Starting phenix.real_space_refine on Thu Feb 5 09:14:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9slj_55003/02_2026/9slj_55003.cif Found real_map, /net/cci-nas-00/data/ceres_data/9slj_55003/02_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_55003/02_2026/9slj_55003.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9slj_55003/02_2026/9slj_55003.map" model { file = "/net/cci-nas-00/data/ceres_data/9slj_55003/02_2026/9slj_55003.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9slj_55003/02_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-2.0-5952/lib/python3.9/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: 3.76, per 1000 atoms: 0.23 Number of scatterers: 16390 At special positions: 0 Unit cell: (133.041, 138.857, 145.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 40 16.00 P 293 15.00 O 3617 8.00 N 3025 7.00 C 9415 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.58 Conformation dependent library (CDL) restraints added in 414.2 milliseconds 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2444 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 10 sheets defined 72.5% alpha, 2.0% beta 147 base pairs and 250 stacking pairs defined. Time for finding SS restraints: 2.52 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: 3.26 Time building geometry restraints manager: 2.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 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=" CB ASP B 24 " pdb=" CG ASP B 24 " ideal model delta sigma weight residual 1.516 1.551 -0.035 2.50e-02 1.60e+03 1.97e+00 bond pdb=" CB GLU D 105 " pdb=" CG GLU D 105 " ideal model delta sigma weight residual 1.520 1.560 -0.040 3.00e-02 1.11e+03 1.79e+00 bond pdb=" CA ASN C 110 " pdb=" CB ASN C 110 " ideal model delta sigma weight residual 1.534 1.564 -0.030 2.33e-02 1.84e+03 1.63e+00 bond pdb=" CB GLU F 52 " pdb=" CG GLU F 52 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.54e+00 bond pdb=" CB GLU A 105 " pdb=" CG GLU A 105 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.35e+00 ... (remaining 17284 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 24066 2.06 - 4.13: 429 4.13 - 6.19: 53 6.19 - 8.26: 15 8.26 - 10.32: 3 Bond angle restraints: 24566 Sorted by residual: 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=" CA LYS P 112 " pdb=" CB LYS P 112 " pdb=" CG LYS P 112 " ideal model delta sigma weight residual 114.10 122.78 -8.68 2.00e+00 2.50e-01 1.89e+01 angle pdb=" CA GLU D 105 " pdb=" CB GLU D 105 " pdb=" CG GLU D 105 " ideal model delta sigma weight residual 114.10 122.08 -7.98 2.00e+00 2.50e-01 1.59e+01 angle pdb=" CA ASP B 24 " pdb=" CB ASP B 24 " pdb=" CG ASP B 24 " ideal model delta sigma weight residual 112.60 116.39 -3.79 1.00e+00 1.00e+00 1.44e+01 angle pdb=" CA GLU O 31 " pdb=" CB GLU O 31 " pdb=" CG GLU O 31 " ideal model delta sigma weight residual 114.10 121.65 -7.55 2.00e+00 2.50e-01 1.43e+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: 2468 0.056 - 0.112: 255 0.112 - 0.168: 20 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: 3.790 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: 17.980 Find NCS groups from input model: 0.140 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: 0.000 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 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 : 0.004 0.043 17289 Z= 0.178 Angle : 0.654 10.319 24566 Z= 0.366 Chirality : 0.036 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 covalent geometry : bond 0.00393 (17289) covalent geometry : angle 0.65402 (24566) hydrogen bonds : bond 0.10358 ( 1065) hydrogen bonds : angle 4.17904 ( 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 : 0.548 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: 0.1820 time to fit residues: 73.5990 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 : 0.503 ------------------------------------------------------------------------------- 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: 5.9990 chunk 10 optimal weight: 0.0570 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 30.0000 overall best weight: 2.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3652 r_free = 0.3652 target = 0.097479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.054470 restraints weight = 60934.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.054561 restraints weight = 29364.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.054926 restraints weight = 20447.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.055160 restraints weight = 17623.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.055267 restraints weight = 16505.939| |-----------------------------------------------------------------------------| r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.0635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 17289 Z= 0.204 Angle : 0.580 7.126 24566 Z= 0.334 Chirality : 0.035 0.221 2748 Planarity : 0.004 0.036 2110 Dihedral : 29.499 95.852 4684 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.54 % Allowed : 22.69 % Favored : 73.77 % 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: 2.82 (0.17), residues: 870 sheet: -3.63 (1.16), residues: 20 loop : -0.56 (0.31), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 71 TYR 0.024 0.002 TYR H 83 PHE 0.009 0.001 PHE A 67 TRP 0.005 0.001 TRP Q 33 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00453 (17289) covalent geometry : angle 0.57971 (24566) hydrogen bonds : bond 