cc_start: 0.9287 (mt-10) cc_final: 0.8620 (pt0) REVERT: G 75 LYS cc_start: 0.9203 (mmpt) cc_final: 0.8997 (mmmm) REVERT: G 95 LYS cc_start: 0.9507 (tppp) cc_final: 0.9192 (tppt) REVERT: H 105 GLU cc_start: 0.8603 (tm-30) cc_final: 0.8181 (tm-30) REVERT: H 106 LEU cc_start: 0.9648 (mt) cc_final: 0.9102 (mt) outliers start: 21 outliers final: 10 residues processed: 147 average time/residue: 0.1085 time to fit residues: 22.5225 Evaluate side-chains 134 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 52 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 78 optimal weight: 20.0000 chunk 42 optimal weight: 0.9990 chunk 92 optimal weight: 20.0000 chunk 32 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 19 optimal weight: 0.0270 chunk 93 optimal weight: 20.0000 chunk 96 optimal weight: 50.0000 chunk 46 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 84 optimal weight: 40.0000 overall best weight: 1.3442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN B 25 ASN E 68 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.064078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.043756 restraints weight = 78810.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.044808 restraints weight = 41545.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.045521 restraints weight = 28809.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.045775 restraints weight = 23612.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.045924 restraints weight = 21579.832| |-----------------------------------------------------------------------------| r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12685 Z= 0.151 Angle : 0.626 7.151 18390 Z= 0.373 Chirality : 0.042 0.265 2096 Planarity : 0.004 0.052 1312 Dihedral : 30.743 143.203 4020 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.95 % Allowed : 18.51 % Favored : 79.55 % 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: 1.87 (0.32), residues: 726 helix: 2.10 (0.23), residues: 516 sheet: None (None), residues: 0 loop : -1.01 (0.41), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 32 TYR 0.014 0.001 TYR F 88 PHE 0.006 0.001 PHE A 78 HIS 0.003 0.001 HIS H 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.15 (12685) covalent geometry : angle 0.62619 / 0.37 (18390) hydrogen bonds : bond 0.04337 / 2.92 ( 738) hydrogen bonds : angle 2.87362 / 1.99 ( 1835) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 142 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8769 (pt0) cc_final: 0.8438 (pm20) REVERT: A 59 GLU cc_start: 0.7600 (tm-30) cc_final: 0.7360 (tm-30) REVERT: A 60 LEU cc_start: 0.9222 (mm) cc_final: 0.8981 (mm) REVERT: A 90 MET cc_start: 0.9310 (mmp) cc_final: 0.8998 (mmp) REVERT: A 120 MET cc_start: 0.8749 (mmm) cc_final: 0.8477 (mmm) REVERT: B 35 ARG cc_start: 0.9500 (mtp85) cc_final: 0.8805 (mtm-85) REVERT: B 63 GLU cc_start: 0.8914 (OUTLIER) cc_final: 0.8513 (pm20) REVERT: C 38 ASN cc_start: 0.8234 (t0) cc_final: 0.7922 (t0) REVERT: C 64 GLU cc_start: 0.9020 (tp30) cc_final: 0.8716 (tp30) REVERT: D 68 ASP cc_start: 0.9070 (t0) cc_final: 0.8865 (t0) REVERT: D 71 GLU cc_start: 0.9138 (tt0) cc_final: 0.8852 (tm-30) REVERT: E 59 GLU cc_start: 0.8495 (mp0) cc_final: 0.8220 (mp0) REVERT: E 60 LEU cc_start: 0.9390 (tp) cc_final: 0.8999 (tt) REVERT: E 90 MET cc_start: 0.9257 (mmm) cc_final: 0.9047 (mmp) REVERT: E 97 GLU cc_start: 0.8364 (mt-10) cc_final: 0.8157 (mt-10) REVERT: E 120 MET cc_start: 0.8544 (mpp) cc_final: 0.8330 (mpp) REVERT: F 37 LEU cc_start: 0.9601 (OUTLIER) cc_final: 0.9342 (mm) REVERT: