Starting phenix.real_space_refine on Thu Aug 6 17:52:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9slj_55003/08_2026/9slj_55003.cif Found real_map, /net/cci-nas-00/data/ceres_data/9slj_55003/08_2026/9slj_55003.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9slj_55003/08_2026/9slj_55003.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9slj_55003/08_2026/9slj_55003.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9slj_55003/08_2026/9slj_55003.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9slj_55003/08_2026/9slj_55003.map" } resolution = 3.8 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 293 5.49 5 S 40 5.16 5 C 9415 2.51 5 N 3025 2.21 5 O 3617 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16390 Number of models: 1 Model: "" Number of chains: 16 Chain: "L" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 633 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "M" Number of atoms: 1118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1118 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 9, 'TRANS': 127} Chain: "N" Number of atoms: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 346 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 2, 'TRANS': 39} Chain: "A" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 811 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "C" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 862 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "D" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 746 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 831 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "F" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 657 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "G" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 871 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 5, 'TRANS': 107} Chain: "H" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 746 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 3034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3034 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2990 Classifications: {'DNA': 147} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 146} Chain: "O" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 633 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "P" Number of atoms: 1118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1118 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 9, 'TRANS': 127} Chain: "Q" Number of atoms: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 346 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 2, 'TRANS': 39} Time building chain proxies: 3.72, per 1000 atoms: 0.23 Number of scatterers: 16390 At special positions: 0 Unit cell: (133.041, 138.857, 145.4, 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 40 16.00 P 293 15.00 O 3617 8.00 N 3025 7.00 C 9415 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: 1.36 Conformation dependent library (CDL) restraints added in 536.2 milliseconds 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2444 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 10 sheets defined 72.5% alpha, 2.0% beta 147 base pairs and 250 stacking pairs defined. Time for finding SS restraints: 2.28 Creating SS restraints... Processing helix chain 'L' and resid 9 through 61 Processing helix chain 'L' and resid 62 through 67 Processing helix chain 'L' and resid 69 through 76 removed outlier: 3.761A pdb=" N TYR L 73 " --> pdb=" O ASN L 69 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU L 76 " --> pdb=" O ASP L 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 10 through 13 Processing helix chain 'M' and resid 14 through 21 removed outlier: 3.650A pdb=" N THR M 21 " --> pdb=" O HIS M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 34 through 42 Processing helix chain 'M' and resid 72 through 81 Processing helix chain 'M' and resid 85 through 89 Processing helix chain 'M' and resid 97 through 141 removed outlier: 3.546A pdb=" N MET M 141 " --> pdb=" O GLN M 137 " (cutoff:3.500A) Processing helix chain 'N' and resid 7 through 9 No H-bonds generated for 'chain 'N' and resid 7 through 9' Processing helix chain 'N' and resid 10 through 46 removed outlier: 4.575A pdb=" N LEU N 31 " --> pdb=" O ASP N 27 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N VAL N 32 " --> pdb=" O ASN N 28 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N MET N 44 " --> pdb=" O GLU N 40 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE N 45 " --> pdb=" O ALA N 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 56 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.934A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.664A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.922A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.555A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.606A 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 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.494A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 91 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.552A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 123 removed outlier: 4.259A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.700A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.693A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.869A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.554A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.662A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.697A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 124 removed outlier: 3.990A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) Processing helix chain 'O' and resid 9 through 61 Processing helix chain 'O' and resid 62 through 67 Processing helix chain 'O' and resid 69 through 76 removed outlier: 3.976A pdb=" N TYR O 73 " --> pdb=" O ASN O 69 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU O 76 " --> pdb=" O ASP O 72 " (cutoff:3.500A) Processing helix chain 'P' and resid 10 through 13 Processing helix chain 'P' and resid 14 through 21 removed outlier: 3.681A pdb=" N THR P 21 " --> pdb=" O HIS P 17 " (cutoff:3.500A) Processing helix chain 'P' and resid 34 through 42 Processing helix chain 'P' and resid 72 through 81 Processing helix chain 'P' and resid 85 through 89 Processing helix chain 'P' and resid 92 through 96 removed outlier: 3.989A pdb=" N GLU P 95 " --> pdb=" O GLN P 92 " (cutoff:3.500A) Processing helix chain 'P' and resid 97 through 141 removed outlier: 3.599A pdb=" N MET P 141 " --> pdb=" O GLN P 137 " (cutoff:3.500A) Processing helix chain 'Q' and resid 7 through 9 No H-bonds generated for 'chain 'Q' and resid 7 through 9' Processing helix chain 'Q' and resid 10 through 46 removed outlier: 4.186A pdb=" N LEU Q 31 " --> pdb=" O ASP Q 27 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N VAL Q 32 " --> pdb=" O ASN Q 28 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N MET Q 44 " --> pdb=" O GLU Q 40 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE Q 45 " --> pdb=" O ALA Q 41 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'M' and resid 43 through 45 Processing sheet with id=AA2, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.415A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.324A 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 'C' and resid 100 through 101 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.045A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.659A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB1, first strand: chain 'P' and resid 43 through 45 688 hydrogen bonds defined for protein. 