0.04209 ( 1065) hydrogen bonds : angle 3.36162 ( 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 320 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 281 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8361 (tt0) cc_final: 0.7717 (tt0) REVERT: A 94 GLU cc_start: 0.8493 (mm-30) cc_final: 0.8183 (tp30) REVERT: B 25 ASN cc_start: 0.8549 (m-40) cc_final: 0.8261 (m110) REVERT: B 93 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.8558 (mp10) REVERT: D 35 GLU cc_start: 0.8841 (tp30) cc_final: 0.8624 (mm-30) REVERT: D 42 TYR cc_start: 0.8327 (t80) cc_final: 0.8016 (t80) REVERT: D 79 ARG cc_start: 0.8811 (mtm-85) cc_final: 0.8131 (mtm-85) REVERT: D 105 GLU cc_start: 0.7675 (tm-30) cc_final: 0.6950 (tm-30) REVERT: D 109 HIS cc_start: 0.8464 (OUTLIER) cc_final: 0.8207 (m-70) REVERT: D 120 LYS cc_start: 0.9538 (tttm) cc_final: 0.9182 (tttm) REVERT: F 74 GLU cc_start: 0.8559 (tm-30) cc_final: 0.8245 (tp30) REVERT: G 90 ASP cc_start: 0.8212 (t70) cc_final: 0.7950 (t70) REVERT: G 91 GLU cc_start: 0.8908 (mp0) cc_final: 0.8628 (mp0) REVERT: G 118 LYS cc_start: 0.8275 (tmtt) cc_final: 0.8000 (tmtt) REVERT: H 33 ARG cc_start: 0.8365 (tpt170) cc_final: 0.8118 (mmt-90) REVERT: H 71 GLU cc_start: 0.8590 (tm-30) cc_final: 0.8382 (tm-30) REVERT: H 93 GLU cc_start: 0.8461 (mp0) cc_final: 0.7976 (mp0) REVERT: H 113 GLU cc_start: 0.8826 (tm-30) cc_final: 0.8486 (tm-30) REVERT: H 120 LYS cc_start: 0.9371 (tmtt) cc_final: 0.9006 (tptm) REVERT: O 17 ARG cc_start: 0.8526 (mtt-85) cc_final: 0.7922 (tpt170) REVERT: P 38 MET cc_start: 0.6903 (OUTLIER) cc_final: 0.5934 (mmm) outliers start: 39 outliers final: 22 residues processed: 303 average time/residue: 0.1746 time to fit residues: 73.5594 Evaluate side-chains 293 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 268 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 109 HIS Chi-restraints excluded: chain E residue 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 85 LEU Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain P residue 38 MET Chi-restraints excluded: chain P residue 91 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 37 optimal weight: 3.9990 chunk 71 optimal weight: 0.5980 chunk 127 optimal weight: 0.0010 chunk 45 optimal weight: 0.9980 chunk 102 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 128 optimal weight: 5.9990 chunk 50 optimal weight: 0.7980 chunk 6 optimal weight: 30.0000 chunk 16 optimal weight: 6.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.098975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.055612 restraints weight = 60957.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.056671 restraints weight = 28684.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.057135 restraints weight = 20223.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.057295 restraints weight = 17586.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.057310 restraints weight = 16420.528| |-----------------------------------------------------------------------------| r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.0848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17289 Z= 0.141 Angle : 0.559 7.850 24566 Z= 0.321 Chirality : 0.034 0.221 2748 Planarity : 0.004 0.037 2110 Dihedral : 29.390 97.326 4629 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 4.08 % Allowed : 23.23 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.75 (0.24), residues: 1257 helix: 2.90 (0.17), residues: 870 sheet: -3.14 (1.13), residues: 20 loop : -0.63 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 71 TYR 0.025 0.001 TYR H 83 PHE 0.010 0.001 PHE A 67 TRP 0.005 0.001 TRP Q 33 HIS 0.003 0.001 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00302 (17289) covalent geometry : angle 0.55856 (24566) hydrogen bonds : bond 0.03652 ( 1065) hydrogen bonds : angle 3.14426 ( 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 336 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 291 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8328 (tt0) cc_final: 0.7640 (tt0) REVERT: A 94 GLU cc_start: 0.8435 (mm-30) cc_final: 0.7968 (tp30) REVERT: B 25 ASN cc_start: 0.8472 (m-40) cc_final: 0.8177 (m110) REVERT: C 61 GLU cc_start: 0.8717 (tp30) cc_final: 0.8439 (tp30) REVERT: D 35 GLU cc_start: 0.8853 (tp30) cc_final: 0.8616 (mm-30) REVERT: D 42 TYR cc_start: 0.8203 (t80) cc_final: 0.7977 (t80) REVERT: D 76 GLU cc_start: 0.8934 (tp30) cc_final: 0.8713 (tp30) REVERT: D 79 ARG cc_start: 0.8790 (mtm-85) cc_final: 0.8221 (mtm-85) REVERT: D 105 GLU cc_start: 0.7575 (tm-30) cc_final: 0.6825 (tm-30) REVERT: D 109 HIS cc_start: 0.8452 (OUTLIER) cc_final: 0.8233 (m-70) REVERT: D 120 LYS cc_start: 0.9544 (tttm) cc_final: 0.9182 (tttm) REVERT: E 59 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.7827 (pm20) REVERT: F 24 ASP cc_start: 0.7460 (t0) cc_final: 0.6247 (t0) REVERT: F 74 GLU cc_start: 0.8526 (tm-30) cc_final: 0.8200 (tp30) REVERT: G 104 GLN cc_start: 0.8679 (mm110) cc_final: 0.8408 (mm110) REVERT: G 118 LYS cc_start: 0.8347 (tmtt) cc_final: 0.8044 (tmtt) REVERT: H 33 ARG cc_start: 0.8279 (tpt170) cc_final: 0.7933 (mmt-90) REVERT: H 71 GLU cc_start: 0.8574 (tm-30) cc_final: 0.8372 (tm-30) REVERT: H 83 TYR cc_start: 0.8546 (m-10) cc_final: 0.8198 (m-80) REVERT: H 93 GLU cc_start: 0.8468 (mp0) cc_final: 0.8107 (mp0) REVERT: H 113 GLU cc_start: 0.8741 (tm-30) cc_final: 0.8394 (tm-30) REVERT: H 120 LYS cc_start: 0.9369 (tmtt) cc_final: 0.9000 (tptm) REVERT: O 17 ARG cc_start: 