F 67 ARG cc_start: 0.9461 (ttm110) cc_final: 0.8846 (mtm-85) REVERT: F 84 MET cc_start: 0.9005 (mmm) cc_final: 0.8240 (mmm) REVERT: F 93 GLN cc_start: 0.8929 (mp10) cc_final: 0.8679 (mp10) REVERT: G 35 ARG cc_start: 0.8483 (ttp-170) cc_final: 0.7845 (ttp-170) REVERT: G 41 GLU cc_start: 0.9323 (mt-10) cc_final: 0.8610 (pt0) REVERT: G 75 LYS cc_start: 0.9184 (mmpt) cc_final: 0.8971 (mmmm) REVERT: G 95 LYS cc_start: 0.9477 (tppp) cc_final: 0.9194 (tppt) REVERT: H 105 GLU cc_start: 0.8590 (tm-30) cc_final: 0.8162 (tm-30) REVERT: H 106 LEU cc_start: 0.9657 (mt) cc_final: 0.9133 (mt) outliers start: 12 outliers final: 9 residues processed: 148 average time/residue: 0.1052 time to fit residues: 21.9443 Evaluate side-chains 144 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 133 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 52 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 1 optimal weight: 3.9990 chunk 51 optimal weight: 8.9990 chunk 35 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 44 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 96 optimal weight: 50.0000 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.060620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.040616 restraints weight = 68133.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.041545 restraints weight = 34584.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.042171 restraints weight = 22966.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.042553 restraints weight = 18364.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.042746 restraints weight = 16314.879| |-----------------------------------------------------------------------------| r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12685 Z= 0.151 Angle : 0.608 7.633 18390 Z= 0.364 Chirality : 0.041 0.267 2096 Planarity : 0.004 0.044 1312 Dihedral : 30.724 143.303 4020 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.41 % Allowed : 17.69 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.32), residues: 726 helix: 2.17 (0.23), residues: 516 sheet: None (None), residues: 0 loop : -0.87 (0.42), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 32 TYR 0.016 0.001 TYR B 98 PHE 0.004 0.001 PHE A 104 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.15 (12685) covalent geometry : angle 0.60805 / 0.36 (18390) hydrogen bonds : bond 0.04245 / 2.87 ( 738) hydrogen bonds : angle 2.78993 / 1.93 ( 1835) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.9490 (ptmt) cc_final: 0.9087 (ptpp) REVERT: A 59 GLU cc_start: 0.7744 (tm-30) cc_final: 0.7370 (tm-30) REVERT: A 60 LEU cc_start: 0.9212 (mm) cc_final: 0.8834 (mm) REVERT: A 61 LEU cc_start: 0.9431 (mp) cc_final: 0.8988 (mp) REVERT: A 90 MET cc_start: 0.9335 (mmp) cc_final: 0.9087 (mmp) REVERT: B 35 ARG cc_start: 0.9513 (mtp85) cc_final: 0.8848 (mtm-85) REVERT: B 63 GLU cc_start: 0.8928 (OUTLIER) cc_final: 0.8530 (pm20) REVERT: B 98 TYR cc_start: 0.9146 (m-80) cc_final: 0.8944 (m-80) REVERT: C 38 ASN cc_start: 0.8240 (t0) cc_final: 0.7907 (t0) REVERT: C 64 GLU cc_start: 0.8998 (tp30) cc_final: 0.8709 (tp30) REVERT: C 79 ILE cc_start: 0.9380 (OUTLIER) cc_final: 0.9100 (tp) REVERT: D 68 ASP cc_start: 0.9108 (t0) cc_final: 0.8906 (t0) REVERT: D 71 GLU cc_start: 0.9187 (tt0) cc_final: 0.8922 (tm-30) REVERT: E 59 GLU cc_start: 0.8551 (mp0) cc_final: 0.8265 (mp0) REVERT: E 60 LEU cc_start: 0.9403 (tp) cc_final: 0.9051 (tt) REVERT: E 90 MET cc_start: 0.9276 (mmm) cc_final: 0.9050 (mmp) REVERT: E 94 GLU cc_start: 0.9208 (mm-30) cc_final: 0.8988 (mm-30) REVERT: E 97 GLU cc_start: 0.8375 (mt-10) cc_final: 0.8069 (mt-10) REVERT: F 37 LEU cc_start: 0.9605 (OUTLIER) cc_final: 0.9334 (mm) REVERT: F 67 ARG cc_start: 0.9461 (ttm110) cc_final: 0.8841 (mtm-85) REVERT: F 93 GLN cc_start: 0.8891 (mp10) cc_final: 0.8612 (mp10) REVERT: G 35 ARG cc_start: 0.8429 (ttp-170) cc_final: 0.8212 (ttm110) REVERT: G 41 GLU cc_start: 0.9284 (mt-10) cc_final: 0.8585 (pt0) REVERT: G 95 LYS cc_start: 0.9452 (tppp) cc_final: 0.9169 (tppt) REVERT: H 105 GLU cc_start: 0.8613 (tm-30) cc_final: 0.8184 (tm-30) REVERT: H 106 LEU cc_start: 0.9651 (mt) cc_final: 0.9113 (mt) outliers start: 21 outliers final: 7 residues processed: 153 average time/residue: 0.0985 time to fit residues: 21.6846 Evaluate side-chains 145 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 135 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain H residue 52 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 38 optimal weight: 0.8980 chunk 86 optimal weight: 20.0000 chunk 65 optimal weight: 0.8980 chunk 79 optimal weight: 20.0000 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 7.9990 chunk 91 optimal weight: 30.0000 chunk 44 optimal weight: 0.8980 chunk 26 optimal weight: 0.4980 chunk 0 optimal weight: 9.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.061304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.040586 restraints weight = 69671.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.041489 restraints weight = 35948.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.042101 restraints weight = 24457.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.042473 restraints weight = 19882.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.042635 restraints weight = 17859.556| |-----------------------------------------------------------------------------| r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12685 Z= 0.141 Angle : 0.617 8.324 18390 Z= 0.363 Chirality : 0.041 0.283 2096 Planarity : 0.004 0.044 1312 Dihedral : 30.716 143.279 4020 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.79 % Allowed : 21.75 % Favored : 76.46 % 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: 1.99 (0.32), residues: 726 helix: 2.16 (0.23), residues: 515 sheet: None (None), residues: 0 loop : -0.83 (0.42), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 71 TYR 0.014 0.001 TYR F 88 PHE 0.007 0.001 PHE A 104 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.14 (12685) covalent geometry : angle 0.61715 / 0.36 (18390) hydrogen bonds : bond 0.04013 / 2.71 ( 738) hydrogen bonds : angle 2.73522 / 1.89 ( 1835) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 148 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.9491 (ptmt) cc_final: 0.9075 (ptpp) REVERT: A 59 GLU cc_start: 0.7765 (tm-30) cc_final: 0.7480 (tm-30) REVERT: A 60 LEU cc_start: 0.9230 (mm) cc_final: 0.8955 (mm) REVERT: A 61 LEU cc_start: 0.9438 (mp) cc_final: 0.9050 (mp) REVERT: A 90 MET cc_start: 0.9319 (mmp) cc_final: 0.9088 (mmp) REVERT: A 120 MET cc_start: 0.8763 (mmm) cc_final: 0.8494 (mmm) REVERT: B 35 ARG cc_start: 0.9520 (mtp85) cc_final: 0.8857 (mtm-85) REVERT: B 63 GLU cc_start: 0.8906 (OUTLIER) cc_final: 0.8536 (pm20) REVERT: C 64 GLU cc_start: 0.8994 (tp30) cc_final: 0.8721 (tp30) REVERT: D 71 GLU cc_start: 0.9160 (tt0) cc_final: 0.8915 (tm-30) REVERT: E 59 GLU cc_start: 0.8546 (mp0) cc_final: 0.8062 (mp0) REVERT: E 60 LEU cc_start: 0.9383 (tp) cc_final: 0.9018 (tt) REVERT: E 90 MET cc_start: 0.9249 (mmm) cc_final: 0.9038 (mmp) REVERT: E 120 MET cc_start: 0.8548 (mpp) cc_final: 