2019 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 377 hydrogen bonds 754 hydrogen bond angles 0 basepair planarities 147 basepair parallelities 250 stacking parallelities Total time for adding SS restraints: 3.27 Time building geometry restraints manager: 1.85 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: 3632 1.33 - 1.45: 4852 1.45 - 1.57: 8158 1.57 - 1.69: 585 1.69 - 1.81: 62 Bond restraints: 17289 Sorted by residual: bond pdb=" C3' DC I 103 " pdb=" C2' DC I 103 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.03e+01 bond pdb=" C3' DG I 135 " pdb=" C2' DG I 135 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.58e+00 bond pdb=" C3' DA J 285 " pdb=" C2' DA J 285 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.98e+00 bond pdb=" C3' DA J 198 " pdb=" C2' DA J 198 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.96e+00 bond pdb=" C3' DG I 63 " pdb=" C2' DG I 63 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.95e+00 ... (remaining 17284 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 23697 2.06 - 4.13: 798 4.13 - 6.19: 53 6.19 - 8.26: 15 8.26 - 10.32: 3 Bond angle restraints: 24566 Sorted by residual: angle pdb=" O4' DC J 289 " pdb=" C4' DC J 289 " pdb=" C3' DC J 289 " ideal model delta sigma weight residual 106.00 103.02 2.98 6.00e-01 2.78e+00 2.47e+01 angle pdb=" O4' DG I 130 " pdb=" C4' DG I 130 " pdb=" C3' DG I 130 " ideal model delta sigma weight residual 106.00 103.10 2.90 6.00e-01 2.78e+00 2.34e+01 angle pdb=" C ASP B 24 " pdb=" CA ASP B 24 " pdb=" CB ASP B 24 " ideal model delta sigma weight residual 110.26 117.44 -7.18 1.50e+00 4.44e-01 2.29e+01 angle pdb=" N3 DT J 178 " pdb=" C4 DT J 178 " pdb=" O4 DT J 178 " ideal model delta sigma weight residual 119.90 122.73 -2.83 6.00e-01 2.78e+00 2.23e+01 angle pdb=" N3 DT I 49 " pdb=" C4 DT I 49 " pdb=" O4 DT I 49 " ideal model delta sigma weight residual 119.90 122.60 -2.70 6.00e-01 2.78e+00 2.02e+01 ... (remaining 24561 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.17: 6758 19.17 - 38.34: 1577 38.34 - 57.51: 1220 57.51 - 76.69: 174 76.69 - 95.86: 21 Dihedral angle restraints: 9750 sinusoidal: 6001 harmonic: 3749 Sorted by residual: dihedral pdb=" CA ASP B 24 " pdb=" C ASP B 24 " pdb=" N ASN B 25 " pdb=" CA ASN B 25 " ideal model delta harmonic sigma weight residual 180.00 161.87 18.13 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA GLN F 27 " pdb=" C GLN F 27 " pdb=" N GLY F 28 " pdb=" CA GLY F 28 " ideal model delta harmonic sigma weight residual 180.00 162.67 17.33 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CB GLU G 61 " pdb=" CG GLU G 61 " pdb=" CD GLU G 61 " pdb=" OE1 GLU G 61 " ideal model delta sinusoidal sigma weight residual 0.00 89.76 -89.76 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 9747 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2280 0.056 - 0.112: 414 0.112 - 0.168: 49 0.168 - 0.224: 3 0.224 - 0.280: 2 Chirality restraints: 2748 Sorted by residual: chirality pdb=" CB VAL O 32 " pdb=" CA VAL O 32 " pdb=" CG1 VAL O 32 " pdb=" CG2 VAL O 32 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CG LEU N 23 " pdb=" CB LEU N 23 " pdb=" CD1 LEU N 23 " pdb=" CD2 LEU N 23 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA ASP B 24 " pdb=" N ASP B 24 " pdb=" C ASP B 24 " pdb=" CB ASP B 24 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.93e-01 ... (remaining 2745 not shown) Planarity restraints: 2110 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 24 " 0.016 2.00e-02 2.50e+03 3.28e-02 1.08e+01 pdb=" C ASP B 24 " -0.057 2.00e-02 2.50e+03 pdb=" O ASP B 24 " 0.022 2.00e-02 2.50e+03 pdb=" N ASN B 25 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 83 " 0.019 2.00e-02 2.50e+03 1.52e-02 4.61e+00 pdb=" CG TYR H 83 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TYR H 83 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR H 83 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR H 83 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR H 83 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR H 83 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR H 83 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU H 71 " 0.009 2.00e-02 2.50e+03 1.89e-02 3.59e+00 pdb=" CD GLU H 71 " -0.033 2.00e-02 2.50e+03 pdb=" OE1 GLU H 71 " 0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU H 71 " 0.012 2.00e-02 2.50e+03 ... (remaining 2107 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.89: 5553 2.89 - 3.39: 16740 3.39 - 3.89: 31958 3.89 - 4.40: 35489 4.40 - 4.90: 50494 Nonbonded interactions: 140234 Sorted by model distance: nonbonded pdb=" O ASP B 24 " pdb=" OD1 ASP B 24 " model vdw 2.381 3.040 nonbonded pdb=" OE1 GLU A 73 " pdb=" ND2 ASN B 25 " model vdw 2.456 3.120 nonbonded pdb=" N GLU F 52 " pdb=" OE1 GLU F 52 " model vdw 2.471 3.120 nonbonded pdb=" O ASN G 68 " pdb=" OD1 ASP G 72 " model vdw 2.473 3.040 nonbonded pdb=" N GLU E 133 " pdb=" OE1 GLU E 133 " model vdw 2.492 3.120 ... (remaining 140229 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' and resid 37 through 134) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 21 through 101) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 9 through 120) } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'L' selection = chain 'O' } ncs_group { reference = chain 'M' selection = chain 'P' } ncs_group { reference = chain 'N' selection = chain 'Q' } 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=0.00 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: 6.