Starting phenix.real_space_refine on Fri Jul 3 22:13:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9slj_55003/07_2026/9slj_55003.cif Found real_map, /net/cci-nas-00/data/ceres_data/9slj_55003/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9slj_55003/07_2026/9slj_55003.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9slj_55003/07_2026/9slj_55003.map" model { file = "/net/cci-nas-00/data/ceres_data/9slj_55003/07_2026/9slj_55003.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9slj_55003/07_2026/9slj_55003.cif" } 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-dev-6108/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: 3.60, per 1000 atoms: 0.22 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: 1.35 Conformation dependent library (CDL) restraints added in 555.3 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: 2.37 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: 3.25 Time building geometry restraints manager: 1.82 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: 23700 2.06 - 4.13: 795 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: 3.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.710 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.520 ------------------------------------------------------------------------------- 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= 0.453 Angle : 0.772 10.319 24566 Z= 0.617 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 0.77248 / 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 : 0.479 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: 0.0496 (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: 0.7870 (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: 0.7664 (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 33 ARG cc_start: 0.8179 (tpt170) cc_final: 0.7979 (mmt-90) 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: 0.5426 (mmm) REVERT: P 58 PHE cc_start: 0.0999 (OUTLIER) cc_final: 0.0294 (p90) REVERT: P 107 GLU cc_start: 0.5659 (OUTLIER) cc_final: 0.5380 (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: 0.1768 time to fit residues: 72.1291 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 : 0.478 ------------------------------------------------------------------------------- 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: 2.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 30.0000 overall best weight: 2.4106 ------------------------------------------------------------------------------- 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 = 0.3648 r_free = 0.3648 target = 0.097362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.054096 restraints weight = 61407.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.054769 restraints weight = 29391.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.054642 restraints weight = 20625.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.054862 restraints weight = 17783.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.054937 restraints weight = 16796.683| |-----------------------------------------------------------------------------| r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.0564 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= 0.190 Angle : 0.641 7.468 24566 Z= 0.368 Chirality : 0.042 0.228 2748 Planarity : 0.004 0.035 2110 Dihedral : 29.656 96.881 4684 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.54 % Allowed : 23.05 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.62 (0.24), residues: 1257 helix: 2.79 (0.17), residues: 867 sheet: -3.52 (1.18), residues: 20 loop : -0.59 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 116 TYR 0.026 0.001 TYR H 83 PHE 0.010 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 0.00360 / 0.19 (17289) covalent geometry : angle 0.64125 / 0.37 (24566) hydrogen bonds : bond 0.04804 / 3.20 ( 1065) hydrogen bonds : angle 3.49826 / 2.56 ( 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 315 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 276 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8392 (tt0) cc_final: 0.7757 (tt0) REVERT: A 94 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8175 (tp30) REVERT: B 25 ASN cc_start: 0.8528 (m-40) cc_final: 0.8178 (m110) REVERT: D 42 TYR cc_start: 0.8343 (t80) cc_final: 0.7999 (t80) REVERT: D 79 ARG cc_start: 0.8802 (mtm-85) cc_final: 0.8143 (mtm-85) REVERT: D 105 GLU cc_start: 0.7828 (tm-30) cc_final: 0.7066 (tm-30) REVERT: D 109 HIS cc_start: 0.8458 (OUTLIER) cc_final: 0.8226 (m-70) REVERT: D 120 LYS cc_start: 0.9537 (tttm) cc_final: 0.9193 (tttm) REVERT: F 74 GLU cc_start: 0.8564 (tm-30) cc_final: 0.8243 (tp30) REVERT: G 74 LYS cc_start: 0.9418 (mppt) cc_final: 0.9150 (mppt) REVERT: G 118 LYS cc_start: 0.8259 (tmtt) cc_final: 0.7998 (tmtt) REVERT: H 33 ARG cc_start: 0.8378 (tpt170) cc_final: 0.8159 (mmt-90) REVERT: H 113 GLU cc_start: 0.8832 (tm-30) cc_final: 0.8498 (tm-30) REVERT: H 120 LYS cc_start: 0.9381 (tmtt) cc_final: 0.9014 (tptm) REVERT: O 17 ARG cc_start: 0.8517 (mtt-85) cc_final: 