0.8618 (mtt-85) cc_final: 0.8217 (mmt90) REVERT: P 38 MET cc_start: 0.6796 (OUTLIER) cc_final: 0.5710 (mmm) REVERT: P 58 PHE cc_start: 0.0889 (OUTLIER) cc_final: 0.0331 (p90) REVERT: P 107 GLU cc_start: 0.5673 (OUTLIER) cc_final: 0.5404 (pp20) outliers start: 45 outliers final: 20 residues processed: 315 average time/residue: 0.1780 time to fit residues: 77.7084 Evaluate side-chains 301 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 276 time to evaluate : 0.466 ------------------------------------------------------------------------------- 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 107 THR 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 58 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain O residue 15 SER Chi-restraints excluded: chain O residue 20 LYS 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 107 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 71 optimal weight: 0.9990 chunk 139 optimal weight: 20.0000 chunk 142 optimal weight: 10.0000 chunk 29 optimal weight: 0.9990 chunk 149 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 chunk 131 optimal weight: 5.9990 chunk 52 optimal weight: 8.9990 chunk 83 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 99 optimal weight: 8.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3650 r_free = 0.3650 target = 0.097068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.053451 restraints weight = 61803.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.054117 restraints weight = 29768.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.054223 restraints weight = 21146.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.054397 restraints weight = 18545.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.054397 restraints weight = 17523.064| |-----------------------------------------------------------------------------| r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.0990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 17289 Z= 0.236 Angle : 0.588 8.449 24566 Z= 0.337 Chirality : 0.036 0.225 2748 Planarity : 0.004 0.037 2110 Dihedral : 29.565 96.746 4622 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 4.26 % Allowed : 23.14 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.79 (0.24), residues: 1257 helix: 2.94 (0.17), residues: 868 sheet: -3.13 (1.13), residues: 20 loop : -0.65 (0.30), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 99 TYR 0.024 0.001 TYR H 83 PHE 0.009 0.001 PHE E 67 TRP 0.004 0.001 TRP N 33 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00528 (17289) covalent geometry : angle 0.58827 (24566) hydrogen bonds : bond 0.04217 ( 1065) hydrogen bonds : angle 3.18096 ( 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 319 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 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: A 73 GLU cc_start: 0.8378 (tt0) cc_final: 0.7708 (tt0) REVERT: A 94 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8173 (tp30) REVERT: B 25 ASN cc_start: 0.8545 (m-40) cc_final: 0.8041 (m-40) REVERT: D 35 GLU cc_start: 0.8814 (tp30) cc_final: 0.8540 (mm-30) REVERT: D 42 TYR cc_start: 0.8308 (t80) cc_final: 0.8009 (t80) REVERT: D 47 GLN cc_start: 0.8623 (mm-40) cc_final: 0.8415 (mm-40) REVERT: D 57 LYS cc_start: 0.8979 (mtmm) cc_final: 0.8759 (mtmm) REVERT: D 76 GLU cc_start: 0.9000 (tp30) cc_final: 0.8778 (tp30) REVERT: D 79 ARG cc_start: 0.8814 (mtm-85) cc_final: 0.8135 (mtm-85) REVERT: D 105 GLU cc_start: 0.7598 (tm-30) cc_final: 0.6856 (tm-30) REVERT: D 120 LYS cc_start: 0.9518 (tttm) cc_final: 0.9167 (tttm) REVERT: E 59 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.7848 (pm20) REVERT: F 74 GLU cc_start: 0.8546 (tm-30) cc_final: 0.8233 (tp30) REVERT: G 64 GLU cc_start: 0.8966 (tp30) cc_final: 0.8728 (tp30) REVERT: G 74 LYS cc_start: 0.9315 (mppt) cc_final: 0.9106 (mppt) REVERT: G 118 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.7946 (tmtt) REVERT: H 33 ARG cc_start: 0.8375 (tpt170) cc_final: 0.7761 (mmt-90) REVERT: H 71 GLU cc_start: 0.8594 (tm-30) cc_final: 0.8392 (tm-30) REVERT: H 83 TYR cc_start: 0.8571 (m-10) cc_final: 0.8366 (m-10) REVERT: H 93 GLU cc_start: 0.8527 (mp0) cc_final: 0.8091 (mp0) REVERT: H 113 GLU cc_start: 0.8817 (tm-30) cc_final: 0.8388 (tm-30) REVERT: H 120 LYS cc_start: 0.9380 (tmtt) cc_final: 0.9000 (tptm) REVERT: O 17 ARG cc_start: 0.8570 (mtt-85) cc_final: 0.8184 (mmt90) REVERT: P 38 MET cc_start: 0.6899 (OUTLIER) cc_final: 0.5888 (mmm) REVERT: P 58 PHE cc_start: 0.1092 (OUTLIER) cc_final: 0.0586 (p90) REVERT: P 107 GLU cc_start: 0.5603 (OUTLIER) cc_final: 0.5343 (pp20) outliers start: 47 outliers final: 34 residues processed: 294 average time/residue: 0.1765 time to fit residues: 71.9758 Evaluate side-chains 304 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 265 time to evaluate : 0.497 ------------------------------------------------------------------------------- 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 A residue 118 THR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 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 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 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 P residue 141 MET 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: 4.9990 chunk 120 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 109 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 148 optimal weight: 8.9990 chunk 59 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 135 optimal weight: 0.9980 chunk 137 optimal weight: 20.0000 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3662 r_free = 0.3662 target = 0.097731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.054752 restraints weight = 60868.