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.640 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 17289 Z= 0.454 Angle : 0.777 10.319 24566 Z= 0.621 Chirality : 0.044 0.280 2748 Planarity : 0.004 0.033 2110 Dihedral : 26.753 95.857 7306 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.99 % Allowed : 25.23 % Favored : 71.78 % 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: 2.35 (0.24), residues: 1257 helix: 2.50 (0.17), residues: 869 sheet: None (None), residues: 0 loop : -0.69 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 79 TYR 0.037 0.002 TYR H 83 PHE 0.009 0.001 PHE E 67 TRP 0.005 0.001 TRP M 25 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.45 (17289) covalent geometry : angle 0.77708 / 0.62 (24566) hydrogen bonds : bond 0.10358 / 7.01 ( 1065) hydrogen bonds : angle 4.17904 / 3.12 ( 2773) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 281 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 58 PHE cc_start: 0.1354 (OUTLIER) cc_final: 0.0493 (p90) REVERT: A 94 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7923 (tp30) REVERT: D 42 TYR cc_start: 0.8247 (t80) cc_final: 0.7914 (t80) REVERT: D 79 ARG cc_start: 0.8471 (mtm-85) cc_final: 0.7956 (mtm-85) REVERT: D 120 LYS cc_start: 0.9445 (tttm) cc_final: 0.9128 (tttm) REVERT: E 59 GLU cc_start: 0.8540 (pm20) cc_final: 0.8048 (pm20) REVERT: E 125 GLN cc_start: 0.8792 (mt0) cc_final: 0.8551 (mp10) REVERT: F 74 GLU cc_start: 0.8040 (tm-30) cc_final: 0.7667 (tp30) REVERT: F 77 LYS cc_start: 0.8859 (mmtm) cc_final: 0.8631 (mmtm) REVERT: G 74 LYS cc_start: 0.9486 (mppt) cc_final: 0.9154 (mppt) REVERT: G 75 LYS cc_start: 0.9487 (OUTLIER) cc_final: 0.9111 (mmmm) REVERT: G 118 LYS cc_start: 0.8207 (tmtt) cc_final: 0.7966 (tmtt) REVERT: H 79 ARG cc_start: 0.8047 (mtm-85) cc_final: 0.7676 (mtm-85) REVERT: H 83 TYR cc_start: 0.8524 (m-10) cc_final: 0.8196 (m-80) REVERT: H 120 LYS cc_start: 0.9431 (tmtt) cc_final: 0.9053 (tptm) REVERT: O 17 ARG cc_start: 0.8433 (mtt-85) cc_final: 0.8001 (ttt180) REVERT: P 38 MET cc_start: 0.6648 (mpt) cc_final: 0.5427 (mmm) REVERT: P 58 PHE cc_start: 0.0999 (OUTLIER) cc_final: 0.0295 (p90) REVERT: P 107 GLU cc_start: 0.5659 (OUTLIER) cc_final: 0.5379 (pp20) REVERT: Q 26 MET cc_start: 0.7152 (ppp) cc_final: 0.6848 (ppp) outliers start: 33 outliers final: 26 residues processed: 294 average time/residue: 0.1742 time to fit residues: 71.3703 Evaluate side-chains 300 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 270 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 12 LYS Chi-restraints excluded: chain M residue 34 THR Chi-restraints excluded: chain M residue 58 PHE Chi-restraints excluded: chain M residue 108 ARG Chi-restraints excluded: chain N residue 20 MET Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain P residue 58 PHE Chi-restraints excluded: chain P residue 107 GLU Chi-restraints excluded: chain Q residue 38 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 0.0570 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 30.0000 overall best weight: 2.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 68 ASN E 85 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.097404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.053932 restraints weight = 60965.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.054741 restraints weight = 29245.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.055135 restraints weight = 20690.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.055342 restraints weight = 17812.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.055455 restraints weight = 16856.389| |-----------------------------------------------------------------------------| r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.0594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17289 Z= 0.179 Angle : 0.648 7.334 24566 Z= 0.369 Chirality : 0.042 0.228 2748 Planarity : 0.004 0.035 2110 Dihedral : 29.593 96.553 4684 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.36 % Allowed : 23.05 % Favored : 73.59 % 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: 2.63 (0.24), residues: 1257 helix: 2.79 (0.17), residues: 867 sheet: -3.53 (1.18), residues: 20 loop : -0.58 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 37 TYR 0.026 0.002 TYR H 83 PHE 0.009 0.001 PHE A 67 TRP 0.005 0.001 TRP Q 33 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.18 (17289) covalent geometry : angle 0.64839 / 0.37 (24566) hydrogen bonds : bond 0.04770 / 3.18 ( 1065) hydrogen bonds : angle 3.46850 / 2.54 ( 2773) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 277 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8354 (tt0) cc_final: 0.7711 (tt0) REVERT: A 94 GLU cc_start: 0.8481 (mm-30) cc_final: 0.8160 (tp30) REVERT: B 25 ASN cc_start: 0.8512 (m-40) cc_final: 0.8159 (m110) REVERT: B 68 ASP cc_start: 0.8695 (m-30) cc_final: 0.8493 (m-30) REVERT: B 93 GLN cc_start: 0.8846 (OUTLIER) cc_final: 0.8562 (mp10) REVERT: D 42 TYR cc_start: 0.8347 (t80) cc_final: 0.8006 (t80) REVERT: D 79 ARG cc_start: 0.8780 (mtm-85) cc_final: 0.8182 (mtm-85) REVERT: D 105 GLU cc_start: 0.7801 (tm-30) cc_final: 0.7022 (tm-30) REVERT: D 109 HIS cc_start: 0.8443 (OUTLIER) cc_final: 0.8174 (m-70) REVERT: D 120 LYS cc_start: 0.9534 (tttm) cc_final: 0.9182 (tttm) REVERT: F 74 GLU cc_start: 0.8523 (tm-30) cc_final: 0.8203 (tp30) REVERT: G 74 LYS cc_start: 0.9417 (mppt) cc_final: 0.9159 (mppt) REVERT: G 90 ASP cc_start: 0.8264 (t70) cc_final: 0.8011 (t70) REVERT: G 91 GLU cc_start: 0.8888 (mp0) cc_final: 0.8687 (mp0) REVERT: G 118 LYS cc_start: 0.8275 (tmtt) cc_final: 0.8015 (tmtt) REVERT: H 93 GLU cc_start: 0.8454 (mp0) cc_final: 0.8149 (mp0) REVERT: H 113 GLU cc_start: 0.8812 (tm-30) cc_final: 0.8482 (tm-30) REVERT: H 120 LYS cc_start: 0.9389 (tmtt) cc_final: 0.9014 (tptm) REVERT: O 17 ARG cc_start: 0.8513 (mtt-85) cc_final: 0.8181 (mmt90) REVERT: P 38 MET cc_start: 0.6657 (OUTLIER) cc_final: 0.5648 (mmm) outliers start: 37 outliers final: 20 residues processed: 299 average time/residue: 0.1673 time to fit residues: 70.4032 Evaluate side-chains 290 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 267 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 109 HIS Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain P residue 38 MET Chi-restraints excluded: chain P residue 91 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 37 optimal weight: 3.9990 chunk 71 optimal weight: 0.0770 chunk 127 optimal weight: 0.0050 chunk 45 optimal weight: 2.9990 chunk 102 optimal weight: 20.0000 chunk 51 optimal weight: 0.0070 chunk 75 optimal weight: 0.9990 chunk 128 optimal weight: 8.9990 chunk 50 optimal weight: 0.6980 chunk 6 optimal weight: 40.0000 chunk 16 optimal weight: 10.0000 overall best weight: 0.3572 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.098781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.055577 restraints weight = 61266.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.056298 restraints weight = 28768.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.056269 restraints weight = 20181.