Starting phenix.real_space_refine on Wed Mar 4 16:57:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6o96_0652/03_2026/6o96_0652.cif Found real_map, /net/cci-nas-00/data/ceres_data/6o96_0652/03_2026/6o96_0652.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6o96_0652/03_2026/6o96_0652.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6o96_0652/03_2026/6o96_0652.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6o96_0652/03_2026/6o96_0652.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6o96_0652/03_2026/6o96_0652.map" } resolution = 3.5 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= -0.007 sd= 0.345 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 292 5.49 5 S 28 5.16 5 C 8657 2.51 5 N 2794 2.21 5 O 3423 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15194 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 663 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 82} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 715 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 663 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 82} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 723 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "K" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2596 Classifications: {'peptide': 321} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 16, 'TRANS': 304} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 594 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 72} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N LEU L 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU L 73 " occ=0.45 residue: pdb=" N ARG L 74 " occ=0.45 ... (9 atoms not shown) pdb=" NH2 ARG L 74 " occ=0.45 residue: pdb=" N GLY L 75 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY L 75 " occ=0.25 Time building chain proxies: 3.58, per 1000 atoms: 0.24 Number of scatterers: 15194 At special positions: 0 Unit cell: (134.55, 119.025, 143.865, 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 28 16.00 P 292 15.00 O 3423 8.00 N 2794 7.00 C 8657 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: 1.22 Conformation dependent library (CDL) restraints added in 352.4 milliseconds 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2190 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 13 sheets defined 61.4% alpha, 5.1% beta 144 base pairs and 261 stacking pairs defined. Time for finding SS restraints: 2.83 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.582A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.860A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.644A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 removed outlier: 3.774A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 45 through 72 removed outlier: 4.600A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 88 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.804A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.532A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 123 removed outlier: 3.613A pdb=" N SER D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 57 removed outlier: 3.848A pdb=" N LYS E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.516A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.755A 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 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.594A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR G 50 " --> pdb=" O GLY G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.583A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.807A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 124 removed outlier: 3.942A pdb=" N ALA H 124 " --> pdb=" O CYS H 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 32 through 48 removed outlier: 3.662A pdb=" N ILE K 48 " --> pdb=" O VAL K 44 " (cutoff:3.500A) Processing helix chain 'K' and resid 48 through 