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.055426 restraints weight = 28758.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.055876 restraints weight = 20181.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.056041 restraints weight = 17634.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.055871 restraints weight = 16693.729| |-----------------------------------------------------------------------------| r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.1012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17289 Z= 0.182 Angle : 0.577 8.780 24566 Z= 0.330 Chirality : 0.034 0.225 2748 Planarity : 0.004 0.037 2110 Dihedral : 29.566 97.257 4622 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 4.81 % Allowed : 22.96 % Favored : 72.23 % 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: 2.77 (0.24), residues: 1257 helix: 2.94 (0.17), residues: 868 sheet: -3.12 (1.14), residues: 20 loop : -0.69 (0.30), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 99 TYR 0.017 0.001 TYR H 83 PHE 0.010 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 covalent geometry : bond 0.00403 (17289) covalent geometry : angle 0.57715 (24566) hydrogen bonds : bond 0.03756 ( 1065) hydrogen bonds : angle 3.10363 ( 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 332 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 279 time to evaluate : 0.531 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 73 GLU cc_start: 0.8408 (tt0) cc_final: 0.7844 (tt0) REVERT: A 94 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8011 (tp30) REVERT: B 25 ASN cc_start: 0.8487 (m-40) cc_final: 0.8021 (m-40) REVERT: D 35 GLU cc_start: 0.8808 (tp30) cc_final: 0.8527 (mm-30) REVERT: D 42 TYR cc_start: 0.8295 (t80) cc_final: 0.8024 (t80) REVERT: D 57 LYS cc_start: 0.8995 (mtmm) cc_final: 0.8757 (mtmm) REVERT: D 76 GLU cc_start: 0.9011 (tp30) cc_final: 0.8803 (tp30) REVERT: D 79 ARG cc_start: 0.8851 (mtm-85) cc_final: 0.8135 (mtm-85) REVERT: D 120 LYS cc_start: 0.9532 (tttm) cc_final: 0.9170 (tttm) REVERT: E 59 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.7821 (pm20) REVERT: F 74 GLU cc_start: 0.8584 (tm-30) cc_final: 0.8263 (tp30) REVERT: G 104 GLN cc_start: 0.8723 (mm110) cc_final: 0.8496 (mm110) REVERT: G 118 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.8000 (tmtt) REVERT: H 33 ARG cc_start: 0.8408 (tpt170) cc_final: 0.7985 (mmt-90) REVERT: H 71 GLU cc_start: 0.8645 (tm-30) cc_final: 0.8422 (tm-30) REVERT: H 93 GLU cc_start: 0.8560 (mp0) cc_final: 0.8078 (mp0) REVERT: H 113 GLU cc_start: 0.8808 (tm-30) cc_final: 0.8353 (tm-30) REVERT: H 120 LYS cc_start: 0.9379 (tmtt) cc_final: 0.9000 (tptm) REVERT: P 38 MET cc_start: 0.6833 (OUTLIER) cc_final: 0.5847 (mmm) REVERT: P 58 PHE cc_start: 0.1136 (OUTLIER) cc_final: 0.0640 (p90) REVERT: P 107 GLU cc_start: 0.5622 (OUTLIER) cc_final: 0.5367 (pp20) outliers start: 53 outliers final: 36 residues processed: 300 average time/residue: 0.1771 time to fit residues: 73.7442 Evaluate side-chains 311 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 270 time to evaluate : 0.510 ------------------------------------------------------------------------------- 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 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 C residue 16 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 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 59 GLU 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 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 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 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 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: 9.9990 chunk 54 optimal weight: 1.9990 chunk 144 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 119 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 chunk 121 optimal weight: 4.9990 chunk 8 optimal weight: 50.0000 chunk 104 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN ** M 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 76 GLN D 49 HIS P 11 GLN Q 38 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.095857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.052605 restraints weight = 61517.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.052848 restraints weight = 29646.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.053368 restraints weight = 21066.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.053597 restraints weight = 18236.