0.8181 (mmt90) REVERT: P 38 MET cc_start: 0.6611 (OUTLIER) cc_final: 0.5587 (mmm) outliers start: 39 outliers final: 23 residues processed: 302 average time/residue: 0.1672 time to fit residues: 70.9726 Evaluate side-chains 290 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 265 time to evaluate : 0.515 ------------------------------------------------------------------------------- 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 C residue 101 THR 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 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 80 THR 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 15 SER Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain P residue 36 GLU 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: 1.9990 chunk 127 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 102 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 128 optimal weight: 0.0570 chunk 50 optimal weight: 8.9990 chunk 6 optimal weight: 40.0000 chunk 16 optimal weight: 4.9990 overall best weight: 2.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN Q 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.097481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.053946 restraints weight = 61430.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.054898 restraints weight = 28831.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.055359 restraints weight = 20206.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.055664 restraints weight = 17692.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.055697 restraints weight = 16521.498| |-----------------------------------------------------------------------------| r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.0679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17289 Z= 0.173 Angle : 0.624 8.291 24566 Z= 0.358 Chirality : 0.041 0.228 2748 Planarity : 0.004 0.037 2110 Dihedral : 29.791 98.412 4626 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.99 % Allowed : 23.23 % Favored : 72.78 % 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: 2.64 (0.24), residues: 1257 helix: 2.80 (0.17), residues: 868 sheet: None (None), residues: 0 loop : -0.79 (0.29), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 71 TYR 0.033 0.002 TYR H 83 PHE 0.012 0.001 PHE E 67 TRP 0.005 0.001 TRP Q 33 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.17 (17289) covalent geometry : angle 0.62396 / 0.36 (24566) hydrogen bonds : bond 0.04463 / 2.99 ( 1065) hydrogen bonds : angle 3.34398 / 2.44 ( 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 319 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 275 time to evaluate : 0.559 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: 0.8385 (tt0) cc_final: 0.7793 (tt0) REVERT: A 94 GLU cc_start: 0.8489 (mm-30) cc_final: 0.8175 (tp30) REVERT: B 25 ASN cc_start: 0.8512 (m-40) cc_final: 0.8247 (m110) REVERT: B 93 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8467 (mp10) REVERT: D 42 TYR cc_start: 0.8360 (t80) cc_final: 0.8072 (t80) REVERT: D 76 GLU cc_start: 0.9006 (tp30) cc_final: 0.8769 (tp30) REVERT: D 79 ARG cc_start: 0.8837 (mtm-85) cc_final: 0.8201 (mtm-85) REVERT: D 105 GLU cc_start: 0.7654 (tm-30) cc_final: 0.6948 (tm-30) REVERT: D 109 HIS cc_start: 0.8469 (OUTLIER) cc_final: 0.8235 (m-70) REVERT: D 120 LYS cc_start: 0.9531 (tttm) cc_final: 0.9178 (tttm) REVERT: F 24 ASP cc_start: 0.7493 (t0) cc_final: 0.6487 (t0) REVERT: F 74 GLU cc_start: 0.8581 (tm-30) cc_final: 0.8265 (tp30) REVERT: F 88 TYR cc_start: 0.8761 (m-10) cc_final: 0.8465 (m-10) REVERT: G 74 LYS cc_start: 0.9338 (mppt) cc_final: 0.9099 (mppt) REVERT: G 118 LYS cc_start: 0.8329 (tmtt) cc_final: 0.8047 (tmtt) REVERT: H 33 ARG cc_start: 0.8319 (tpt170) cc_final: 0.7918 (mmt-90) REVERT: H 83 TYR cc_start: 0.8652 (m-10) cc_final: 0.8298 (m-80) REVERT: H 93 GLU cc_start: 0.8419 (mp0) cc_final: 0.7902 (mp0) REVERT: H 113 GLU cc_start: 0.8826 (tm-30) cc_final: 0.8403 (tm-30) REVERT: H 120 LYS cc_start: 0.9372 (tmtt) cc_final: 0.9001 (tptm) REVERT: O 17 ARG cc_start: 0.8566 (mtt-85) cc_final: 0.8049 (tpt170) REVERT: P 38 MET cc_start: 0.6668 (OUTLIER) cc_final: 0.5516 (mmm) REVERT: P 58 PHE cc_start: 0.0609 (OUTLIER) cc_final: 0.0067 (p90) REVERT: P 107 GLU cc_start: 0.5773 (OUTLIER) cc_final: 0.5512 (pp20) outliers start: 44 outliers final: 27 residues processed: 296 average time/residue: 0.1724 time to fit residues: 71.4970 Evaluate side-chains 301 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 269 time to evaluate : 0.500 ------------------------------------------------------------------------------- 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 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 62 ILE 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 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 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 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: 0.0470 chunk 139 optimal weight: 8.9990 chunk 142 optimal weight: 6.9990 chunk 29 optimal weight: 0.8980 chunk 149 optimal weight: 5.9990 chunk 122 optimal weight: 10.0000 chunk 131 optimal weight: 6.9990 chunk 52 optimal weight: 0.8980 chunk 83 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 chunk 99 optimal weight: 20.0000 overall best weight: 1.7480 ------------------------------------------------------------------------------- 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 = 0.3657 r_free = 0.3657 target = 0.097674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.054680 restraints weight = 61094.