55 removed outlier: 3.863A pdb=" N LYS K 52 " --> pdb=" O ILE K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 90 removed outlier: 4.046A pdb=" N MET K 71 " --> pdb=" O SER K 67 " (cutoff:3.500A) Processing helix chain 'K' and resid 103 through 119 removed outlier: 3.759A pdb=" N LEU K 107 " --> pdb=" O SER K 103 " (cutoff:3.500A) Processing helix chain 'K' and resid 121 through 127 removed outlier: 3.669A pdb=" N LYS K 124 " --> pdb=" O ASP K 121 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN K 127 " --> pdb=" O LYS K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 140 through 151 removed outlier: 3.979A pdb=" N VAL K 144 " --> pdb=" O SER K 140 " (cutoff:3.500A) Processing helix chain 'K' and resid 167 through 177 Processing helix chain 'K' and resid 188 through 210 removed outlier: 3.515A pdb=" N ALA K 192 " --> pdb=" O ALA K 188 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N THR K 197 " --> pdb=" O LYS K 193 " (cutoff:3.500A) Processing helix chain 'K' and resid 225 through 235 removed outlier: 4.144A pdb=" N GLU K 230 " --> pdb=" O GLU K 226 " (cutoff:3.500A) Processing helix chain 'K' and resid 241 through 245 removed outlier: 4.529A pdb=" N ALA K 244 " --> pdb=" O ASN K 241 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N PHE K 245 " --> pdb=" O ASN K 242 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 241 through 245' Processing helix chain 'K' and resid 246 through 258 removed outlier: 3.593A pdb=" N ASP K 250 " --> pdb=" O GLY K 246 " (cutoff:3.500A) Processing helix chain 'K' and resid 286 through 289 removed outlier: 3.698A pdb=" N THR K 289 " --> pdb=" O ASP K 286 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 286 through 289' Processing helix chain 'K' and resid 320 through 329 Processing helix chain 'L' and resid 22 through 35 removed outlier: 3.506A pdb=" N VAL L 26 " --> pdb=" O THR L 22 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 60 removed outlier: 3.641A pdb=" N TYR L 59 " --> pdb=" O LEU L 56 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.930A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 removed outlier: 3.594A pdb=" N TYR B 98 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.486A 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 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.567A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.984A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.693A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 6 through 9 Processing sheet with id=AB3, first strand: chain 'K' and resid 215 through 216 removed outlier: 7.033A pdb=" N PHE K 159 " --> pdb=" O TYR K 183 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL K 160 " --> pdb=" O PHE K 239 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 12 through 16 removed outlier: 4.669A pdb=" N SER L 65 " --> pdb=" O GLN L 2 " (cutoff:3.500A) 520 hydrogen bonds defined for protein. 1542 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 367 hydrogen bonds 734 hydrogen bond angles 0 basepair planarities 144 basepair parallelities 261 stacking parallelities Total time for adding SS restraints: 3.58 Time building geometry restraints manager: 1.70 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: 2804 1.33 - 1.45: 5104 1.45 - 1.57: 7536 1.57 - 1.69: 582 1.69 - 1.81: 49 Bond restraints: 16075 Sorted by residual: bond pdb=" C4 SAH K 401 " pdb=" C5 SAH K 401 " ideal model delta sigma weight residual 1.386 1.470 -0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" C5 SAH K 401 " pdb=" C6 SAH K 401 " ideal model delta sigma weight residual 1.407 1.489 -0.082 2.00e-02 2.50e+03 1.68e+01 bond pdb=" C TRP K 22 " pdb=" N PRO K 23 " ideal model delta sigma weight residual 1.332 1.382 -0.050 1.34e-02 5.57e+03 1.40e+01 bond pdb=" N ARG E 42 " pdb=" CA ARG E 42 " ideal model delta sigma weight residual 1.453 1.488 -0.035 1.16e-02 7.43e+03 9.10e+00 bond pdb=" N ARG E 40 " pdb=" CA ARG E 40 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.23e-02 6.61e+03 7.10e+00 ... (remaining 16070 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 22036 2.25 - 4.50: 854 4.50 - 6.76: 84 6.76 - 9.01: 17 9.01 - 11.26: 8 Bond angle restraints: 22999 Sorted by residual: angle pdb=" N ASN K 178 " pdb=" CA ASN K 178 " pdb=" C ASN K 178 " ideal model delta sigma weight residual 110.44 117.63 -7.19 1.20e+00 6.94e-01 3.59e+01 angle pdb=" C LEU K 60 " pdb=" N ILE K 61 " pdb=" CA ILE K 61 " ideal model delta sigma weight residual 120.62 128.00 -7.38 1.64e+00 3.72e-01 2.03e+01 angle pdb=" C TYR K 312 " pdb=" N TYR K 313 " pdb=" CA TYR K 313 " ideal model delta sigma weight residual 120.71 127.08 -6.37 1.42e+00 4.96e-01 2.01e+01 angle pdb=" C LYS K 10 " pdb=" N SER K 11 " pdb=" CA SER K 11 " ideal model delta sigma weight residual 120.86 127.51 -6.65 1.60e+00 3.91e-01 1.73e+01 angle pdb=" CA ARG F 95 " pdb=" C ARG F 95 " pdb=" N THR F 96 " ideal model delta sigma weight residual 114.76 119.32 -4.56 1.14e+00 7.69e-01 1.60e+01 ... (remaining 22994 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.83: 7099 31.83 - 63.65: 1750 63.65 - 95.48: 51 95.48 - 127.30: 0 127.30 - 159.13: 3 Dihedral angle restraints: 8903 sinusoidal: 5517 harmonic: 3386 Sorted by residual: dihedral pdb=" CA ASN K 57 " pdb=" C ASN K 57 " pdb=" N TYR K 58 " pdb=" CA TYR K 58 " ideal model delta harmonic sigma weight residual 180.00 152.56 27.44 0 5.00e+00 4.00e-02 3.01e+01 dihedral pdb=" CA THR K 306 " pdb=" C THR K 306 " pdb=" N GLY K 307 " pdb=" CA GLY K 307 " ideal model delta harmonic sigma weight residual -180.00 -153.38 -26.62 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" CA THR K 177 " pdb=" C THR K 177 " pdb=" N ASN K 178 " pdb=" CA ASN K 178 " ideal model delta harmonic sigma weight residual -180.00 -154.98 -25.02 0 5.00e+00 4.00e-02 2.50e+01 ... (remaining 8900 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 2117 0.067 - 0.134: 428 0.134 - 0.201: 59 0.201 - 0.268: 10 0.268 - 0.336: 1 Chirality restraints: 2615 Sorted by residual: chirality pdb=" CB ILE H 54 " pdb=" CA ILE H 54 " pdb=" CG1 ILE H 54 " pdb=" CG2 ILE H 54 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" CB VAL C 100 " pdb=" CA VAL C 100 " pdb=" CG1 VAL C 100 " pdb=" CG2 VAL C 100 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CB ILE D 54 " pdb=" CA ILE D 54 " pdb=" CG1 ILE D 54 " pdb=" CG2 ILE D 54 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 2612 not shown) Planarity restraints: 1909 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC J 142 " -0.045 2.00e-02 2.50e+03 2.26e-02 1.15e+01 pdb=" N1 DC J 142 " 0.042 2.00e-02 2.50e+03 pdb=" C2 DC J 142 " -0.006 2.00e-02 2.50e+03 pdb=" O2 DC J 142 " 0.016 2.00e-02 2.50e+03 pdb=" N3 DC J 142 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DC J 142 " -0.009 2.00e-02 2.50e+03 pdb=" N4 DC J 142 " -0.011 2.00e-02 2.50e+03 pdb=" C5 DC J 142 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DC J 142 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " 0.046 5.00e-02 4.00e+02 6.95e-02 7.72e+00 pdb=" N PRO G 80 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " -0.046 5.00e-02 4.00e+02 6.85e-02 7.51e+00 pdb=" N PRO C 80 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " -0.038 5.00e-02 4.00e+02 ... (remaining 1906 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2225 2.75 - 3.28: 12913 3.28 - 3.82: 29735 3.82 - 4.36: 34215 4.36 - 4.90: 50375 Nonbonded interactions: 129463 Sorted by model distance: nonbonded pdb=" NH2 ARG E 40 " pdb=" O2 DT J 83 " model vdw 2.207 3.120 nonbonded pdb=" OH TYR D 40 " pdb=" OP1 DG I 122 " model vdw 2.277 3.040 nonbonded pdb=" O THR C 16 " pdb=" OG SER C 19 " model vdw 2.303 3.040 nonbonded pdb=" OG1 THR B 73 " pdb=" OD2 ASP B 85 " model vdw 2.305 3.040 nonbonded pdb=" O