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.056433 restraints weight = 17373.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.056609 restraints weight = 16518.894| |-----------------------------------------------------------------------------| r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.0757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17289 Z= 0.140 Angle : 0.610 8.191 24566 Z= 0.352 Chirality : 0.041 0.238 2748 Planarity : 0.004 0.038 2110 Dihedral : 29.581 98.506 4626 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.63 % Allowed : 23.14 % Favored : 73.23 % 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: 2.66 (0.24), residues: 1257 helix: 2.82 (0.17), residues: 868 sheet: -3.09 (1.13), residues: 20 loop : -0.64 (0.30), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 71 TYR 0.025 0.001 TYR H 83 PHE 0.012 0.001 PHE E 67 TRP 0.005 0.001 TRP Q 33 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.14 (17289) covalent geometry : angle 0.61045 / 0.35 (24566) hydrogen bonds : bond 0.04203 / 2.82 ( 1065) hydrogen bonds : angle 3.25787 / 2.38 ( 2773) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 294 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8396 (tt0) cc_final: 0.7739 (tt0) REVERT: A 94 GLU cc_start: 0.8473 (mm-30) cc_final: 0.7999 (tp30) REVERT: B 25 ASN cc_start: 0.8489 (m-40) cc_final: 0.8163 (m110) REVERT: C 61 GLU cc_start: 0.8711 (tp30) cc_final: 0.8443 (tp30) REVERT: D 79 ARG cc_start: 0.8835 (mtm-85) cc_final: 0.8272 (mtm-85) REVERT: D 105 GLU cc_start: 0.7635 (tm-30) cc_final: 0.6833 (tm-30) REVERT: D 109 HIS cc_start: 0.8454 (OUTLIER) cc_final: 0.8197 (m-70) REVERT: D 120 LYS cc_start: 0.9547 (tttm) cc_final: 0.9173 (tttm) REVERT: F 24 ASP cc_start: 0.7423 (t0) cc_final: 0.6538 (t0) REVERT: F 74 GLU cc_start: 0.8542 (tm-30) cc_final: 0.8212 (tp30) REVERT: G 74 LYS cc_start: 0.9305 (mppt) cc_final: 0.9092 (mppt) REVERT: G 90 ASP cc_start: 0.8134 (t70) cc_final: 0.7914 (t70) REVERT: G 91 GLU cc_start: 0.8886 (mp0) cc_final: 0.8666 (mp0) REVERT: G 104 GLN cc_start: 0.8681 (mm110) cc_final: 0.8402 (mm110) REVERT: G 118 LYS cc_start: 0.8346 (tmtt) cc_final: 0.8059 (tmtt) REVERT: H 83 TYR cc_start: 0.8603 (m-10) cc_final: 0.8217 (m-80) REVERT: H 93 GLU cc_start: 0.8475 (mp0) cc_final: 0.8160 (mp0) REVERT: H 113 GLU cc_start: 0.8769 (tm-30) cc_final: 0.8410 (tm-30) REVERT: H 120 LYS cc_start: 0.9362 (tmtt) cc_final: 0.8992 (tptm) REVERT: O 17 ARG cc_start: 0.8595 (mtt-85) cc_final: 0.8212 (mmt90) REVERT: P 38 MET cc_start: 0.6674 (OUTLIER) cc_final: 0.5536 (mmm) REVERT: P 58 PHE cc_start: 0.0691 (OUTLIER) cc_final: 0.0137 (p90) REVERT: P 107 GLU cc_start: 0.5672 (OUTLIER) cc_final: 0.5400 (pp20) outliers start: 40 outliers final: 21 residues processed: 313 average time/residue: 0.1605 time to fit residues: 70.2820 Evaluate side-chains 302 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 277 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 58 PHE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 109 HIS Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain O residue 15 SER Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain P residue 38 MET Chi-restraints excluded: chain P residue 58 PHE Chi-restraints excluded: chain P residue 91 LYS Chi-restraints excluded: chain P residue 107 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 71 optimal weight: 0.7980 chunk 139 optimal weight: 2.9990 chunk 142 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 149 optimal weight: 8.9990 chunk 122 optimal weight: 20.0000 chunk 131 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 chunk 99 optimal weight: 20.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Q 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.097181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.053900 restraints weight = 61460.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.054643 restraints weight = 29334.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.054730 restraints weight = 20692.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.054884 restraints weight = 18063.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.054884 restraints weight = 17115.194| |-----------------------------------------------------------------------------| r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.0916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17289 Z= 0.198 Angle : 0.652 8.512 24566 Z= 0.365 Chirality : 0.042 0.236 2748 Planarity : 0.004 0.037 2110 Dihedral : 29.775 99.277 4622 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 4.54 % Allowed : 22.41 % Favored : 73.05 % 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: 2.71 (0.24), residues: 1257 helix: 2.88 (0.17), residues: 868 sheet: -3.05 (1.14), residues: 20 loop : -0.69 (0.30), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 35 TYR 0.024 0.001 TYR H 83 PHE 0.010 0.001 PHE A 67 TRP 0.004 0.001 TRP Q 33 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.20 (17289) covalent geometry : angle 0.65175 / 0.37 (24566) hydrogen bonds : bond 0.04730 / 3.15 ( 1065) hydrogen bonds : angle 3.29285 / 2.40 ( 2773) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 274 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 18 ARG cc_start: 0.8774 (ptp90) cc_final: 0.8452 (ptp-170) REVERT: A 73 GLU cc_start: 0.8388 (tt0) cc_final: 0.7829 (tt0) REVERT: A 94 GLU cc_start: 0.8496 (mm-30) cc_final: 0.8194 (tp30) REVERT: B 25 ASN cc_start: 0.8518 (m-40) cc_final: 0.8195 (m110) REVERT: B 93 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.8540 (mp10) REVERT: C 89 ASN cc_start: 0.8912 (m-40) cc_final: 0.8685 (m-40) REVERT: D 76 GLU cc_start: 0.8997 (tp30) cc_final: 0.8733 (tp30) REVERT: D 79 ARG cc_start: 0.8810 (mtm-85) cc_final: 0.8186 (mtm-85) REVERT: D 105 GLU cc_start: 0.7614 (tm-30) cc_final: 0.6890 (tm-30) REVERT: D 120 LYS cc_start: 0.9527 (tttm) cc_final: 0.9161 (tttm) REVERT: E 59 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.7811 (pm20) REVERT: F 24 ASP cc_start: 0.7919 (t0) cc_final: 0.7694 (t0) REVERT: F 74 GLU cc_start: 0.8571 (tm-30) cc_final: 0.8272 (tp30) REVERT: G 74 LYS cc_start: 0.9332 (mppt) cc_final: 0.9104 (mppt) REVERT: G 90 ASP cc_start: 0.8174 (t70) cc_final: 0.7931 (t70) REVERT: G 118 LYS cc_start: 0.8300 (tmtt) cc_final: 0.7965 (tmtt) REVERT: H 93 GLU cc_start: 0.8483 (mp0) cc_final: 0.8104 (mp0) REVERT: H 105 GLU cc_start: 0.9155 (tp30) cc_final: 0.8888 (tp30) REVERT: H 113 GLU cc_start: 0.8818 (tm-30) cc_final: 0.8384 (tm-30) REVERT: H 120 LYS cc_start: 0.9374 (tmtt) cc_final: 0.9004 (tptm) REVERT: O 17 ARG cc_start: 0.8596 (mtt-85) cc_final: 0.8090 (ttt180) REVERT: P 38 MET cc_start: 0.6778 (OUTLIER) cc_final: 0.5831 (mmm) REVERT: P 107 GLU cc_start: 0.5658 (OUTLIER) cc_final: 0.5427 (pp20) outliers start: 50 outliers final: 35 residues processed: 297 average time/residue: 0.1633 time to fit residues: 67.5777 Evaluate side-chains 306 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 267 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 12 LYS Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain M residue 58 PHE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain O residue 15 SER Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain P residue 38 MET Chi-restraints excluded: chain P residue 91 LYS Chi-restraints excluded: chain P residue 107 GLU Chi-restraints excluded: chain Q residue 20 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 105 optimal weight: 10.0000 chunk 120 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 109 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 80 optimal weight: 0.9980 chunk 148 optimal weight: 40.0000 chunk 59 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 135 optimal weight: 6.9990 chunk 137 optimal weight: 20.0000 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.097194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.053804 restraints weight = 61373.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.054198 restraints weight = 29294.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.054700 restraints weight = 20864.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.054929 restraints weight = 17911.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.054894 restraints weight = 16905.988| |-----------------------------------------------------------------------------| r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.0957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17289 Z= 0.195 Angle : 0.652 9.398 24566 Z= 0.364 Chirality : 0.042 0.229 2748 Planarity : 0.004 0.036 2110 Dihedral : 29.862 100.894 4622 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 4.90 % Allowed : 22.60 % Favored : 72.50 % 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: 2.74 (0.24), residues: 1257 helix: 2.91 (0.17), residues: 868 sheet: -3.07 (1.13), residues: 20 loop : -0.68 (0.30), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 79 TYR 0.032 0.002 TYR H 83 PHE 0.010 0.001 PHE A 67 TRP 0.003 0.001 TRP Q 33 HIS 0.014 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.20 (17289) covalent geometry : angle 0.65180 / 0.36 (24566) hydrogen bonds : bond 0.04408 / 2.96 ( 1065) hydrogen bonds : angle 3.27824 / 2.39 ( 2773) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 271 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 18 ARG cc_start: 0.8806 (ptp90) cc_final: 0.8486 (ptp-170) REVERT: A 73 GLU cc_start: 0.8377 (tt0) cc_final: 0.7827 (tt0) REVERT: A 94 GLU cc_start: 0.8499 (mm-30) cc_final: 0.8181 (tp30) REVERT: B 25 ASN cc_start: 0.8466 (m-40) cc_final: 0.8029 (m-40) REVERT: C 89 ASN cc_start: 0.8902 (m-40) cc_final: 0.8691 (m-40) REVERT: D 57 LYS cc_start: 0.8963 (mtmm) cc_final: 0.8753 (mtmm) REVERT: D 79 ARG cc_start: 0.8821 (mtm-85) cc_final: 0.8139 (mtm-85) REVERT: D 120 LYS cc_start: 0.9522 (tttm) cc_final: 0.9175 (tttm) REVERT: E 59 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7745 (pm20) REVERT: F 24 ASP cc_start: 0.7940 (t0) cc_final: 0.7606 (t0) REVERT: F 74 GLU cc_start: 0.8581 (tm-30) cc_final: 0.8275 (tp30) REVERT: F 79 LYS cc_start: 0.9261 (mtpp) cc_final: 0.8979 (mtmm) REVERT: G 64 GLU cc_start: 0.8934 (tp30) cc_final: 0.8693 (tp30) REVERT: G 74 LYS cc_start: 0.9315 (mppt) cc_final: 0.9082 (mppt) REVERT: G 118 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.7979 (tmtt) REVERT: H 83 TYR cc_start: 0.8607 (m-10) cc_final: 0.8249 (m-80) REVERT: H 93 GLU cc_start: 0.8503 (mp0) cc_final: 0.8165 (mp0) REVERT: H 105 GLU cc_start: 0.9153 (tp30) cc_final: 0.8879 (tp30) REVERT: H 113 GLU cc_start: 0.8835 (tm-30) cc_final: 0.8387 (tm-30) REVERT: H 120 LYS cc_start: 0.9382 (tmtt) cc_final: 0.9015 (tptm) REVERT: O 17 ARG cc_start: 0.8594 (mtt-85) cc_final: 0.8104 (ttt180) REVERT: P 38 MET cc_start: 0.6809 (OUTLIER) cc_final: 0.5868 (mmm) REVERT: P 107 GLU cc_start: 0.5717 (OUTLIER) cc_final: 0.5490 (pp20) outliers start: 54 outliers final: 40 residues processed: 292 average time/residue: 0.1542 time to fit residues: 62.7540 Evaluate side-chains 306 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 262 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 12 LYS Chi-restraints excluded: chain M residue 58 PHE Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain P residue 38 MET Chi-restraints excluded: chain P residue 91 LYS Chi-restraints excluded: chain P residue 107 GLU Chi-restraints excluded: chain P residue 141 MET Chi-restraints excluded: chain Q residue 20 MET Chi-restraints excluded: chain Q residue 38 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 146 optimal weight: 10.0000 chunk 54 optimal weight: 0.9980 chunk 144 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 19 optimal weight: 5.9990 chunk 119 optimal weight: 10.0000 chunk 14 optimal weight: 0.5980 chunk 121 optimal weight: 9.9990 chunk 8 optimal weight: 50.0000 chunk 104 optimal weight: 20.0000 overall best weight: 2.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.097102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.053955 restraints weight = 61114.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.054646 restraints weight = 28434.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.055115 restraints weight = 19909.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.055415 restraints weight = 17319.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.055437 restraints weight = 16190.728| |-----------------------------------------------------------------------------| r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.1038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17289 Z= 0.186 Angle : 0.651 9.242 24566 Z= 0.364 Chirality : 0.042 0.234 2748 Planarity : 0.004 0.036 2110 Dihedral : 29.906 102.047 4622 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 5.08 % Allowed : 23.23 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.72 (0.24), residues: 1257 helix: 2.89 (0.17), residues: 868 sheet: -3.09 (1.14), residues: 20 loop : -0.69 (0.30), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 79 TYR 0.027 0.002 TYR H 83 PHE 0.011 0.001 PHE A 67 TRP 0.004 0.001 TRP N 33 HIS 0.017 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.19 (17289) covalent geometry : angle 0.65121 / 0.36 (24566) hydrogen bonds : bond 0.04349 / 2.92 ( 1065) hydrogen bonds : angle 3.24554 / 2.38 ( 2773) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 275 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 18 ARG cc_start: 0.8696 (ptp90) cc_final: 0.8424 (ptp-170) REVERT: A 73 GLU cc_start: 0.8447 (tt0) cc_final: 0.7875 (tt0) REVERT: A 94 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8198 (tp30) REVERT: B 25 ASN cc_start: 0.8482 (m-40) cc_final: 0.7973 (m-40) REVERT: B 59 LYS cc_start: 0.9036 (OUTLIER) cc_final: 0.8438 (tppp) REVERT: C 74 LYS cc_start: 0.9254 (mmmt) cc_final: 0.9046 (mmmt) REVERT: D 57 LYS cc_start: 0.8981 (mtmm) cc_final: 0.8760 (mtmm) REVERT: D 79 ARG cc_start: 0.8830 (mtm-85) cc_final: 0.8201 (mtm-85) REVERT: D 120 LYS cc_start: 0.9530 (tttm) cc_final: 0.9178 (tttm) REVERT: E 59 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7709 (pm20) REVERT: E 126 LEU cc_start: 0.9102 (tp) cc_final: 0.8898 (tp) REVERT: F 74 GLU cc_start: 0.8618 (tm-30) cc_final: 0.8309 (tp30) REVERT: F 79 LYS cc_start: 0.9264 (mtpp) cc_final: 0.8947 (mtmm) REVERT: G 74 LYS cc_start: 0.9293 (mppt) cc_final: 0.9039 (mppt) REVERT: G 118 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.7934 (tmtt) REVERT: H 83 TYR cc_start: 0.8587 (m-10) cc_final: 0.8378 (m-10) REVERT: H 93 GLU cc_start: 0.8527 (mp0) cc_final: 0.8163 (mp0) REVERT: H 105 GLU cc_start: 0.9167 (tp30) cc_final: 0.8874 (tp30) REVERT: H 113 GLU cc_start: 0.8835 (tm-30) cc_final: 0.8357 (tm-30) REVERT: H 120 LYS cc_start: 0.9374 (tmtt) cc_final: 0.9014 (tptm) REVERT: P 38 MET cc_start: 0.7142 (OUTLIER) cc_final: 0.6194 (mmm) REVERT: P 107 GLU cc_start: 0.5705 (OUTLIER) cc_final: 0.5466 (pp20) outliers start: 56 outliers final: 43 residues processed: 299 average time/residue: 0.1566 time to fit residues: 65.2480 Evaluate side-chains 315 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 267 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 12 LYS Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain M residue 58 PHE Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain P residue 38 MET Chi-restraints excluded: chain P residue 91 LYS Chi-restraints excluded: chain P residue 107 GLU Chi-restraints excluded: chain P residue 141 MET Chi-restraints excluded: chain Q residue 20 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 103 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 143 optimal weight: 50.0000 chunk 16 optimal weight: 10.0000 chunk 36 optimal weight: 0.6980 chunk 6 optimal weight: 6.9990 chunk 104 optimal weight: 10.0000 chunk 80 optimal weight: 0.1980 chunk 89 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 111 optimal weight: 20.0000 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.097251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.053872 restraints weight = 61143.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.054635 restraints weight = 28520.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.055094 restraints weight = 20101.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.055367 restraints weight = 17496.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.055121 restraints weight = 16350.825| |-----------------------------------------------------------------------------| r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.1077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17289 Z= 0.175 Angle : 0.659 9.783 24566 Z= 0.367 Chirality : 0.042 0.248 2748 Planarity : 0.004 0.037 2110 Dihedral : 29.934 103.482 4622 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 4.81 % Allowed : 23.50 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.72 (0.24), residues: 1257 helix: 2.88 (0.17), residues: 868 sheet: -3.11 (1.14), residues: 20 loop : -0.66 (0.30), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 79 TYR 0.024 0.002 TYR H 83 PHE 0.011 0.001 PHE A 67 TRP 0.003 0.001 TRP Q 33 HIS 0.013 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.17 (17289) covalent geometry : angle 0.65940 / 0.37 (24566) hydrogen bonds : bond 0.04253 / 2.85 ( 1065) hydrogen bonds : angle 3.22528 / 2.36 ( 2773) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 278 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 18 ARG cc_start: 0.8811 (ptp90) cc_final: 0.8495 (ptp-170) REVERT: A 73 GLU cc_start: 0.8441 (tt0) cc_final: 0.7998 (tt0) REVERT: A 94 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8198 (tp30) REVERT: B 25 ASN cc_start: 0.8474 (m-40) cc_final: 0.8014 (m-40) REVERT: B 59 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8446 (tppp) REVERT: D 57 LYS cc_start: 0.8974 (mtmm) cc_final: 0.8770 (mtmm) REVERT: D 79 ARG cc_start: 0.8812 (mtm-85) cc_final: 0.8227 (mtm-85) REVERT: D 120 LYS cc_start: 0.9530 (tttm) cc_final: 0.9166 (tttm) REVERT: E 59 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7704 (pm20) REVERT: F 74 GLU cc_start: 0.8620 (tm-30) cc_final: 0.8311 (tp30) REVERT: F 79 LYS cc_start: 0.9251 (mtpp) cc_final: 0.8953 (mtmm) REVERT: G 64 GLU cc_start: 0.8943 (tp30) cc_final: 0.8725 (tp30) REVERT: G 118 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.7909 (tmtt) REVERT: H 79 ARG cc_start: 0.8168 (mtm-85) cc_final: 0.7829 (mtm-85) REVERT: H 83 TYR cc_start: 0.8589 (m-10) cc_final: 0.8368 (m-10) REVERT: H 93 GLU cc_start: 0.8555 (mp0) cc_final: 0.8187 (mp0) REVERT: H 105 GLU cc_start: 0.9168 (tp30) cc_final: 0.8867 (tp30) REVERT: H 113 GLU cc_start: 0.8825 (tm-30) cc_final: 0.8365 (tm-30) REVERT: H 120 LYS cc_start: 0.9373 (tmtt) cc_final: 0.9010 (tptm) REVERT: P 38 MET cc_start: 0.6890 (OUTLIER) cc_final: 0.5947 (mmm) REVERT: P 107 GLU cc_start: 0.5666 (OUTLIER) cc_final: 0.5422 (pp20) outliers start: 53 outliers final: 41 residues processed: 298 average time/residue: 0.1619 time to fit residues: 67.5605 Evaluate side-chains 311 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 265 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 12 LYS Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain M residue 58 PHE Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain P residue 38 MET Chi-restraints excluded: chain P residue 91 LYS Chi-restraints excluded: chain P residue 107 GLU Chi-restraints excluded: chain P residue 141 MET Chi-restraints excluded: chain Q residue 20 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 11 optimal weight: 8.9990 chunk 53 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 113 optimal weight: 30.0000 chunk 23 optimal weight: 20.0000 chunk 13 optimal weight: 0.9990 chunk 10 optimal weight: 8.9990 chunk 74 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.098017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.054638 restraints weight = 61247.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.054877 restraints weight = 28519.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.055368 restraints weight = 19999.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.055537 restraints weight = 17273.