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.053644 restraints weight = 17057.241| |-----------------------------------------------------------------------------| r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 17289 Z= 0.308 Angle : 0.637 9.118 24566 Z= 0.363 Chirality : 0.038 0.228 2748 Planarity : 0.004 0.035 2110 Dihedral : 29.797 95.838 4622 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 5.26 % Allowed : 22.87 % Favored : 71.87 % 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: 871 sheet: -3.13 (1.15), residues: 20 loop : -0.74 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 79 TYR 0.035 0.002 TYR H 83 PHE 0.011 0.001 PHE G 25 TRP 0.005 0.001 TRP O 70 HIS 0.012 0.001 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00692 (17289) covalent geometry : angle 0.63689 (24566) hydrogen bonds : bond 0.04839 ( 1065) hydrogen bonds : angle 3.26827 ( 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 327 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 269 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8374 (tt0) cc_final: 0.8004 (tt0) REVERT: A 94 GLU cc_start: 0.8507 (mm-30) cc_final: 0.8188 (tp30) REVERT: B 25 ASN cc_start: 0.8447 (m-40) cc_final: 0.8007 (m-40) REVERT: C 74 LYS cc_start: 0.9273 (mmmt) cc_final: 0.9046 (mmmt) REVERT: D 42 TYR cc_start: 0.8437 (t80) cc_final: 0.8066 (t80) REVERT: D 47 GLN cc_start: 0.8681 (mm-40) cc_final: 0.8379 (mm-40) REVERT: D 57 LYS cc_start: 0.8983 (mtmm) cc_final: 0.8769 (mtmm) REVERT: D 79 ARG cc_start: 0.8827 (mtm-85) cc_final: 0.8034 (mtm-85) REVERT: D 120 LYS cc_start: 0.9501 (tttm) cc_final: 0.9150 (tttm) REVERT: E 59 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.7918 (pm20) REVERT: F 74 GLU cc_start: 0.8567 (tm-30) cc_final: 0.8269 (tp30) REVERT: G 118 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.7931 (tmtt) REVERT: H 33 ARG cc_start: 0.8482 (tpt170) cc_final: 0.7860 (mmt-90) REVERT: H 71 GLU cc_start: 0.8641 (tm-30) cc_final: 0.8413 (tm-30) REVERT: H 79 ARG cc_start: 0.8222 (mtm-85) cc_final: 0.7886 (mtm-85) REVERT: H 93 GLU cc_start: 0.8581 (mp0) cc_final: 0.8299 (mp0) REVERT: H 105 GLU cc_start: 0.9153 (tp30) cc_final: 0.8919 (tp30) REVERT: H 113 GLU cc_start: 0.8857 (tm-30) cc_final: 0.8334 (tm-30) REVERT: H 120 LYS cc_start: 0.9394 (tmtt) cc_final: 0.9028 (tptm) REVERT: P 38 MET cc_start: 0.6994 (OUTLIER) cc_final: 0.5988 (mmm) REVERT: P 58 PHE cc_start: 0.1153 (OUTLIER) cc_final: 0.0644 (p90) REVERT: P 107 GLU cc_start: 0.5622 (OUTLIER) cc_final: 0.5370 (pp20) outliers start: 58 outliers final: 46 residues processed: 294 average time/residue: 0.1789 time to fit residues: 72.5450 Evaluate side-chains 309 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 258 time to evaluate : 0.497 ------------------------------------------------------------------------------- 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 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 A residue 118 THR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 62 ILE 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 48 LEU Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 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 86 VAL 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 61 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 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 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: 4.9990 chunk 37 optimal weight: 0.8980 chunk 143 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 36 optimal weight: 0.7980 chunk 6 optimal weight: 9.9990 chunk 104 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 89 optimal weight: 0.0020 chunk 30 optimal weight: 0.8980 chunk 111 optimal weight: 5.9990 overall best weight: 1.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 76 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 = 0.3660 r_free = 0.3660 target = 0.097632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.054584 restraints weight = 60774.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.054883 restraints weight = 28710.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.055380 restraints weight = 20212.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.055562 restraints weight = 17465.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.055574 restraints weight = 16355.516| |-----------------------------------------------------------------------------| r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17289 Z= 0.166 Angle : 0.604 9.561 24566 Z= 0.341 Chirality : 0.035 0.248 2748 Planarity : 0.004 0.037 2110 Dihedral : 29.708 96.839 4622 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.72 % Allowed : 24.32 % Favored : 70.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.76 (0.24), residues: 1257 helix: 2.92 (0.17), residues: 870 sheet: -3.10 (1.16), residues: 20 loop : -0.70 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 99 TYR 0.039 0.002 TYR H 83 PHE 0.010 0.001 PHE A 67 TRP 0.004 0.001 TRP N 33 HIS 0.014 0.001 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00367 (17289) covalent geometry : angle 0.60370 (24566) hydrogen bonds : bond 0.03680 ( 1065) hydrogen bonds : angle 3.10225 ( 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 334 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 282 time to evaluate : 0.528 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 73 GLU cc_start: 0.8381 (tt0) cc_final: 0.8004 (tt0) REVERT: A 94 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8168 (tp30) REVERT: B 25 ASN cc_start: 0.8431 (m-40) cc_final: 0.7930 (m-40) REVERT: C 74 LYS cc_start: 0.9265 (mmmt) cc_final: 0.9047 (mmmt) REVERT: D 35 GLU cc_start: 0.8837 (tp30) cc_final: 0.8598 (mm-30) REVERT: D 42 TYR cc_start: 0.8295 (t80) cc_final: 0.8042 (t80) REVERT: D 71 GLU cc_start: 0.8574 (tm-30) cc_final: 0.8367 (tm-30) REVERT: D 79 ARG cc_start: 0.8835 (mtm-85) cc_final: 0.8292 (mtm-85) REVERT: D 105 GLU cc_start: 0.7826 (tm-30) cc_final: 0.7582 (tm-30) REVERT: D 120 LYS cc_start: 0.9539 (tttm) cc_final: 0.9172 (tttm) REVERT: E 59 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.7856 (pm20) REVERT: F 74 GLU cc_start: 0.8586 (tm-30) cc_final: 