SER D 123 " pdb=" OG SER D 123 " model vdw 2.325 3.040 ... (remaining 129458 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = (chain 'C' and (resid 12 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 118)) selection = (chain 'G' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 118)) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 32 through 33 or (resid 34 and (name N or name CA or name \ C or name O or name CB )) or resid 35 through 56 or (resid 57 through 58 and (na \ me N or name CA or name C or name O or name CB )) or resid 59 through 124)) } 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=0.25 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: 3.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.750 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 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 : 0.011 0.090 16075 Z= 0.460 Angle : 1.027 11.260 22999 Z= 0.585 Chirality : 0.056 0.336 2615 Planarity : 0.008 0.069 1909 Dihedral : 27.276 159.131 6713 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.41 % Allowed : 9.21 % Favored : 90.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.03 (0.18), residues: 1139 helix: -2.83 (0.13), residues: 686 sheet: -0.32 (0.63), residues: 62 loop : -2.40 (0.26), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 45 TYR 0.022 0.003 TYR K 183 PHE 0.029 0.003 PHE E 67 TRP 0.017 0.002 TRP K 208 HIS 0.012 0.002 HIS K 109 Details of bonding type rmsd covalent geometry : bond 0.01073 (16075) covalent geometry : angle 1.02737 (22999) hydrogen bonds : bond 0.10890 ( 887) hydrogen bonds : angle 5.50282 ( 2276) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 610 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.7279 (tt0) cc_final: 0.6698 (tt0) REVERT: A 116 ARG cc_start: 0.7277 (mtm110) cc_final: 0.6723 (mtp180) REVERT: A 120 MET cc_start: 0.6506 (mtp) cc_final: 0.6011 (mtm) REVERT: C 57 TYR cc_start: 0.7821 (t80) cc_final: 0.7311 (t80) REVERT: C 94 ASN cc_start: 0.8289 (t0) cc_final: 0.8026 (t0) REVERT: D 68 ASP cc_start: 0.7915 (t0) cc_final: 0.7628 (t0) REVERT: D 89 ILE cc_start: 0.8832 (mm) cc_final: 0.8620 (mm) REVERT: F 39 ARG cc_start: 0.8166 (mmt-90) cc_final: 0.7958 (mmt180) REVERT: G 50 TYR cc_start: 0.7895 (t80) cc_final: 0.7620 (t80) REVERT: G 57 TYR cc_start: 0.7630 (t80) cc_final: 0.7317 (t80) REVERT: G 100 VAL cc_start: 0.8659 (m) cc_final: 0.8379 (m) REVERT: K 241 ASN cc_start: 0.8129 (t0) cc_final: 0.7490 (t0) REVERT: K 312 TYR cc_start: 0.7937 (m-80) cc_final: 0.7687 (m-80) outliers start: 4 outliers final: 1 residues processed: 613 average time/residue: 0.1596 time to fit residues: 131.1613 Evaluate side-chains 492 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 491 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 316 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN D 49 HIS D 63 ASN E 68 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 HIS G 73 ASN G 89 ASN G 104 GLN H 84 ASN H 95 GLN K 99 ASN K 113 GLN K 116 ASN ** K 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 315 HIS ** L 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 60 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.102096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.063186 restraints weight = 42606.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.065251 restraints weight = 17206.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.066424 restraints weight = 10800.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.067077 restraints weight = 8590.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.067388 restraints weight = 7689.865| |-----------------------------------------------------------------------------| r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2980 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2975 r_free = 0.2975 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2975 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 16075 Z= 0.293 Angle : 0.717 8.345 22999 Z= 0.414 Chirality : 0.041 0.211 2615 Planarity : 0.006 0.054 1909 Dihedral : 29.749 168.756 4480 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 6.94 % Allowed : 24.22 % Favored : 68.