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.055265 restraints weight = 28981.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.055759 restraints weight = 20599.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.056023 restraints weight = 17887.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.056048 restraints weight = 16707.885| |-----------------------------------------------------------------------------| r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.0854 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= 0.162 Angle : 0.617 8.969 24566 Z= 0.353 Chirality : 0.041 0.228 2748 Planarity : 0.004 0.038 2110 Dihedral : 29.826 100.144 4622 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 4.72 % Allowed : 22.50 % Favored : 72.78 % 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: 2.67 (0.24), residues: 1257 helix: 2.86 (0.17), residues: 869 sheet: -3.07 (1.13), residues: 20 loop : -0.73 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 23 TYR 0.019 0.001 TYR H 83 PHE 0.011 0.001 PHE E 67 TRP 0.004 0.001 TRP Q 33 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.16 (17289) covalent geometry : angle 0.61714 / 0.35 (24566) hydrogen bonds : bond 0.04240 / 2.85 ( 1065) hydrogen bonds : angle 3.24262 / 2.37 ( 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 332 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 280 time to evaluate : 0.521 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: A 94 GLU cc_start: 0.8476 (mm-30) cc_final: 0.8178 (tp30) REVERT: B 93 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.8473 (mp10) REVERT: D 42 TYR cc_start: 0.8344 (t80) cc_final: 0.8092 (t80) REVERT: D 79 ARG cc_start: 0.8831 (mtm-85) cc_final: 0.8136 (mtm-85) REVERT: D 105 GLU cc_start: 0.7617 (tm-30) cc_final: 0.6851 (tm-30) REVERT: D 113 GLU cc_start: 0.8990 (tt0) cc_final: 0.8757 (mt-10) REVERT: D 120 LYS cc_start: 0.9528 (tttm) cc_final: 0.9184 (tttm) REVERT: F 74 GLU cc_start: 0.8534 (tm-30) cc_final: 0.8221 (tp30) REVERT: F 79 LYS cc_start: 0.8963 (mtmm) cc_final: 0.8649 (mtmm) REVERT: F 88 TYR cc_start: 0.8751 (m-10) cc_final: 0.8442 (m-10) REVERT: G 74 LYS cc_start: 0.9331 (mppt) cc_final: 0.9102 (mppt) REVERT: G 90 ASP cc_start: 0.8057 (t70) cc_final: 0.7662 (t0) REVERT: G 92 GLU cc_start: 0.8931 (mp0) cc_final: 0.8557 (mp0) REVERT: G 118 LYS cc_start: 0.8324 (tmtt) cc_final: 0.8004 (tmtt) REVERT: H 33 ARG cc_start: 0.8347 (tpt170) cc_final: 0.7944 (mmt-90) REVERT: H 83 TYR cc_start: 0.8629 (m-10) cc_final: 0.8352 (m-10) REVERT: H 93 GLU cc_start: 0.8441 (mp0) cc_final: 0.8137 (mp0) REVERT: H 113 GLU cc_start: 0.8817 (tm-30) cc_final: 0.8392 (tm-30) REVERT: H 120 LYS cc_start: 0.9372 (tmtt) cc_final: 0.8998 (tptm) REVERT: O 17 ARG cc_start: 0.8598 (mtt-85) cc_final: 0.8058 (tpt170) REVERT: P 38 MET cc_start: 0.6879 (OUTLIER) cc_final: 0.5746 (mmm) REVERT: P 58 PHE cc_start: 0.0914 (OUTLIER) cc_final: 0.0337 (p90) REVERT: P 107 GLU cc_start: 0.5698 (OUTLIER) cc_final: 0.5420 (pp20) outliers start: 52 outliers final: 36 residues processed: 306 average time/residue: 0.1749 time to fit residues: 74.3995 Evaluate side-chains 308 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 268 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 E residue 48 LEU Chi-restraints excluded: chain E residue 58 THR 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 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 H residue 122 THR 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 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: 10.0000 chunk 35 optimal weight: 1.9990 chunk 109 optimal weight: 10.0000 chunk 15 optimal weight: 8.9990 chunk 80 optimal weight: 6.9990 chunk 148 optimal weight: 40.0000 chunk 59 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 135 optimal weight: 0.6980 chunk 137 optimal weight: 30.0000 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3644 r_free = 0.3644 target = 0.096961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.054078 restraints weight = 61171.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.054528 restraints weight = 29438.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.055007 restraints weight = 21019.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.055356 restraints weight = 18348.