0.8253 (tp30) REVERT: F 77 LYS cc_start: 0.9125 (mmtm) cc_final: 0.8859 (mmtm) REVERT: F 88 TYR cc_start: 0.8687 (m-10) cc_final: 0.8288 (m-10) REVERT: G 118 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.8028 (tmtt) REVERT: H 33 ARG cc_start: 0.8469 (tpt170) cc_final: 0.8018 (mmt-90) REVERT: H 71 GLU cc_start: 0.8654 (tm-30) cc_final: 0.8400 (tm-30) REVERT: H 72 ARG cc_start: 0.9206 (OUTLIER) cc_final: 0.8129 (mtt180) REVERT: H 83 TYR cc_start: 0.8552 (m-10) cc_final: 0.8223 (m-80) REVERT: H 93 GLU cc_start: 0.8593 (mp0) cc_final: 0.8301 (mp0) REVERT: H 105 GLU cc_start: 0.9177 (tp30) cc_final: 0.8872 (tp30) REVERT: H 113 GLU cc_start: 0.8870 (tm-30) cc_final: 0.8431 (tm-30) REVERT: H 120 LYS cc_start: 0.9377 (tmtt) cc_final: 0.9005 (tptm) REVERT: O 14 ASN cc_start: 0.9423 (m-40) cc_final: 0.9220 (m-40) REVERT: P 38 MET cc_start: 0.6922 (OUTLIER) cc_final: 0.5925 (mmm) REVERT: P 58 PHE cc_start: 0.1015 (OUTLIER) cc_final: 0.0530 (p90) REVERT: P 107 GLU cc_start: 0.5617 (OUTLIER) cc_final: 0.5377 (pp20) outliers start: 52 outliers final: 38 residues processed: 302 average time/residue: 0.1729 time to fit residues: 71.7686 Evaluate side-chains 312 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 268 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 12 LYS 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 47 SER 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 48 LEU Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 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 72 ARG 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 58 PHE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 11 optimal weight: 40.0000 chunk 53 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 113 optimal weight: 7.9990 chunk 23 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 chunk 74 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 11 GLN A 76 GLN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN Q 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.098346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.054541 restraints weight = 61044.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.055553 restraints weight = 28633.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.056005 restraints weight = 20028.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.056241 restraints weight = 17504.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.056302 restraints weight = 16359.174| |-----------------------------------------------------------------------------| r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17289 Z= 0.153 Angle : 0.612 9.790 24566 Z= 0.342 Chirality : 0.035 0.260 2748 Planarity : 0.004 0.038 2110 Dihedral : 29.581 97.332 4622 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.17 % Allowed : 25.41 % Favored : 70.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.74 (0.24), residues: 1257 helix: 2.89 (0.17), residues: 870 sheet: -3.08 (1.17), residues: 20 loop : -0.66 (0.31), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 99 TYR 0.033 0.002 TYR H 83 PHE 0.011 0.001 PHE E 67 TRP 0.003 0.001 TRP N 33 HIS 0.012 0.001 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00337 (17289) covalent geometry : angle 0.61178 (24566) hydrogen bonds : bond 0.03612 ( 1065) hydrogen bonds : angle 3.07665 ( 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 329 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 283 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8393 (tt0) cc_final: 0.8103 (tt0) REVERT: A 94 GLU cc_start: 0.8457 (mm-30) cc_final: 0.8166 (tp30) REVERT: B 25 ASN cc_start: 0.8391 (m-40) cc_final: 0.7917 (m-40) REVERT: C 74 LYS cc_start: 0.9264 (mmmt) cc_final: 0.9051 (mmmt) REVERT: D 35 GLU cc_start: 0.8836 (tp30) cc_final: 0.8573 (mm-30) REVERT: D 42 TYR cc_start: 0.8263 (t80) cc_final: 0.8035 (t80) REVERT: D 71 GLU cc_start: 0.8555 (tm-30) cc_final: 0.8340 (tm-30) REVERT: D 79 ARG cc_start: 0.8837 (mtm-85) cc_final: 0.8286 (mtm-85) REVERT: D 105 GLU cc_start: 0.7801 (tm-30) cc_final: 0.7535 (tm-30) REVERT: D 120 LYS cc_start: 0.9538 (tttm) cc_final: 0.9167 (tttm) REVERT: E 59 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.7833 (pm20) REVERT: F 74 GLU cc_start: 0.8579 (tm-30) cc_final: 0.8246 (tp30) REVERT: F 77 LYS cc_start: 0.9114 (mmtm) cc_final: 0.8859 (mmtm) REVERT: G 118 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8123 (tmtt) REVERT: H 33 ARG cc_start: 0.8443 (tpt170) cc_final: 0.7997 (mmt-90) REVERT: H 34 LYS cc_start: 0.8930 (mmtt) cc_final: 0.8697 (mmtm) REVERT: H 71 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8395 (tm-30) REVERT: H 83 TYR cc_start: 0.8527 (m-10) cc_final: 0.8184 (m-80) REVERT: H 93 GLU cc_start: 0.8578 (mp0) cc_final: 0.8293 (mp0) REVERT: H 105 GLU cc_start: 0.9127 (tp30) cc_final: 0.8803 (tp30) REVERT: H 113 GLU cc_start: 0.8838 (tm-30) cc_final: 0.8434 (tm-30) REVERT: H 120 LYS cc_start: 0.9357 (tmtt) cc_final: 0.8988 (tptm) REVERT: O 14 ASN cc_start: 0.9421 (m-40) cc_final: 0.9202 (m-40) REVERT: O 17 ARG cc_start: 0.8625 (mtt-85) cc_final: 0.8162 (mmt90) REVERT: P 38 MET cc_start: 0.6890 (OUTLIER) cc_final: 0.5872 (mmm) REVERT: P 58 PHE cc_start: 0.0836 (OUTLIER) cc_final: 0.0381 (p90) REVERT: P 107 GLU cc_start: 0.5610 (OUTLIER) cc_final: 0.5379 (pp20) outliers start: 46 outliers final: 31 residues processed: 300 average time/residue: 0.1663 time to fit residues: 68.9236 Evaluate side-chains 312 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 276 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 12 LYS Chi-restraints excluded: chain M residue 58 PHE Chi-restraints excluded: chain N residue 20 MET Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain H residue 63 ASN 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 20 LYS 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 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: 7.9990 chunk 66 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 150 optimal weight: 10.0000 chunk 82 optimal weight: 7.9990 chunk 78 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 41 optimal weight: 7.9990 chunk 84 optimal weight: 1.