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.22), residues: 1139 helix: -0.37 (0.18), residues: 694 sheet: -0.32 (0.55), residues: 72 loop : -1.84 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 55 TYR 0.023 0.002 TYR B 88 PHE 0.037 0.003 PHE A 67 TRP 0.014 0.002 TRP K 305 HIS 0.012 0.002 HIS K 109 Details of bonding type rmsd covalent geometry : bond 0.00643 (16075) covalent geometry : angle 0.71664 (22999) hydrogen bonds : bond 0.05011 ( 887) hydrogen bonds : angle 4.03651 ( 2276) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 538 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.9157 (m-80) cc_final: 0.8686 (m-80) REVERT: A 59 GLU cc_start: 0.8477 (pm20) cc_final: 0.8251 (pm20) REVERT: A 73 GLU cc_start: 0.8256 (tt0) cc_final: 0.8033 (mt-10) REVERT: A 85 GLN cc_start: 0.8840 (mt0) cc_final: 0.8600 (mt0) REVERT: A 87 SER cc_start: 0.9110 (p) cc_final: 0.8910 (p) REVERT: A 93 GLN cc_start: 0.8916 (tt0) cc_final: 0.8120 (tt0) REVERT: A 94 GLU cc_start: 0.9142 (mm-30) cc_final: 0.8725 (mm-30) REVERT: A 97 GLU cc_start: 0.8330 (mt-10) cc_final: 0.7779 (mp0) REVERT: A 120 MET cc_start: 0.8135 (mtp) cc_final: 0.7726 (mtp) REVERT: A 126 LEU cc_start: 0.9553 (tp) cc_final: 0.9318 (tp) REVERT: A 129 ARG cc_start: 0.9153 (tpt-90) cc_final: 0.8899 (tpp80) REVERT: B 25 ASN cc_start: 0.8197 (t0) cc_final: 0.7069 (t0) REVERT: B 44 LYS cc_start: 0.9430 (ttpp) cc_final: 0.8645 (mtpt) REVERT: B 71 THR cc_start: 0.9751 (m) cc_final: 0.9480 (p) REVERT: B 77 LYS cc_start: 0.9486 (mmtt) cc_final: 0.9275 (mmmm) REVERT: B 79 LYS cc_start: 0.8809 (mtmt) cc_final: 0.8405 (mtmm) REVERT: B 85 ASP cc_start: 0.8987 (m-30) cc_final: 0.8596 (m-30) REVERT: B 88 TYR cc_start: 0.9177 (m-80) cc_final: 0.8722 (m-80) REVERT: B 98 TYR cc_start: 0.9288 (m-80) cc_final: 0.9059 (m-80) REVERT: C 24 GLN cc_start: 0.8955 (mm-40) cc_final: 0.8482 (mm-40) REVERT: C 72 ASP cc_start: 0.8745 (m-30) cc_final: 0.8408 (m-30) REVERT: C 73 ASN cc_start: 0.9116 (t0) cc_final: 0.8732 (t0) REVERT: C 82 HIS cc_start: 0.9463 (m170) cc_final: 0.9025 (m90) REVERT: D 47 GLN cc_start: 0.9544 (mt0) cc_final: 0.9041 (mt0) REVERT: D 68 ASP cc_start: 0.9276 (t0) cc_final: 0.8792 (t0) REVERT: D 86 ARG cc_start: 0.8951 (tpp80) cc_final: 0.8531 (tpp80) REVERT: D 113 GLU cc_start: 0.9148 (tt0) cc_final: 0.8912 (tt0) REVERT: E 63 ARG cc_start: 0.8842 (mmp80) cc_final: 0.8328 (mmm-85) REVERT: E 68 GLN cc_start: 0.9358 (tt0) cc_final: 0.9135 (tt0) REVERT: E 85 GLN cc_start: 0.9145 (OUTLIER) cc_final: 0.8734 (mt0) REVERT: E 120 MET cc_start: 0.8367 (mtp) cc_final: 0.7765 (mtp) REVERT: E 125 GLN cc_start: 0.8933 (mt0) cc_final: 0.8695 (mt0) REVERT: F 27 GLN cc_start: 0.9358 (mm-40) cc_final: 0.8931 (pm20) REVERT: F 44 LYS cc_start: 0.9326 (ttmm) cc_final: 0.9112 (ttpt) REVERT: F 45 ARG cc_start: 0.8569 (mtp85) cc_final: 0.8012 (mtp85) REVERT: F 84 MET cc_start: 0.9098 (mmm) cc_final: 0.8087 (mmm) REVERT: F 98 TYR cc_start: 0.9474 (m-10) cc_final: 0.8920 (m-80) REVERT: G 25 PHE cc_start: 0.9295 (m-80) cc_final: 0.8993 (m-80) REVERT: G 42 ARG cc_start: 0.9219 (ptp-110) cc_final: 0.8919 (ptm160) REVERT: G 50 TYR cc_start: 0.9440 (t80) cc_final: 0.8895 (t80) REVERT: G 57 TYR cc_start: 0.9175 (t80) cc_final: 0.8940 (t80) REVERT: G 84 GLN cc_start: 0.9372 (tp-100) cc_final: 0.8590 (tp-100) REVERT: G 89 ASN cc_start: 0.9294 (m-40) cc_final: 0.9020 (m110) REVERT: G 90 ASP cc_start: 0.8549 (t70) cc_final: 0.8210 (t70) REVERT: H 63 ASN cc_start: 0.9502 (t0) cc_final: 0.9246 (t0) REVERT: H 68 ASP cc_start: 0.9381 (t0) cc_final: 0.9136 (t0) REVERT: H 95 GLN cc_start: 