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.055103 restraints weight = 17241.635| |-----------------------------------------------------------------------------| r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.0951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17289 Z= 0.204 Angle : 0.641 8.803 24566 Z= 0.362 Chirality : 0.042 0.230 2748 Planarity : 0.004 0.036 2110 Dihedral : 29.980 101.550 4622 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.90 % Allowed : 22.78 % Favored : 72.32 % 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: 2.69 (0.24), residues: 1257 helix: 2.88 (0.17), residues: 869 sheet: -3.08 (1.13), residues: 20 loop : -0.73 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 35 TYR 0.018 0.001 TYR H 83 PHE 0.010 0.001 PHE A 67 TRP 0.004 0.001 TRP Q 33 HIS 0.013 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.20 (17289) covalent geometry : angle 0.64107 / 0.36 (24566) hydrogen bonds : bond 0.04583 / 3.07 ( 1065) hydrogen bonds : angle 3.28401 / 2.40 ( 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 327 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 273 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8512 (mm-30) cc_final: 0.8194 (tp30) REVERT: B 25 ASN cc_start: 0.8457 (m-40) cc_final: 0.8174 (m110) REVERT: B 59 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8426 (tppp) REVERT: B 93 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.8481 (mp10) REVERT: D 42 TYR cc_start: 0.8397 (t80) cc_final: 0.8106 (t80) REVERT: D 57 LYS cc_start: 0.8972 (mtmm) cc_final: 0.8753 (mtmm) REVERT: D 76 GLU cc_start: 0.8968 (tp30) cc_final: 0.8753 (tp30) REVERT: D 79 ARG cc_start: 0.8808 (mtm-85) cc_final: 0.8194 (mtm-85) REVERT: D 113 GLU cc_start: 0.9027 (tt0) cc_final: 0.8773 (mt-10) REVERT: D 120 LYS cc_start: 0.9520 (tttm) cc_final: 0.9167 (tttm) REVERT: F 74 GLU cc_start: 0.8568 (tm-30) cc_final: 0.8264 (tp30) REVERT: F 79 LYS cc_start: 0.8983 (mtmm) cc_final: 0.8678 (mtmm) REVERT: G 64 GLU cc_start: 0.8952 (tp30) cc_final: 0.8715 (tp30) REVERT: G 74 LYS cc_start: 0.9329 (mppt) cc_final: 0.9081 (mppt) REVERT: G 92 GLU cc_start: 0.8880 (mp0) cc_final: 0.8552 (mp0) REVERT: G 118 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.7994 (tmtt) REVERT: H 34 LYS cc_start: 0.8936 (mmtt) cc_final: 0.8731 (mmtm) REVERT: H 83 TYR cc_start: 0.8646 (m-10) cc_final: 0.8427 (m-10) REVERT: H 93 GLU cc_start: 0.8479 (mp0) cc_final: 0.8079 (mp0) REVERT: H 105 GLU cc_start: 0.9128 (tp30) cc_final: 0.8846 (tp30) REVERT: H 113 GLU cc_start: 0.8834 (tm-30) cc_final: 0.8365 (tm-30) REVERT: H 120 LYS cc_start: 0.9372 (tmtt) cc_final: 0.9007 (tptm) REVERT: O 17 ARG cc_start: 0.8570 (mtt-85) cc_final: 0.8099 (ttt180) REVERT: P 38 MET cc_start: 0.6728 (OUTLIER) cc_final: 0.5776 (mmm) REVERT: P 107 GLU cc_start: 0.5720 (OUTLIER) cc_final: 0.5490 (pp20) outliers start: 54 outliers final: 39 residues processed: 298 average time/residue: 0.1743 time to fit residues: 72.2899 Evaluate side-chains 309 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 265 time to evaluate : 0.514 ------------------------------------------------------------------------------- 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 59 LYS Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 93 GLN 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 87 SER Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 58 THR 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 146 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 144 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 119 optimal weight: 10.0000 chunk 14 optimal weight: 0.0570 chunk 121 optimal weight: 10.0000 chunk 8 optimal weight: 50.0000 chunk 104 optimal weight: 10.0000 overall best weight: 3.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 11 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 = 0.3637 r_free = 0.3637 target = 0.096405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.052709 restraints weight = 60952.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.053606 restraints weight = 29352.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.054013 restraints weight = 20782.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.054190 restraints weight = 18100.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.054374 restraints weight = 17134.403| |-----------------------------------------------------------------------------| r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.1061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17289 Z= 0.217 Angle : 0.663 9.591 24566 Z= 0.370 Chirality : 0.042 0.235 2748 Planarity : 0.004 0.036 2110 Dihedral : 30.073 103.034 4622 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.90 % Allowed : 23.87 % Favored : 71.23 % 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: 2.85 (0.17), residues: 870 sheet: -3.11 (1.13), residues: 20 loop : -0.73 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 79 TYR 0.019 0.002 TYR H 121 PHE 0.010 0.001 PHE A 67 TRP 0.004 0.001 TRP N 33 HIS 0.018 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.22 (17289) covalent geometry : angle 0.66286 / 0.37 (24566) hydrogen bonds : bond 0.04570 / 3.07 ( 1065) hydrogen