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 63 ASN ** Q 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.097068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.053864 restraints weight = 61840.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.053843 restraints weight = 29489.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.054279 restraints weight = 20715.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.054546 restraints weight = 17945.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.054692 restraints weight = 16732.123| |-----------------------------------------------------------------------------| r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 17289 Z= 0.229 Angle : 0.645 10.066 24566 Z= 0.360 Chirality : 0.037 0.262 2748 Planarity : 0.004 0.036 2110 Dihedral : 29.687 97.054 4622 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.81 % Allowed : 25.95 % Favored : 70.24 % 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: 2.81 (0.17), residues: 872 sheet: -3.05 (1.18), residues: 20 loop : -0.69 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 71 TYR 0.035 0.002 TYR H 83 PHE 0.012 0.001 PHE H 65 TRP 0.003 0.001 TRP N 33 HIS 0.011 0.001 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00514 (17289) covalent geometry : angle 0.64504 (24566) hydrogen bonds : bond 0.04190 ( 1065) hydrogen bonds : angle 3.19408 ( 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 316 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 274 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8418 (tt0) cc_final: 0.8096 (tt0) REVERT: A 94 GLU cc_start: 0.8477 (mm-30) cc_final: 0.8185 (tp30) REVERT: B 25 ASN cc_start: 0.8427 (m-40) cc_final: 0.7882 (m-40) REVERT: C 74 LYS cc_start: 0.9301 (mmmt) cc_final: 0.9081 (mmmt) REVERT: D 35 GLU cc_start: 0.8774 (tp30) cc_final: 0.8488 (mm-30) REVERT: D 42 TYR cc_start: 0.8324 (t80) cc_final: 0.8022 (t80) REVERT: D 79 ARG cc_start: 0.8830 (mtm-85) cc_final: 0.8219 (mtm-85) REVERT: D 105 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7580 (tm-30) REVERT: D 120 LYS cc_start: 0.9547 (tttm) cc_final: 0.9189 (tttm) REVERT: E 59 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.7883 (pm20) REVERT: E 125 GLN cc_start: 0.9154 (mt0) cc_final: 0.8710 (mp10) REVERT: F 74 GLU cc_start: 0.8600 (tm-30) cc_final: 0.8291 (tp30) REVERT: G 118 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.7970 (tmtt) REVERT: H 33 ARG cc_start: 0.8527 (tpt170) cc_final: 0.8099 (mmt-90) REVERT: H 71 GLU cc_start: 0.8653 (tm-30) cc_final: 0.8409 (tm-30) REVERT: H 72 ARG cc_start: 0.9220 (OUTLIER) cc_final: 0.8161 (mtt180) REVERT: H 79 ARG cc_start: 0.8170 (mtm-85) cc_final: 0.7694 (mtm-85) REVERT: H 83 TYR cc_start: 0.8568 (m-10) cc_final: 0.8175 (m-80) REVERT: H 93 GLU cc_start: 0.8611 (mp0) cc_final: 0.8330 (mp0) REVERT: H 105 GLU cc_start: 0.9177 (tp30) cc_final: 0.8855 (tp30) REVERT: H 113 GLU cc_start: 0.8886 (tm-30) cc_final: 0.8463 (tm-30) REVERT: H 120 LYS cc_start: 0.9369 (tmtt) cc_final: 0.9004 (tptm) REVERT: O 14 ASN cc_start: 0.9421 (m-40) cc_final: 0.9215 (m-40) REVERT: O 17 ARG cc_start: 0.8612 (mtt-85) cc_final: 0.8235 (mtt180) REVERT: P 38 MET cc_start: 0.6846 (OUTLIER) cc_final: 0.5845 (mmm) REVERT: P 58 PHE cc_start: 0.0814 (OUTLIER) cc_final: 0.0370 (p90) REVERT: P 107 GLU cc_start: 0.5614 (OUTLIER) cc_final: 0.5394 (pp20) outliers start: 42 outliers final: 33 residues processed: 293 average time/residue: 0.1687 time to fit residues: 67.8586 Evaluate side-chains 310 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 271 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 12 LYS Chi-restraints excluded: chain M residue 58 PHE Chi-restraints excluded: chain N residue 20 MET Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain 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 72 ARG Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain O residue 20 LYS 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 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 119 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 149 optimal weight: 20.0000 chunk 140 optimal weight: 5.9990 chunk 9 optimal weight: 8.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 63 ASN ** Q 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.097392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.053456 restraints weight = 61463.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.054218 restraints weight = 29018.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.054592 restraints weight = 20414.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.054991 restraints weight = 17973.