0.8226 (mpp) REVERT: F 37 LEU cc_start: 0.9594 (OUTLIER) cc_final: 0.9333 (mm) REVERT: F 53 GLU cc_start: 0.8872 (mp0) cc_final: 0.8580 (mp0) REVERT: F 67 ARG cc_start: 0.9464 (ttm110) cc_final: 0.8873 (mtm-85) REVERT: F 93 GLN cc_start: 0.8864 (mp10) cc_final: 0.8575 (mp10) REVERT: G 35 ARG cc_start: 0.8392 (ttp-170) cc_final: 0.8123 (ttm110) REVERT: G 95 LYS cc_start: 0.9432 (tppp) cc_final: 0.9157 (tppt) REVERT: H 105 GLU cc_start: 0.8611 (tm-30) cc_final: 0.8174 (tm-30) REVERT: H 106 LEU cc_start: 0.9655 (mt) cc_final: 0.9100 (mt) outliers start: 11 outliers final: 8 residues processed: 153 average time/residue: 0.1011 time to fit residues: 22.2086 Evaluate side-chains 145 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 135 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 52 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 63 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 35 optimal weight: 10.0000 chunk 95 optimal weight: 30.0000 chunk 94 optimal weight: 30.0000 chunk 48 optimal weight: 4.9990 chunk 57 optimal weight: 0.3980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.061452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.040669 restraints weight = 69432.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.041558 restraints weight = 36192.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.042137 restraints weight = 24744.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.042539 restraints weight = 20199.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.042713 restraints weight = 18128.560| |-----------------------------------------------------------------------------| r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12685 Z= 0.141 Angle : 0.618 7.727 18390 Z= 0.365 Chirality : 0.041 0.268 2096 Planarity : 0.004 0.059 1312 Dihedral : 30.705 142.911 4020 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.27 % Allowed : 20.94 % Favored : 76.79 % 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: 1.97 (0.32), residues: 726 helix: 2.14 (0.23), residues: 515 sheet: None (None), residues: 0 loop : -0.81 (0.41), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 71 TYR 0.015 0.001 TYR H 40 PHE 0.021 0.001 PHE E 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.14 (12685) covalent geometry : angle 0.61763 / 0.36 (18390) hydrogen bonds : bond 0.03918 / 2.66 ( 738) hydrogen bonds : angle 2.70730 / 1.87 ( 1835) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 146 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.9172 (tt) cc_final: 0.8905 (mt) REVERT: A 56 LYS cc_start: 0.9481 (ptmt) cc_final: 0.9047 (ptpp) REVERT: A 59 GLU cc_start: 0.7745 (tm-30) cc_final: 0.7479 (tm-30) REVERT: A 60 LEU cc_start: 0.9236 (mm) cc_final: 0.8963 (mm) REVERT: A 61 LEU cc_start: 0.9449 (mp) cc_final: 0.9051 (mp) REVERT: A 120 MET cc_start: 0.8815 (mmm) cc_final: 0.8525 (mmm) REVERT: B 35 ARG cc_start: 0.9517 (mtp85) cc_final: 0.8894 (mtm-85) REVERT: B 63 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.8523 (pm20) REVERT: C 56 GLU cc_start: 0.8696 (tm-30) cc_final: 0.8251 (tm-30) REVERT: C 64 GLU cc_start: 0.8966 (tp30) cc_final: 0.8700 (tp30) REVERT: D 68 ASP cc_start: 0.9046 (t0) cc_final: 0.8838 (t0) REVERT: D 71 GLU cc_start: 0.9118 (tt0) cc_final: 0.8906 (tm-30) REVERT: D 113 GLU cc_start: 0.9170 (mm-30) cc_final: 0.8723 (mt-10) REVERT: E 56 LYS cc_start: 0.9245 (pttm) cc_final: 0.9007 (pttm) REVERT: E 59 GLU cc_start: 0.8565 (mp0) cc_final: 0.8033 (mp0) REVERT: E 60 LEU cc_start: 0.9405 (tp) cc_final: 0.9003 (tt) REVERT: E 90 MET cc_start: 0.9251 (mmm) cc_final: 0.9022 (mmp) REVERT: F 37 LEU cc_start: 0.9586 (OUTLIER) cc_final: 0.9318 (mm) REVERT: F 53 GLU cc_start: 0.8894 (mp0) cc_final: 0.8614 (mp0) REVERT: F 67 ARG cc_start: 0.9452 (ttm110) cc_final: 0.8891 (mtm-85) REVERT: F 84 MET cc_start: 0.9008 (mmm) cc_final: 0.8083 (mmm) REVERT: F 93 GLN cc_start: 0.8851 (mp10) cc_final: 0.8547 (mp10) REVERT: G 35 ARG cc_start: 0.8369 (ttp-170) cc_final: 0.8119 (ttm110) REVERT: G 95 LYS cc_start: 0.9430 (tppp) cc_final: 0.9154 (tppt) REVERT: H 105 GLU cc_start: 0.8585 (tm-30) cc_final: 0.8383 (tm-30) REVERT: H 106 LEU cc_start: 0.9646 (mt) cc_final: 0.9247 (mt) outliers start: 14 outliers final: 10 residues processed: 153 average time/residue: 0.0981 time to fit residues: 21.4794 Evaluate side-chains 147 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 135 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 100 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 12 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 60 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 90 optimal weight: 20.0000 chunk 77 optimal weight: 20.0000 chunk 68 optimal weight: 3.9990 chunk 33 optimal weight: 0.4980 chunk 89 optimal weight: 20.0000 chunk 19 optimal weight: 0.3980 chunk 54 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.061654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.040952 restraints weight = 68609.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.041877 restraints weight = 35519.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.042470 restraints weight = 24150.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.042866 restraints weight = 19623.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.043074 restraints weight = 17532.903| |-----------------------------------------------------------------------------| r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 12685 Z= 0.142 Angle : 0.650 14.725 18390 Z= 0.374 Chirality : 0.042 0.554 2096 Planarity : 0.004 0.078 1312 Dihedral : 30.717 142.703 4020 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.44 % Allowed : 21.75 % Favored : 75.81 % 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: 1.92 (0.32), residues: 726 helix: 2.09 (0.23), residues: 515 sheet: None (None), residues: 0 loop : -0.79 (0.41), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 71 TYR 0.017 0.001 TYR H 40 PHE 0.009 0.001 PHE E 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.14 (12685) covalent geometry : angle 0.64952 / 0.37 (18390) hydrogen bonds : bond 0.03886 / 2.64 ( 738) hydrogen bonds : angle 2.72456 / 1.89 ( 1835) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 143 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.9131 (tt) cc_final: 0.8843 (mt) REVERT: A 56 LYS cc_start: 0.9465 (ptmt) cc_final: 0.9026 (ptpp) REVERT: A 59 GLU cc_start: 0.7730 (tm-30) cc_final: 0.7414 (tm-30) REVERT: A 60 LEU cc_start: 0.9258 (mm) cc_final: 0.9018 (mm) REVERT: A 61 LEU cc_start: 0.9417 (mp) cc_final: 0.8912 (mt) REVERT: A 120 MET cc_start: 0.8814 (mmm) cc_final: 0.8531 (mmm) REVERT: B 35 ARG cc_start: 0.9522 (mtp85) cc_final: 0.8894 (mtm-85) REVERT: B 63 GLU cc_start: 0.8900 (OUTLIER) cc_final: 0.8520 (pm20) REVERT: B 98 TYR cc_start: 0.8994 (m-80) cc_final: 0.8567 (m-80) REVERT: C 56 GLU cc_start: 0.8735 (tm-30) cc_final: 0.8293 (tm-30) REVERT: C 64 GLU cc_start: 0.8991 (tp30) cc_final: 0.8722 (tp30) REVERT: D 68 ASP cc_start: 0.9062 (t0) cc_final: 0.8848 (t0) REVERT: D 71 GLU cc_start: 0.9115 (tt0) cc_final: 0.8894 (tm-30) REVERT: D 113 GLU cc_start: 0.9183 (mm-30) cc_final: 0.8741 (mt-10) REVERT: E 59 GLU cc_start: 0.8562 (mp0) cc_final: 0.8050 (mp0) REVERT: E 60 LEU cc_start: 0.9400 (tp) cc_final: 0.9065 (tt) REVERT: E 90 MET cc_start: 0.9262 (mmm) cc_final: 0.8960 (mmp) REVERT: E 93 GLN cc_start: 0.9409 (tp40) cc_final: 0.8880 (mm-40) REVERT: E 94 GLU cc_start: 0.9240 (mm-30) cc_final: 0.8978 (mm-30) REVERT: E 97 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7922 (mt-10) REVERT: E 120 MET cc_start: 0.8581 (mpp) cc_final: 0.8269 (mpp) REVERT: F 37 LEU cc_start: 0.9578 (OUTLIER) cc_final: 0.9309 (mm) REVERT: F 53 GLU cc_start: 0.8941 (mp0) cc_final: 0.8642 (mp0) REVERT: F 67 ARG cc_start: 0.9468 (ttm110) cc_final: 0.8909 (mtm-85) REVERT: G 35 ARG cc_start: 0.8358 (ttp-170) cc_final: 0.8108 (ttm110) REVERT: G 95 LYS cc_start: 0.9424 (tppp) cc_final: 0.9135 (tppt) REVERT: H 105 GLU cc_start: 0.8636 (tm-30) cc_final: 0.8411 (tm-30) REVERT: H 106 LEU cc_start: 0.9650 (mt) cc_final: 0.9249 (mt) outliers start: 15 outliers final: 12 residues processed: 150 average time/residue: 0.0944 time to fit residues: 20.5240 Evaluate side-chains 146 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 132 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 100 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 42 optimal weight: 0.2980 chunk 2 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 85 optimal weight: 30.0000 chunk 62 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 82 optimal weight: 50.0000 chunk 38 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.064621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.044339 restraints weight = 78195.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.045387 restraints weight = 41806.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.046113 restraints weight = 29048.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.046419 restraints weight = 23769.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.046611 restraints weight = 21600.268| |-----------------------------------------------------------------------------| r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12685 Z= 0.151 Angle : 0.642 11.578 18390 Z= 0.371 Chirality : 0.041 0.389 2096 Planarity : 0.004 0.074 1312 Dihedral : 30.737 142.567 4020 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.92 % Allowed : 22.24 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.32), residues: 726 helix: 2.10 (0.23), residues: 515 sheet: None (None), residues: 0 loop : -0.81 (0.41), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 86 TYR 0.018 0.001 TYR H 40 PHE 0.017 0.001 PHE E 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.15 (12685) covalent geometry : angle 0.64241 / 0.37 (18390) hydrogen bonds : bond 0.04090 / 2.81 ( 738) hydrogen bonds : angle 2.79718 / 1.93 ( 1835) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.9167 (tt) cc_final: 0.8854 (mt) REVERT: A 59 GLU cc_start: 0.7784 (tm-30) cc_final: 0.7527 (tm-30) REVERT: A 60 LEU cc_start: 0.9277 (mm) cc_final: 0.9009 (mm) REVERT: A 61 LEU cc_start: 0.9426 (mp) cc_final: 0.9013 (mp) REVERT: B 35 ARG cc_start: 0.9517 (mtp85) cc_final: 0.8860 (mtm-85) REVERT: B 63 GLU cc_start: 0.8886 (OUTLIER) cc_final: 0.8498 (pm20) REVERT: C 56 GLU cc_start: 0.8756 (tm-30) cc_final: 0.8499 (tm-30) REVERT: C 64 GLU cc_start: 0.9000 (tp30) cc_final: 0.8724 (tp30) REVERT: D 68 ASP cc_start: 0.9074 (t0) cc_final: 0.8862 (t0) REVERT: D 71 GLU cc_start: 0.9104 (tt0) cc_final: 0.8896 (tm-30) REVERT: D 113 GLU cc_start: 0.9184 (mm-30) cc_final: 0.8885 (mt-10) REVERT: E 56 LYS cc_start: 0.9194 (pttm) cc_final: 0.8900 (pttm) REVERT: E 59 GLU cc_start: 0.8557 (mp0) cc_final: 0.8002 (mp0) REVERT: E 60 LEU cc_start: 0.9391 (tp) cc_final: 0.9072 (tt) REVERT: E 67 PHE cc_start: 0.9172 (t80) cc_final: 0.8785 (t80) REVERT: E 90 MET cc_start: 0.9273 (mmm) cc_final: 0.9009 (mmp) REVERT: E 94 GLU cc_start: 0.9263 (mm-30) cc_final: 0.8988 (mm-30) REVERT: E 97 GLU cc_start: 0.8265 (mt-10) cc_final: 0.7865 (mt-10) REVERT: E 120 MET cc_start: 0.8550 (mpp) cc_final: 0.8255 (mpp) REVERT: E 129 ARG cc_start: 0.9126 (OUTLIER) cc_final: 0.8364 (ttp80) REVERT: F 37 LEU cc_start: 0.9590 (OUTLIER) cc_final: 0.9314 (mm) REVERT: F 53 GLU cc_start: 0.8993 (mp0) cc_final: 0.8674 (mp0) REVERT: F 67 ARG cc_start: 0.9466 (ttm110) cc_final: 0.9013 (mtm-85) REVERT: F 84 MET cc_start: 0.9082 (mmm) cc_final: 0.8232 (mmm) REVERT: G 35 ARG cc_start: 0.8417 (ttp-170) cc_final: 0.8149 (ttm110) REVERT: G 95 LYS cc_start: 0.9424 (tppp) cc_final: 0.9151 (tppt) REVERT: H 105 GLU cc_start: 0.8606 (tm-30) cc_final: 0.8383 (tm-30) REVERT: H 106 LEU cc_start: 0.9652 (mt) cc_final: 0.9240 (mt) outliers start: 18 outliers final: 10 residues processed: 143 average time/residue: 0.0862 time to fit residues: 17.9214 Evaluate side-chains 147 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 134 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain H residue 52 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 91 optimal weight: 30.0000 chunk 90 optimal weight: 20.0000 chunk 1 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 31 optimal weight: 0.0050 chunk 13 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 11 optimal weight: 0.0670 chunk 83 optimal weight: 30.0000 chunk 42 optimal weight: 0.9980 overall best weight: 0.5732 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 63 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.061776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.041379 restraints weight = 69279.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.042300 restraints weight = 35237.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.042924 restraints weight = 23780.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.043299 restraints weight = 19155.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.043477 restraints weight = 17122.848| |-----------------------------------------------------------------------------| r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 12685 Z= 0.142 Angle : 0.650 12.728 18390 Z= 0.373 Chirality : 0.041 0.373 2096 Planarity : 0.004 0.058 1312 Dihedral : 30.754 142.625 4020 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.27 % Allowed : 23.21 % Favored : 74.51 % 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: 1.94 (0.32), residues: 726 helix: 2.09 (0.23), residues: 515 sheet: None (None), residues: 0 loop : -0.78 (0.42), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 86 TYR 0.018 0.001 TYR H 40 PHE 0.018 0.001 PHE E 67 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.14 (12685) covalent geometry : angle 0.65001 / 0.37 (18390) hydrogen bonds : bond 0.03779 / 2.58 ( 738) hydrogen bonds : angle 2.72231 / 1.89 ( 1835) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 140 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.9530 (ptmt) cc_final: 0.9144 (ptpp) REVERT: A 59 GLU cc_start: 0.7750 (tm-30) cc_final: 0.7461 (tm-30) REVERT: A 60 LEU cc_start: 0.9266 (mm) cc_final: 0.8960 (mm) REVERT: A 61 LEU cc_start: 0.9423 (mp) cc_final: 0.8858 (mt) REVERT: B 35 ARG cc_start: 0.9513 (mtp85) cc_final: 0.8899 (mtm-85) REVERT: B 63 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.8513 (pm20) REVERT: C 56 GLU cc_start: 0.8704 (tm-30) cc_final: 0.8240 (tm-30) REVERT: C 64 GLU cc_start: 0.8956 (tp30) cc_final: 0.8686 (tp30) REVERT: D 71 GLU cc_start: 0.9095 (tt0) cc_final: 0.8868 (tm-30) REVERT: D 113 GLU cc_start: 0.9155 (mm-30) cc_final: 0.8726 (mt-10) REVERT: E 59 GLU cc_start: 0.8525 (mp0) cc_final: 0.7976 (mp0) REVERT: E 60 LEU cc_start: 0.9361 (tp) cc_final: 0.9031 (tt) REVERT: E 90 MET cc_start: 0.9224 (mmm) cc_final: 0.8946 (mmp) REVERT: E 94 GLU cc_start: 0.9232 (mm-30) cc_final: 0.8930 (mm-30) REVERT: E 97 GLU cc_start: 0.8278 (mt-10) cc_final: 0.7888 (mt-10) REVERT: E 120 MET cc_start: 0.8569 (mpp) cc_final: 0.8303 (mpp) REVERT: E 129 ARG cc_start: 0.9122 (OUTLIER) cc_final: 0.8374 (ttp80) REVERT: F 37 LEU cc_start: 0.9579 (OUTLIER) cc_final: 0.9312 (mm) REVERT: F 53 GLU cc_start: 0.8905 (mp0) cc_final: 0.8635 (mp0) REVERT: F 67 ARG cc_start: 0.9471 (ttm110) cc_final: 0.8912 (mtm-85) REVERT: F 84 MET cc_start: 0.9075 (mmm) cc_final: 0.8191 (mmm) REVERT: G 35 ARG cc_start: 0.8299 (ttp-170) cc_final: 0.8047 (ttm110) REVERT: G 95 LYS cc_start: 0.9420 (tppp) cc_final: 0.9139 (tppt) REVERT: H 105 GLU cc_start: 0.8590 (tm-30) cc_final: 0.8368 (tm-30) REVERT: H 106 LEU cc_start: 0.9654 (mt) cc_final: 0.9241 (mt) outliers start: 14 outliers final: 10 residues processed: 147 average time/residue: 0.0904 time to fit residues: 19.2371 Evaluate side-chains 146 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 133 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 63 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 40 optimal weight: 2.9990 chunk 37 optimal weight: 0.0470 chunk 55 optimal weight: 1.9990 chunk 93 optimal weight: 20.0000 chunk 24 optimal weight: 0.9990 chunk 25 optimal weight: 0.0570 chunk 23 optimal weight: 2.9990 chunk 79 optimal weight: 20.0000 chunk 60 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.0202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.061732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.041577 restraints weight = 67809.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.042528 restraints weight = 34449.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.043146 restraints weight = 23017.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.043547 restraints weight = 18427.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.043730 restraints weight = 16407.901| |-----------------------------------------------------------------------------| r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.207 12685 Z= 0.196 Angle : 0.882 59.121 18390 Z= 0.537 Chirality : 0.041 0.365 2096 Planarity : 0.004 0.059 1312 Dihedral : 30.754 142.626 4020 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.27 % Allowed : 23.21 % Favored : 74.51 % Cbeta Deviations : 0.14 % 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: 1.92 (0.32), residues: 726 helix: 2.08 (0.23), residues: 515 sheet: None (None), residues: 0 loop : -0.78 (0.42), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 86 TYR 0.017 0.001 TYR H 40 PHE 0.017 0.001 PHE E 67 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.20 (12685) covalent geometry : angle 0.88151 / 0.54 (18390) hydrogen bonds : bond 0.03801 / 2.60 ( 738) hydrogen bonds : angle 2.72578 / 1.89 ( 1835) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1685.42 seconds wall clock time: 29 minutes 38.64 seconds (1778.64 seconds total)