bonds : angle 3.30047 / 2.42 ( 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 326 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 272 time to evaluate : 0.495 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: 0.8723 (ptp90) cc_final: 0.8423 (ptp-170) REVERT: A 94 GLU cc_start: 0.8512 (mm-30) cc_final: 0.8193 (tp30) REVERT: B 25 ASN cc_start: 0.8403 (m-40) cc_final: 0.7970 (m-40) REVERT: B 93 GLN cc_start: 0.8738 (OUTLIER) cc_final: 0.8490 (mp10) REVERT: C 74 LYS cc_start: 0.9276 (mmmt) cc_final: 0.9060 (mmmt) REVERT: D 42 TYR cc_start: 0.8405 (t80) cc_final: 0.8134 (t80) REVERT: D 57 LYS cc_start: 0.8970 (mtmm) cc_final: 0.8741 (mtmm) REVERT: D 79 ARG cc_start: 0.8819 (mtm-85) cc_final: 0.8138 (mtm-85) REVERT: D 120 LYS cc_start: 0.9522 (tttm) cc_final: 0.9182 (tttm) REVERT: F 74 GLU cc_start: 0.8569 (tm-30) cc_final: 0.8271 (tp30) REVERT: F 79 LYS cc_start: 0.8972 (mtmm) cc_final: 0.8666 (mtmm) REVERT: G 74 LYS cc_start: 0.9316 (mppt) cc_final: 0.9061 (mppt) REVERT: G 118 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7916 (tmtt) REVERT: H 79 ARG cc_start: 0.8203 (mtm-85) cc_final: 0.7890 (mtm-85) REVERT: H 93 GLU cc_start: 0.8493 (mp0) cc_final: 0.8080 (mp0) REVERT: H 105 GLU cc_start: 0.9155 (tp30) cc_final: 0.8877 (tp30) REVERT: H 113 GLU cc_start: 0.8843 (tm-30) cc_final: 0.8350 (tm-30) REVERT: H 120 LYS cc_start: 0.9388 (tmtt) cc_final: 0.9026 (tptm) REVERT: O 17 ARG cc_start: 0.8585 (mtt-85) cc_final: 0.8132 (tpt-90) REVERT: P 38 MET cc_start: 0.7002 (OUTLIER) cc_final: 0.6074 (mmm) REVERT: P 107 GLU cc_start: 0.5608 (OUTLIER) cc_final: 0.5371 (pp20) outliers start: 54 outliers final: 46 residues processed: 296 average time/residue: 0.1774 time to fit residues: 72.9208 Evaluate side-chains 315 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 265 time to evaluate : 0.496 ------------------------------------------------------------------------------- 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 42 ARG 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 62 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 93 GLN 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 87 SER Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 58 THR 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 Chi-restraints excluded: chain Q residue 38 GLN 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: 0.9990 chunk 143 optimal weight: 7.9990 chunk 16 optimal weight: 9.9990 chunk 36 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 80 optimal weight: 0.8980 chunk 89 optimal weight: 8.9990 chunk 30 optimal weight: 0.9980 chunk 111 optimal weight: 20.0000 overall best weight: 1.9784 ------------------------------------------------------------------------------- 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 = 0.3647 r_free = 0.3647 target = 0.096976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.054203 restraints weight = 61279.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.054746 restraints weight = 29159.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.055137 restraints weight = 20868.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 71)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.054910 restraints weight = 18245.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.055055 restraints weight = 16840.658| |-----------------------------------------------------------------------------| r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.1062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17289 Z= 0.170 Angle : 0.648 9.965 24566 Z= 0.363 Chirality : 0.041 0.245 2748 Planarity : 0.004 0.037 2110 Dihedral : 30.071 104.692 4622 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.45 % Allowed : 24.32 % Favored : 71.23 % 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: 2.67 (0.24), residues: 1257 helix: 2.86 (0.17), residues: 869 sheet: -3.15 (1.13), residues: 20 loop : -0.73 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 99 TYR 0.032 0.002 TYR H 83 PHE 0.011 0.001 PHE A 67 TRP 0.003 0.001 TRP Q 33 HIS 0.015 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.17 (17289) covalent geometry : angle 0.64781 / 0.36 (24566) hydrogen bonds : bond 0.04237 / 2.85 ( 1065) hydrogen bonds : angle 3.23196 / 2.37 ( 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 328 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 279 time to evaluate : 0.488 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: A 94 GLU cc_start: 0.8492 (mm-30) cc_final: 0.8163 (tp30) REVERT: B 93 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.8476 (mp10) REVERT: D 42 TYR cc_start: 0.8356 (t80) cc_final: 0.8144 (t80) REVERT: D 57 LYS cc_start: 0.8954 (mtmm) cc_final: 0.8746 (mtmm) REVERT: D 79 ARG cc_start: 0.8803 (mtm-85) cc_final: 0.8218 (mtm-85) REVERT: D 120 LYS cc_start: 0.9527 (tttm) cc_final: 0.9164 (tttm) REVERT: F 74 GLU cc_start: 0.8554 (tm-30) cc_final: 0.8248 (tp30) REVERT: F 79 LYS cc_start: 0.8928 (mtmm) cc_final: 0.8672 (mtmm) REVERT: G 64 GLU cc_start: 