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.055113 restraints weight = 16909.379| |-----------------------------------------------------------------------------| r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.1377 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= 0.199 Angle : 0.641 10.386 24566 Z= 0.358 Chirality : 0.036 0.268 2748 Planarity : 0.004 0.036 2110 Dihedral : 29.710 97.399 4622 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.81 % Allowed : 26.04 % Favored : 70.15 % 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: 2.79 (0.17), residues: 873 sheet: -3.05 (1.18), residues: 20 loop : -0.66 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 71 TYR 0.039 0.002 TYR H 83 PHE 0.010 0.001 PHE E 67 TRP 0.003 0.001 TRP M 25 HIS 0.010 0.001 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00447 (17289) covalent geometry : angle 0.64055 (24566) hydrogen bonds : bond 0.03847 ( 1065) hydrogen bonds : angle 3.15614 ( 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 316 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 274 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 18 ARG cc_start: 0.8659 (ptp90) cc_final: 0.8410 (ptp-170) REVERT: A 73 GLU cc_start: 0.8410 (tt0) cc_final: 0.7910 (tt0) REVERT: A 94 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8196 (tp30) REVERT: B 25 ASN cc_start: 0.8436 (m-40) cc_final: 0.7791 (m-40) REVERT: B 93 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.8424 (mp10) REVERT: C 74 LYS cc_start: 0.9314 (mmmt) cc_final: 0.9109 (mmmt) REVERT: D 35 GLU cc_start: 0.8792 (tp30) cc_final: 0.8484 (mm-30) REVERT: D 42 TYR cc_start: 0.8242 (t80) cc_final: 0.8001 (t80) REVERT: D 79 ARG cc_start: 0.8846 (mtm-85) cc_final: 0.8279 (mtm-85) REVERT: D 120 LYS cc_start: 0.9555 (tttm) cc_final: 0.9192 (tttm) REVERT: E 59 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.7894 (pm20) REVERT: F 74 GLU cc_start: 0.8599 (tm-30) cc_final: 0.8266 (tp30) REVERT: F 77 LYS cc_start: 0.9088 (mmtm) cc_final: 0.8821 (mmtm) REVERT: F 88 TYR cc_start: 0.8821 (m-10) cc_final: 0.8308 (m-10) REVERT: G 118 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.8066 (tmtt) REVERT: H 33 ARG cc_start: 0.8547 (tpt170) cc_final: 0.8104 (mmt-90) REVERT: H 34 LYS cc_start: 0.8964 (mmtt) cc_final: 0.8750 (mmtm) REVERT: H 71 GLU cc_start: 0.8656 (tm-30) cc_final: 0.8387 (tm-30) REVERT: H 72 ARG cc_start: 0.9209 (OUTLIER) cc_final: 0.8160 (mtt180) REVERT: H 79 ARG cc_start: 0.8208 (mtm-85) cc_final: 0.7746 (mtm-85) REVERT: H 83 TYR cc_start: 0.8509 (m-10) cc_final: 0.8211 (m-10) REVERT: H 93 GLU cc_start: 0.8614 (mp0) cc_final: 0.8325 (mp0) REVERT: H 105 GLU cc_start: 0.9155 (tp30) cc_final: 0.8821 (tp30) REVERT: H 113 GLU cc_start: 0.8868 (tm-30) cc_final: 0.8440 (tm-30) REVERT: H 120 LYS cc_start: 0.9366 (tmtt) cc_final: 0.8999 (tptm) REVERT: O 14 ASN cc_start: 0.9423 (m-40) cc_final: 0.9206 (m-40) REVERT: O 17 ARG cc_start: 0.8604 (mtt-85) cc_final: 0.8227 (mtt180) REVERT: P 38 MET cc_start: 0.6939 (OUTLIER) cc_final: 0.5951 (mmm) REVERT: P 58 PHE cc_start: 0.1017 (OUTLIER) cc_final: 0.0553 (p90) REVERT: P 107 GLU cc_start: 0.5561 (OUTLIER) cc_final: 0.5343 (pp20) outliers start: 42 outliers final: 32 residues processed: 293 average time/residue: 0.1787 time to fit residues: 71.8857 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 : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 12 LYS Chi-restraints excluded: chain M residue 58 PHE Chi-restraints excluded: chain N residue 20 MET Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain 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 72 ARG Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain O residue 20 LYS 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 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: 1.9990 chunk 20 optimal weight: 50.0000 chunk 127 optimal weight: 4.9990 chunk 114 optimal weight: 7.9990 chunk 61 optimal weight: 0.9990 chunk 57 optimal weight: 0.0270 chunk 85 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 overall best weight: 1.1444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3681 r_free = 0.3681 target = 0.098088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.053919 restraints weight = 61033.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.054798 restraints weight = 29563.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.055240 restraints weight = 20926.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.055549 restraints weight = 18271.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.055616 restraints weight = 17125.677| |-----------------------------------------------------------------------------| r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17289 Z= 0.158 Angle : 0.629 10.271 24566 Z= 0.351 Chirality : 0.035 0.280 2748 Planarity : 0.004 0.037 2110 Dihedral : 29.545 98.350 4622 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.09 % Allowed : 26.95 % Favored : 69.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.70 (0.24), residues: 1257 helix: 2.84 (0.17), residues: 873 sheet: -3.03 (1.18), residues: 20 loop : -0.63 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 71 TYR 0.032 0.002 TYR H 83 PHE 0.010 0.001 PHE E 67 TRP 0.004 0.001 TRP M 25 HIS 0.010 0.001 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00352 (17289) covalent geometry : angle 0.62942 (24566) hydrogen bonds : bond 0.03616 ( 1065) hydrogen bonds : angle 3.08606 ( 2773) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4598.47 seconds wall clock time: 79 minutes 27.05 seconds (4767.05 seconds total)