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.055703 restraints weight = 16345.761| |-----------------------------------------------------------------------------| r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17289 Z= 0.150 Angle : 0.651 9.808 24566 Z= 0.363 Chirality : 0.041 0.256 2748 Planarity : 0.004 0.037 2110 Dihedral : 29.893 105.876 4622 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.63 % Allowed : 24.41 % Favored : 70.96 % 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: 2.72 (0.24), residues: 1257 helix: 2.88 (0.17), residues: 871 sheet: -3.15 (1.14), residues: 20 loop : -0.68 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 99 TYR 0.022 0.002 TYR C 57 PHE 0.011 0.001 PHE E 67 TRP 0.004 0.001 TRP N 33 HIS 0.008 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.15 (17289) covalent geometry : angle 0.65067 / 0.36 (24566) hydrogen bonds : bond 0.03991 / 2.68 ( 1065) hydrogen bonds : angle 3.14919 / 2.31 ( 2773) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 280 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8430 (tt0) cc_final: 0.7993 (tt0) REVERT: A 94 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8182 (tp30) REVERT: B 25 ASN cc_start: 0.8395 (m-40) cc_final: 0.7917 (m-40) REVERT: B 59 LYS cc_start: 0.9019 (OUTLIER) cc_final: 0.8417 (tppp) REVERT: D 57 LYS cc_start: 0.8958 (mtmm) cc_final: 0.8730 (mtmm) REVERT: D 79 ARG cc_start: 0.8813 (mtm-85) cc_final: 0.8236 (mtm-85) REVERT: D 105 GLU cc_start: 0.7751 (tm-30) cc_final: 0.7535 (tm-30) REVERT: D 120 LYS cc_start: 0.9534 (tttm) cc_final: 0.9161 (tttm) REVERT: E 59 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7652 (pm20) REVERT: F 74 GLU cc_start: 0.8600 (tm-30) cc_final: 0.8295 (tp30) REVERT: F 79 LYS cc_start: 0.9222 (mtpp) cc_final: 0.8956 (mtmm) REVERT: G 13 LYS cc_start: 0.9076 (tppt) cc_final: 0.8808 (tptp) REVERT: G 64 GLU cc_start: 0.8965 (tp30) cc_final: 0.8734 (tp30) REVERT: G 118 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.8032 (tttt) REVERT: H 83 TYR cc_start: 0.8569 (m-10) cc_final: 0.8365 (m-10) REVERT: H 93 GLU cc_start: 0.8544 (mp0) cc_final: 0.8245 (mp0) REVERT: H 105 GLU cc_start: 0.9141 (tp30) cc_final: 0.8842 (tp30) REVERT: H 113 GLU cc_start: 0.8799 (tm-30) cc_final: 0.8341 (tm-30) REVERT: H 120 LYS cc_start: 0.9372 (tmtt) cc_final: 0.9006 (tptm) REVERT: O 17 ARG cc_start: 0.8632 (mtt-85) cc_final: 0.8124 (tpt-90) REVERT: P 38 MET cc_start: 0.6698 (OUTLIER) cc_final: 0.5803 (mmm) REVERT: P 107 GLU cc_start: 0.5684 (OUTLIER) cc_final: 0.5442 (pp20) outliers start: 51 outliers final: 34 residues processed: 300 average time/residue: 0.1502 time to fit residues: 62.5830 Evaluate side-chains 311 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 272 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 12 LYS Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain M residue 58 PHE Chi-restraints excluded: chain N residue 20 MET Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain P residue 38 MET Chi-restraints excluded: chain P residue 107 GLU Chi-restraints excluded: chain P residue 141 MET Chi-restraints excluded: chain Q residue 20 MET Chi-restraints excluded: chain Q residue 38 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 114 optimal weight: 20.0000 chunk 66 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 123 optimal weight: 10.0000 chunk 150 optimal weight: 9.9990 chunk 82 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 chunk 115 optimal weight: 20.0000 chunk 55 optimal weight: 0.9990 chunk 41 optimal weight: 10.0000 chunk 84 optimal weight: 0.5980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 11 GLN Q 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.098274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.054165 restraints weight = 61522.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.054696 restraints weight = 28879.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.055185 restraints weight = 20251.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.055421 restraints weight = 17556.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.055483 restraints weight = 16460.909| |-----------------------------------------------------------------------------| r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17289 Z= 0.151 Angle : 0.668 10.729 24566 Z= 0.369 Chirality : 0.041 0.256 2748 Planarity : 0.004 0.037 2110 Dihedral : 29.890 107.120 4622 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.17 % Allowed : 25.23 % Favored : 70.60 % 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: 2.71 (0.24), residues: 1257 helix: 2.86 (0.17), residues: 872 sheet: -3.17 (1.14), residues: 20 loop : -0.65 (0.30), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 79 TYR 0.021 0.002 TYR C 57 PHE 0.010 0.001 PHE A 67 TRP 0.003 0.001 TRP M 25 HIS 0.011 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.15 (17289) covalent geometry : angle 0.66840 / 0.37 (24566) hydrogen bonds : bond 0.04005 / 2.68 ( 1065) hydrogen bonds : angle 3.15985 / 2.32 ( 2773) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 281 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8430 (tt0) cc_final: 0.8014 (tt0) REVERT: A 94 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8168 (tp30) REVERT: B 25 ASN cc_start: 0.8404 (m-40) cc_final: 0.7878 (m-40) REVERT: B 59 LYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8419 (tppp) REVERT: C 61 GLU cc_start: 0.8684 (tp30) cc_final: 0.8449 (tp30) REVERT: D 47 GLN cc_start: 0.8390 (mm-40) cc_final: 0.7967 (mm-40) REVERT: D 57 LYS cc_start: 0.8951 (mtmm) cc_final: 0.8725 (mtmm) REVERT: D 79 ARG cc_start: 0.8810 (mtm-85) cc_final: 0.8233 (mtm-85) REVERT: D 105 GLU cc_start: 0.7778 (tm-30) cc_final: 0.7529 (tm-30) REVERT: D 120 LYS cc_start: 0.9531 (tttm) cc_final: 0.9167 (tttm) REVERT: E 59 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7640 (pm20) REVERT: E 125 GLN cc_start: 0.9091 (mt0) cc_final: 0.8642 (mp10) REVERT: F 74 GLU cc_start: 0.8592 (tm-30) cc_final: 0.8286 (tp30) REVERT: F 79 LYS cc_start: 0.9215 (mtpp) cc_final: 0.8958 (mtmm) REVERT: G 13 LYS cc_start: 0.9089 (tppt) cc_final: 0.8836 (tptp) REVERT: G 64 GLU cc_start: 0.8973 (tp30) cc_final: 0.8727 (tp30) REVERT: G 118 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.8101 (tttt) REVERT: H 79 ARG cc_start: 0.8132 (mtm-85) cc_final: 0.7757 (mtm-85) REVERT: H 83 TYR cc_start: 0.8531 (m-10) cc_final: 0.8328 (m-10) REVERT: H 93 GLU cc_start: 0.8534 (mp0) cc_final: 0.8153 (mp0) REVERT: H 105 GLU cc_start: 0.9129 (tp30) cc_final: 0.8820 (tp30) REVERT: H 113 GLU cc_start: 0.8792 (tm-30) cc_final: 0.8345 (tm-30) REVERT: H 120 LYS cc_start: 0.9377 (tmtt) cc_final: 0.9016 (tptm) REVERT: P 38 MET cc_start: 0.6698 (OUTLIER) cc_final: 0.5787 (mmm) REVERT: P 107 GLU