0.8926 (tp30) cc_final: 0.8713 (tp30) REVERT: G 74 LYS cc_start: 0.9298 (mppt) cc_final: 0.9066 (mppt) REVERT: G 118 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.7939 (tmtt) REVERT: H 83 TYR cc_start: 0.8598 (m-10) cc_final: 0.8233 (m-80) REVERT: H 90 THR cc_start: 0.9357 (p) cc_final: 0.8823 (p) REVERT: H 93 GLU cc_start: 0.8503 (mp0) cc_final: 0.7951 (mp0) REVERT: H 105 GLU cc_start: 0.9137 (tp30) cc_final: 0.8847 (tp30) REVERT: H 113 GLU cc_start: 0.8853 (tm-30) cc_final: 0.8409 (tm-30) REVERT: H 120 LYS cc_start: 0.9378 (tmtt) cc_final: 0.9011 (tptm) REVERT: O 17 ARG cc_start: 0.8601 (mtt-85) cc_final: 0.8132 (tpt-90) REVERT: P 38 MET cc_start: 0.6863 (OUTLIER) cc_final: 0.5938 (mmm) REVERT: P 107 GLU cc_start: 0.5626 (OUTLIER) cc_final: 0.5382 (pp20) outliers start: 49 outliers final: 41 residues processed: 300 average time/residue: 0.1594 time to fit residues: 66.5439 Evaluate side-chains 313 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 268 time to evaluate : 0.437 ------------------------------------------------------------------------------- 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 42 ARG 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 93 GLN 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 87 SER Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 58 THR 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: 7.9990 chunk 53 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 113 optimal weight: 30.0000 chunk 23 optimal weight: 20.0000 chunk 13 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 74 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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** ** Q 38 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 = 0.3671 r_free = 0.3671 target = 0.098289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.055158 restraints weight = 61324.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.055806 restraints weight = 28957.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.055715 restraints weight = 20464.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.055943 restraints weight = 17558.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.055982 restraints weight = 16471.874| |-----------------------------------------------------------------------------| r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17289 Z= 0.144 Angle : 0.639 9.786 24566 Z= 0.360 Chirality : 0.041 0.255 2748 Planarity : 0.004 0.038 2110 Dihedral : 29.953 107.385 4622 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.81 % Allowed : 24.86 % Favored : 71.32 % 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: 2.68 (0.24), residues: 1257 helix: 2.84 (0.17), residues: 874 sheet: -3.18 (1.13), residues: 20 loop : -0.69 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 79 TYR 0.025 0.002 TYR H 83 PHE 0.011 0.001 PHE E 67 TRP 0.003 0.001 TRP M 25 HIS 0.008 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.14 (17289) covalent geometry : angle 0.63886 / 0.36 (24566) hydrogen bonds : bond 0.03953 / 2.65 ( 1065) hydrogen bonds : angle 3.15160 / 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 325 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 283 time to evaluate : 0.509 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 94 GLU cc_start: 0.8493 (mm-30) cc_final: 0.7974 (tp30) REVERT: B 25 ASN cc_start: 0.8173 (m-40) cc_final: 0.7921 (m110) REVERT: C 61 GLU cc_start: 0.8655 (tp30) cc_final: 0.8431 (tp30) REVERT: D 57 LYS cc_start: 0.8960 (mtmm) cc_final: 0.8736 (mtmm) REVERT: D 68 ASP cc_start: 0.8742 (t0) cc_final: 0.8355 (t0) REVERT: D 79 ARG cc_start: 0.8816 (mtm-85) cc_final: 0.8274 (mtm-85) REVERT: D 120 LYS cc_start: 0.9538 (tttm) cc_final: 0.9161 (tttm) REVERT: F 24 ASP cc_start: 0.7209 (t0) cc_final: 0.6349 (t0) REVERT: F 74 GLU cc_start: 0.8565 (tm-30) cc_final: 0.8238 (tp30) REVERT: F 77 LYS cc_start: 0.9128 (mmtm) cc_final: 0.8890 (mmtm) REVERT: G 64 GLU cc_start: 0.8967 (tp30) cc_final: 0.8731 (tp30) REVERT: G 92 GLU cc_start: 0.8947 (mp0) cc_final: 0.8743 (mp0) REVERT: G 104 GLN cc_start: 0.8671 (mm110) cc_final: 0.8407 (mm110) REVERT: G 118 LYS cc_start: 0.8397 (OUTLIER) cc_final: 0.8047 (tmtt) REVERT: H 79 ARG cc_start: 0.8238 (mtm-85) cc_final: 0.7884 (mtm-85) REVERT: H 83 TYR cc_start: 0.8518 (m-10) cc_final: 0.8228 (m-80) REVERT: H 90 THR cc_start: 0.9365 (p) cc_final: 0.8799 (p) REVERT: H 93 GLU cc_start: 0.8493 (mp0) cc_final: 0.7991 (mp0) REVERT: H 113 GLU cc_start: 0.8824 (tm-30) cc_final: 0.8437 (tm-30) REVERT: H 120 LYS cc_start: 0.9355 (tmtt) cc_final: 0.8993 (tptm) REVERT: P 38 MET cc_start: 0.6744 (OUTLIER) cc_final: 0.5854 (mmm) REVERT: P 107 GLU cc_start: 0.5660 (OUTLIER) cc_final: 0.5408 (pp20) outliers start: 42 outliers final: 33 residues processed: 302 average time/residue: 0.1695 time to fit residues: 71.1390 Evaluate side-chains 306 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 270 time to evaluate : 0.644 ------------------------------------------------------------------------------- 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 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 116 LYS 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 47 SER Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 96 THR 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 89 ASN 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 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: 4.9990 chunk 78 optimal weight: 2.9990 chunk 115 optimal weight: 10.0000 chunk 55 optimal weight: 0.6980 chunk 41 optimal weight: 20.0000 chunk 84 optimal weight: 5.