0.9451 (tt0) cc_final: 0.8793 (tp40) outliers start: 67 outliers final: 35 residues processed: 551 average time/residue: 0.1406 time to fit residues: 108.4491 Evaluate side-chains 537 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 501 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 85 GLN Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain K residue 86 HIS Chi-restraints excluded: chain K residue 177 THR Chi-restraints excluded: chain K residue 190 ILE Chi-restraints excluded: chain K residue 316 THR Chi-restraints excluded: chain K residue 317 ILE Chi-restraints excluded: chain L residue 4 PHE Chi-restraints excluded: chain L residue 68 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 4 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 111 optimal weight: 20.0000 chunk 67 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 73 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 118 optimal weight: 6.9990 chunk 42 optimal weight: 0.5980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.103449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.064841 restraints weight = 42416.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.066899 restraints weight = 16858.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.068136 restraints weight = 10533.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.068779 restraints weight = 8298.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.069083 restraints weight = 7442.583| |-----------------------------------------------------------------------------| r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3024 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3024 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16075 Z= 0.192 Angle : 0.671 11.998 22999 Z= 0.380 Chirality : 0.039 0.178 2615 Planarity : 0.005 0.046 1909 Dihedral : 29.531 170.430 4480 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 6.31 % Allowed : 27.23 % Favored : 66.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.24), residues: 1139 helix: 0.57 (0.19), residues: 698 sheet: -0.43 (0.55), residues: 79 loop : -1.49 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 42 TYR 0.020 0.002 TYR D 40 PHE 0.035 0.002 PHE A 67 TRP 0.011 0.001 TRP K 305 HIS 0.010 0.001 HIS L 68 Details of bonding type rmsd covalent geometry : bond 0.00430 (16075) covalent geometry : angle 0.67111 (22999) hydrogen bonds : bond 0.03982 ( 887) hydrogen bonds : angle 3.72273 ( 2276) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 538 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.9245 (m-80) cc_final: 0.8780 (m-80) REVERT: A 63 ARG cc_start: 0.9156 (mmp-170) cc_final: 0.8422 (mmm-85) REVERT: A 87 SER cc_start: 0.9090 (p) cc_final: 0.8874 (p) REVERT: A 93 GLN cc_start: 0.8922 (tt0) cc_final: 0.8269 (tt0) REVERT: A 94 GLU cc_start: 0.9156 (mm-30) cc_final: 0.8732 (mm-30) REVERT: A 97 GLU cc_start: 0.8327 (mt-10) cc_final: 0.7788 (mp0) REVERT: A 120 MET cc_start: 0.8107 (mtp) cc_final: 0.7632 (mtp) REVERT: A 129 ARG cc_start: 0.9163 (tpt-90) cc_final: 0.8866 (tpp80) REVERT: B 25 ASN cc_start: 0.8113 (t0) cc_final: 0.7637 (t0) REVERT: B 30 THR cc_start: 0.9199 (p) cc_final: 0.8859 (t) REVERT: B 35 ARG cc_start: 0.9404 (ttm-80) cc_final: 0.9202 (ttm-80) REVERT: B 44 LYS cc_start: 0.9449 (ttpp) cc_final: 0.8630 (mtmt) REVERT: B 45 ARG cc_start: 0.8351 (mmm-85) cc_final: 0.8084 (mmm-85) REVERT: B 74 GLU cc_start: 0.9104 (tt0) cc_final: 0.8883 (tt0) REVERT: B 77 LYS cc_start: 0.9455 (mmtt) cc_final: 0.9238 (mmmm) REVERT: B 79 LYS cc_start: 0.8653 (mtmt) cc_final: 0.8140 (mtmm) REVERT: B 82 THR cc_start: 0.9175 (OUTLIER) cc_final: 0.8722 (t) REVERT: B 85 ASP cc_start: 0.8901 (m-30) cc_final: 0.8551 (m-30) REVERT: B 88 TYR cc_start: 0.8997 (m-10) cc_final: 0.8491 (m-80) REVERT: B 98 TYR cc_start: 0.9325 (m-80) cc_final: 0.8971 (m-80) REVERT: C 24 GLN cc_start: 0.8768 (mm-40) cc_final: 0.8331 (mm-40) REVERT: C 42 ARG cc_start: 0.9178 (OUTLIER) cc_final: 0.8814 (mtp-110) REVERT: C 58 LEU cc_start: 0.9611 (OUTLIER) cc_final: 0.9393 (mm) REVERT: C 72 ASP cc_start: 0.8634 (m-30) cc_final: 0.8406 (m-30) REVERT: C 73 ASN cc_start: 0.9252 (OUTLIER) cc_final: 0.8736 (t0) REVERT: C 82 HIS cc_start: 0.9449 (m170) cc_final: 0.8964 (m90) REVERT: C 84 GLN cc_start: 0.9556 (tp-100) cc_final: 0.9333 (tp-100) REVERT: D 47 GLN cc_start: 0.9523 (mt0) cc_final: 0.8947 (mt0) REVERT: D 68 ASP cc_start: 0.9227 (t0) cc_final: 0.8664 (t0) REVERT: D 83 TYR cc_start: 0.8357 (m-10) cc_final: 0.6477 (m-10) REVERT: D 121 TYR cc_start: 0.9465 (t80) cc_final: 0.9240 (t80) REVERT: E 68 GLN cc_start: 0.9305 (tt0) cc_final: 0.9029 (tt0) REVERT: E 73 GLU cc_start: 0.8614 (tt0) cc_final: 0.7737 (tt0) REVERT: E 85 GLN cc_start: 0.9064 (OUTLIER) cc_final: 0.8799 (mt0) REVERT: E 120 MET cc_start: 0.8437 (mtp) cc_final: 0.7676 (mtp) REVERT: E 125 GLN cc_start: 0.8946 (mt0) cc_final: 0.8644 (mt0) REVERT: E 133 GLU cc_start: 0.7610 (mp0) cc_final: 0.7244 (mp0) REVERT: F 30 THR cc_start: 0.9101 (p) cc_final: 0.8693 (t) REVERT: F 45 ARG cc_start: 0.8943 (mtp85) cc_final: 0.8228 (mtp85) REVERT: F 98 TYR cc_start: 0.9541 (m-10) cc_final: 0.8883 (m-80) REVERT: G 25 PHE cc_start: 0.9303 (m-80) cc_final: 0.9076 (m-80) REVERT: G 42 ARG cc_start: 0.9164 (ptp-110) cc_final: 0.8821 (ptm160) REVERT: G 56 GLU cc_start: 0.8709 (tm-30) cc_final: 0.8321 (tt0) REVERT: G 57 TYR cc_start: 0.9212 (t80) cc_final: 0.8801 (t80) REVERT: G 71 ARG cc_start: 0.9227 (ttp80) cc_final: 0.8660 (ttp80) REVERT: G 84 GLN cc_start: 0.9332 (tp-100) cc_final: 0.8492 (tp-100) REVERT: G 89 ASN cc_start: 0.9418 (m-40) cc_final: 0.9049 (m-40) REVERT: G 90 ASP cc_start: 0.8444 (t70) cc_final: 0.8122 (t70) REVERT: H 37 TYR cc_start: 0.9372 (m-80) cc_final: 0.8828 (m-80) REVERT: H 47 GLN cc_start: 0.9427 (mt0) cc_final: 0.9167 (tm-30) REVERT: H 64 SER cc_start: 0.9597 (t) cc_final: 0.9327 (t) REVERT: H 68 ASP cc_start: 0.9401 (t0) cc_final: 0.9130 (t0) REVERT: H 86 ARG cc_start: 0.9195 (mmm-85) cc_final: 0.8773 (mmm160) REVERT: H 95 GLN cc_start: 0.9389 (tt0) cc_final: 0.8393 (tp40) REVERT: H 96 THR cc_start: 0.9642 (m) cc_final: 0.9232 (t) REVERT: K 55 MET cc_start: -0.0804 (mmt) cc_final: -0.1426 (tpp) REVERT: K 101 ARG cc_start: 0.7456 (mmt90) cc_final: 0.5969 (mmp80) REVERT: K 113 GLN cc_start: 0.8220 (pt0) cc_final: 0.8010 (pp30) outliers start: 61 outliers final: 37 residues processed: 557 average time/residue: 0.1362 time to fit residues: 107.0851 Evaluate side-chains 540 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 498 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 85 GLN Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 52 LYS Chi-restraints excluded: chain K residue 160 VAL Chi-restraints excluded: chain K residue 177 THR Chi-restraints excluded: chain K residue 190 ILE Chi-restraints excluded: chain K residue 286 ASP Chi-restraints excluded: chain K residue 316 THR Chi-restraints excluded: chain K residue 317 ILE Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 68 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 31 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 chunk 117 optimal weight: 10.0000 chunk 42 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 49 HIS ** K 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.103322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.064839 restraints weight = 42163.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.066876 restraints weight = 16964.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.068080 restraints weight = 10607.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.068733 restraints weight = 8370.