cc_start: 0.5700 (OUTLIER) cc_final: 0.5482 (pp20) outliers start: 46 outliers final: 37 residues processed: 299 average time/residue: 0.1643 time to fit residues: 68.6827 Evaluate side-chains 319 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 277 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 12 LYS Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain M residue 58 PHE Chi-restraints excluded: chain N residue 20 MET Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain P residue 38 MET Chi-restraints excluded: chain P residue 107 GLU Chi-restraints excluded: chain P residue 141 MET Chi-restraints excluded: chain Q residue 20 MET Chi-restraints excluded: chain Q residue 38 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 119 optimal weight: 10.0000 chunk 92 optimal weight: 9.9990 chunk 121 optimal weight: 10.9990 chunk 38 optimal weight: 4.9990 chunk 32 optimal weight: 0.3980 chunk 42 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 71 optimal weight: 8.9990 chunk 149 optimal weight: 20.0000 chunk 140 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 76 GLN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.098375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.054847 restraints weight = 61328.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.055077 restraints weight = 28931.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.055556 restraints weight = 20179.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.055747 restraints weight = 17500.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.055800 restraints weight = 16522.458| |-----------------------------------------------------------------------------| r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17289 Z= 0.149 Angle : 0.680 10.638 24566 Z= 0.376 Chirality : 0.041 0.266 2748 Planarity : 0.004 0.037 2110 Dihedral : 29.878 108.701 4622 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.90 % Allowed : 25.59 % Favored : 70.51 % 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: 2.65 (0.24), residues: 1257 helix: 2.81 (0.17), residues: 873 sheet: -3.16 (1.14), residues: 20 loop : -0.66 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 79 TYR 0.021 0.001 TYR C 57 PHE 0.011 0.001 PHE E 67 TRP 0.003 0.001 TRP M 25 HIS 0.011 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.15 (17289) covalent geometry : angle 0.67980 / 0.38 (24566) hydrogen bonds : bond 0.04055 / 2.69 ( 1065) hydrogen bonds : angle 3.17914 / 2.33 ( 2773) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 278 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8433 (tt0) cc_final: 0.8000 (tt0) REVERT: A 94 GLU cc_start: 0.8481 (mm-30) cc_final: 0.8173 (tp30) REVERT: B 25 ASN cc_start: 0.8416 (m-40) cc_final: 0.7862 (m-40) REVERT: C 61 GLU cc_start: 0.8685 (tp30) cc_final: 0.8450 (tp30) REVERT: D 47 GLN cc_start: 0.8424 (mm-40) cc_final: 0.7993 (mm-40) REVERT: D 57 LYS cc_start: 0.8951 (mtmm) cc_final: 0.8721 (mtmm) REVERT: D 79 ARG cc_start: 0.8820 (mtm-85) cc_final: 0.8269 (mtm-85) REVERT: D 105 GLU cc_start: 0.7757 (tm-30) cc_final: 0.7493 (tm-30) REVERT: D 120 LYS cc_start: 0.9545 (tttm) cc_final: 0.9173 (tttm) REVERT: E 59 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7625 (pm20) REVERT: E 125 GLN cc_start: 0.9100 (mt0) cc_final: 0.8650 (mp10) REVERT: F 24 ASP cc_start: 0.7796 (t0) cc_final: 0.7468 (t0) REVERT: F 74 GLU cc_start: 0.8591 (tm-30) cc_final: 0.8287 (tp30) REVERT: F 79 LYS cc_start: 0.9215 (mtpp) cc_final: 0.8993 (mtmm) REVERT: G 13 LYS cc_start: 0.9094 (tppt) cc_final: 0.8846 (tptp) REVERT: G 64 GLU cc_start: 0.8955 (tp30) cc_final: 0.8713 (tp30) REVERT: G 118 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.8071 (tttt) REVERT: H 79 ARG cc_start: 0.8121 (mtm-85) cc_final: 0.7760 (mtm-85) REVERT: H 83 TYR cc_start: 0.8547 (m-10) cc_final: 0.8325 (m-10) REVERT: H 93 GLU cc_start: 0.8533 (mp0) cc_final: 0.8142 (mp0) REVERT: H 105 GLU cc_start: 0.9117 (tp30) cc_final: 0.8804 (tp30) REVERT: H 113 GLU cc_start: 0.8797 (tm-30) cc_final: 0.8343 (tm-30) REVERT: H 120 LYS cc_start: 0.9366 (tmtt) cc_final: 0.9005 (tptm) REVERT: P 38 MET cc_start: 0.6702 (OUTLIER) cc_final: 0.5807 (mmm) REVERT: P 107 GLU cc_start: 0.5678 (OUTLIER) cc_final: 0.5472 (pp20) outliers start: 43 outliers final: 37 residues processed: 296 average time/residue: 0.1667 time to fit residues: 68.8181 Evaluate side-chains 312 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 271 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 12 LYS Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain M residue 58 PHE Chi-restraints excluded: chain N residue 20 MET Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain P residue 38 MET Chi-restraints excluded: chain P residue 107 GLU Chi-restraints excluded: chain P residue 141 MET Chi-restraints excluded: chain Q residue 20 MET Chi-restraints excluded: chain Q residue 38 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 48 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 127 optimal weight: 0.8980 chunk 114 optimal weight: 20.0000 chunk 61 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 101 optimal weight: 20.0000 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.098265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.055032 restraints weight = 61202.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.055236 restraints weight = 28821.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.055656 restraints weight = 20257.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.055973 restraints weight = 17618.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.056029 restraints weight = 16558.191| |-----------------------------------------------------------------------------| r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.236 17289 Z= 0.213 Angle : 0.867 59.186 24566 Z= 0.508 Chirality : 0.048 1.332 2748 Planarity : 0.005 0.148 2110 Dihedral : 29.876 108.713 4622 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.02 % Favored : 96.90 % Rotamer: Outliers : 3.72 % Allowed : 25.95 % Favored : 70.33 % Cbeta Deviations : 0.08 % 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: 2.64 (0.24), residues: 1257 helix: 2.80 (0.17), residues: 873 sheet: -3.16 (1.14), residues: 20 loop : -0.67 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 29 TYR 0.019 0.001 TYR C 57 PHE 0.010 0.001 PHE E 67 TRP 0.003 0.001 TRP M 25 HIS 0.010 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.21 (17289) covalent geometry : angle 0.86735 / 0.51 (24566) hydrogen bonds : bond 0.04054 / 2.69 ( 1065) hydrogen bonds : angle 3.17943 / 2.34 ( 2773) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4297.23 seconds wall clock time: 74 minutes 14.02 seconds (4454.02 seconds total)