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 38 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.096927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.055888 restraints weight = 61819.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 78)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.053338 restraints weight = 31651.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.053896 restraints weight = 20903.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.054142 restraints weight = 17620.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.054200 restraints weight = 16281.896| |-----------------------------------------------------------------------------| r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 17289 Z= 0.217 Angle : 0.691 9.930 24566 Z= 0.383 Chirality : 0.042 0.253 2748 Planarity : 0.004 0.036 2110 Dihedral : 30.095 108.550 4622 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.90 % Allowed : 24.95 % Favored : 71.14 % 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: 2.64 (0.24), residues: 1257 helix: 2.82 (0.17), residues: 872 sheet: -3.15 (1.14), residues: 20 loop : -0.74 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 99 TYR 0.031 0.002 TYR H 83 PHE 0.013 0.001 PHE P 93 TRP 0.003 0.001 TRP N 33 HIS 0.011 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.22 (17289) covalent geometry : angle 0.69145 / 0.38 (24566) hydrogen bonds : bond 0.04617 / 3.07 ( 1065) hydrogen bonds : angle 3.27287 / 2.40 ( 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 320 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 277 time to evaluate : 0.609 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8518 (mm-30) cc_final: 0.8199 (tp30) REVERT: B 59 LYS cc_start: 0.9040 (OUTLIER) cc_final: 0.8450 (tppp) REVERT: D 57 LYS cc_start: 0.9003 (mtmm) cc_final: 0.8760 (mtmm) REVERT: D 79 ARG cc_start: 0.8835 (mtm-85) cc_final: 0.8237 (mtm-85) REVERT: D 113 GLU cc_start: 0.9016 (tt0) cc_final: 0.8773 (mt-10) REVERT: D 120 LYS cc_start: 0.9524 (tttm) cc_final: 0.9157 (tttm) REVERT: F 24 ASP cc_start: 0.7532 (t0) cc_final: 0.7269 (t0) REVERT: F 74 GLU cc_start: 0.8623 (tm-30) cc_final: 0.8321 (tp30) REVERT: G 64 GLU cc_start: 0.8996 (tp30) cc_final: 0.8757 (tp30) REVERT: G 118 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.7969 (tmtt) REVERT: H 51 ASP cc_start: 0.9031 (p0) cc_final: 0.8771 (p0) REVERT: H 83 TYR cc_start: 0.8561 (m-10) cc_final: 0.8307 (m-10) REVERT: H 93 GLU cc_start: 0.8540 (mp0) cc_final: 0.8022 (mp0) REVERT: H 105 GLU cc_start: 0.9177 (tp30) cc_final: 0.8848 (tp30) REVERT: H 113 GLU cc_start: 0.8881 (tm-30) cc_final: 0.8467 (tm-30) REVERT: H 120 LYS cc_start: 0.9361 (tmtt) cc_final: 0.9001 (tptm) REVERT: P 13 PHE cc_start: 0.7303 (m-80) cc_final: 0.6864 (m-80) REVERT: P 38 MET cc_start: 0.7407 (OUTLIER) cc_final: 0.6439 (mmm) REVERT: P 58 PHE cc_start: 0.0916 (p90) cc_final: 0.0346 (p90) REVERT: P 107 GLU cc_start: 0.5666 (OUTLIER) cc_final: 0.5415 (pp20) REVERT: P 123 GLU cc_start: 0.9480 (pp20) cc_final: 0.9221 (pp20) REVERT: P 124 PHE cc_start: 0.9183 (t80) cc_final: 0.8770 (m-80) outliers start: 43 outliers final: 34 residues processed: 296 average time/residue: 0.1759 time to fit residues: 72.4870 Evaluate side-chains 311 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 273 time to evaluate : 0.480 ------------------------------------------------------------------------------- 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 59 LYS Chi-restraints excluded: chain B residue 62 LEU 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 108 LYS Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 61 LEU 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 86 VAL Chi-restraints excluded: chain F residue 96 THR 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 89 ASN 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: 10.0000 chunk 121 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 94 optimal weight: 0.8980 chunk 71 optimal weight: 8.9990 chunk 149 optimal weight: 20.0000 chunk 140 optimal weight: 9.9990 chunk 9 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 11 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 = 0.3648 r_free = 0.3648 target = 0.097104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.053949 restraints weight = 61475.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 83)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.053809 restraints weight = 29731.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.054283 restraints weight = 20770.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.054540 restraints weight = 17996.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.054555 restraints weight = 16740.254| |-----------------------------------------------------------------------------| r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.236 17289 Z= 0.250 Angle : 0.846 59.171 24566 Z= 0.486 Chirality : 0.042 0.312 2748 Planarity : 0.004 0.036 2110 Dihedral : 30.105 108.606 4622 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.54 % Allowed : 26.32 % Favored : 70.15 % 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: 2.83 (0.17), residues: 872 sheet: -3.14 (1.14), residues: 20 loop : -0.75 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 79 TYR 0.026 0.002 TYR H 83 PHE 0.011 0.001 PHE A 67 TRP 0.003 0.001 TRP N 33 HIS 0.022 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.25 (17289) covalent geometry : angle 0.84618 / 0.49 (24566) hydrogen bonds : bond 0.04615 / 3.07 ( 1065) hydrogen bonds : angle 3.28424 / 2.41 ( 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 313 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 274 time to evaluate : 0.536 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8192 (tp30) REVERT: D 57 LYS cc_start: 0.8995 (mtmm) cc_final: 0.8752 (mtmm) REVERT: D 79 ARG cc_start: 0.8830 (mtm-85) cc_final: 0.8231 (mtm-85) REVERT: D 113 GLU cc_start: 0.9010 (tt0) cc_final: 0.8767 (mt-10) REVERT: D 120 LYS cc_start: 0.9523 (tttm) cc_final: 0.9157 (tttm) REVERT: F 74 GLU cc_start: 0.8615 (tm-30) cc_final: 0.8312 (tp30) REVERT: G 64 GLU cc_start: 0.8999 (tp30) cc_final: 0.8755 (tp30) REVERT: G 118 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.7932 (tmtt) REVERT: H 51 ASP cc_start: 0.9028 (p0) cc_final: 0.8759 (p0) REVERT: H 71 GLU cc_start: 0.8634 (tm-30) cc_final: 0.8411 (tm-30) REVERT: H 79 ARG cc_start: 0.8029 (mtm-85) cc_final: 0.7695 (mtm-85) REVERT: H 93 GLU cc_start: 0.8537 (mp0) cc_final: 0.8206 (mp0) REVERT: H 105 GLU cc_start: 0.9174 (tp30) cc_final: 0.8843 (tp30) REVERT: H 113 GLU cc_start: 0.8878 (tm-30) cc_final: 0.8467 (tm-30) REVERT: H 120 LYS cc_start: 0.9361 (tmtt) cc_final: 0.8998 (tptm) REVERT: P 13 PHE cc_start: 0.7117 (m-80) cc_final: 0.6848 (m-80) REVERT: P 38 MET cc_start: 0.6734 (OUTLIER) cc_final: 0.5780 (mmm) REVERT: P 58 PHE cc_start: 0.0574 (p90) cc_final: 0.0217 (p90) REVERT: P 107 GLU cc_start: 0.5755 (OUTLIER) cc_final: 0.5509 (pp20) REVERT: P 123 GLU cc_start: 0.9474 (pp20) cc_final: 0.9139 (pp20) REVERT: P 124 PHE cc_start: 0.9150 (t80) cc_final: 0.8735 (m-80) outliers start: 39 outliers final: 36 residues processed: 291 average time/residue: 0.1737 time to fit residues: 70.3658 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 : 0.504 ------------------------------------------------------------------------------- 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 C residue 114 VAL Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 53 GLU 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 89 ASN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 48 optimal weight: 0.8980 chunk 20 optimal weight: 50.0000 chunk 127 optimal weight: 7.9990 chunk 114 optimal weight: 20.0000 chunk 61 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 101 optimal weight: 20.0000 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 38 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 = 0.3649 r_free = 0.3649 target = 0.097133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.053885 restraints weight = 61311.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.054060 restraints weight = 29096.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.054454 restraints weight = 20556.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.054752 restraints weight = 17917.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.054791 restraints weight = 16781.217| |-----------------------------------------------------------------------------| r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.236 17289 Z= 0.250 Angle : 0.846 59.171 24566 Z= 0.486 Chirality : 0.042 0.312 2748 Planarity : 0.004 0.036 2110 Dihedral : 30.105 108.606 4622 Min Nonbonded Distance : 1.253 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.54 % Allowed : 26.23 % Favored : 70.24 % 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: 2.83 (0.17), residues: 872 sheet: -3.14 (1.14), residues: 20 loop : -0.75 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 79 TYR 0.026 0.002 TYR H 83 PHE 0.011 0.001 PHE A 67 TRP 0.003 0.001 TRP N 33 HIS 0.022 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.25 (17289) covalent geometry : angle 0.84618 / 0.49 (24566) hydrogen bonds : bond 0.04615 / 3.07 ( 1065) hydrogen bonds : angle 3.28424 / 2.41 ( 2773) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4416.52 seconds wall clock time: 76 minutes 34.59 seconds (4594.59 seconds total)