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.069048 restraints weight = 7482.047| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3027 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3027 r_free = 0.3027 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3027 r_free = 0.3027 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3027 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16075 Z= 0.192 Angle : 0.664 11.214 22999 Z= 0.374 Chirality : 0.039 0.177 2615 Planarity : 0.004 0.044 1909 Dihedral : 29.414 172.214 4480 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 7.04 % Allowed : 28.67 % Favored : 64.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.25), residues: 1139 helix: 1.04 (0.19), residues: 698 sheet: -0.38 (0.57), residues: 79 loop : -1.36 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 36 TYR 0.020 0.002 TYR C 57 PHE 0.034 0.002 PHE A 67 TRP 0.010 0.001 TRP K 305 HIS 0.008 0.001 HIS K 109 Details of bonding type rmsd covalent geometry : bond 0.00428 (16075) covalent geometry : angle 0.66403 (22999) hydrogen bonds : bond 0.03927 ( 887) hydrogen bonds : angle 3.65617 ( 2276) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 520 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.9265 (m-80) cc_final: 0.8805 (m-80) REVERT: A 63 ARG cc_start: 0.9113 (mmp-170) cc_final: 0.8540 (mmp80) REVERT: A 87 SER cc_start: 0.9106 (p) cc_final: 0.8883 (p) REVERT: A 93 GLN cc_start: 0.8933 (tt0) cc_final: 0.8678 (mt0) REVERT: A 94 GLU cc_start: 0.9159 (mm-30) cc_final: 0.8684 (mm-30) REVERT: A 97 GLU cc_start: 0.8337 (mt-10) cc_final: 0.7850 (mp0) REVERT: A 118 THR cc_start: 0.9704 (m) cc_final: 0.9480 (p) REVERT: A 120 MET cc_start: 0.8142 (mtp) cc_final: 0.7634 (mtp) REVERT: A 122 LYS cc_start: 0.9006 (mtmt) cc_final: 0.8771 (mtmt) REVERT: A 129 ARG cc_start: 0.9113 (tpt-90) cc_final: 0.8843 (tpp80) REVERT: B 25 ASN cc_start: 0.8118 (t0) cc_final: 0.7690 (t0) REVERT: B 30 THR cc_start: 0.9240 (p) cc_final: 0.8965 (t) REVERT: B 44 LYS cc_start: 0.9460 (ttpp) cc_final: 0.8695 (mtpt) REVERT: B 45 ARG cc_start: 0.8470 (mmm-85) cc_final: 0.8264 (mmm-85) REVERT: B 51 TYR cc_start: 0.8948 (m-80) cc_final: 0.8326 (m-10) REVERT: B 74 GLU cc_start: 0.9107 (tt0) cc_final: 0.8877 (tt0) REVERT: B 77 LYS cc_start: 0.9447 (mmtt) cc_final: 0.9216 (mmmm) REVERT: B 79 LYS cc_start: 0.8683 (mtmt) cc_final: 0.8317 (mtmm) REVERT: B 82 THR cc_start: 0.9152 (OUTLIER) cc_final: 0.8914 (t) REVERT: B 85 ASP cc_start: 0.9019 (m-30) cc_final: 0.8655 (m-30) REVERT: B 88 TYR cc_start: 0.8999 (m-10) cc_final: 0.8548 (m-80) REVERT: B 98 TYR cc_start: 0.9320 (m-10) cc_final: 0.8932 (m-80) REVERT: C 24 GLN cc_start: 0.8755 (mm-40) cc_final: 0.8550 (mm-40) REVERT: C 42 ARG cc_start: 0.9221 (OUTLIER) cc_final: 0.8905 (mtp85) REVERT: C 58 LEU cc_start: 0.9624 (OUTLIER) cc_final: 0.9404 (mm) REVERT: C 72 ASP cc_start: 0.8677 (m-30) cc_final: 0.8395 (m-30) REVERT: D 37 TYR cc_start: 0.9222 (OUTLIER) cc_final: 0.8924 (m-10) REVERT: D 68 ASP cc_start: 0.9242 (t0) cc_final: 0.8698 (t0) REVERT: D 83 TYR cc_start: 0.8472 (m-10) cc_final: 0.6689 (m-10) REVERT: D 93 GLU cc_start: 0.9053 (mp0) cc_final: 0.8647 (mp0) REVERT: D 108 LYS cc_start: 0.8910 (mtmt) cc_final: 0.8704 (ttmt) REVERT: D 121 TYR cc_start: 0.9480 (t80) cc_final: 0.9233 (t80) REVERT: E 68 GLN cc_start: 0.9318 (tt0) cc_final: 0.9033 (tt0) REVERT: E 90 MET cc_start: 0.9165 (mmt) cc_final: 0.8918 (mmp) REVERT: E 120 MET cc_start: 0.8537 (mtp) cc_final: 0.7976 (mtp) REVERT: E 125 GLN cc_start: 0.8953 (mt0) cc_final: 0.8603 (mt0) REVERT: E 133 GLU cc_start: 0.7674 (mp0) cc_final: 0.7455 (mp0) REVERT: F 30 THR cc_start: 0.9164 (p) cc_final: 0.8526 (t) REVERT: F 36 ARG cc_start: 0.8808 (mtm-85) cc_final: 0.7272 (mtm-85) REVERT: F 45 ARG cc_start: 0.8881 (mtp85) cc_final: 0.8264 (mtp85) REVERT: F 51 TYR cc_start: 0.8788 (m-80) cc_final: 0.8254 (m-10) REVERT: F 55 ARG cc_start: 0.9322 (mtt90) cc_final: 0.8258 (mtt90) REVERT: F 84 MET cc_start: 0.9084 (mmm) cc_final: 0.8821 (tpp) REVERT: F 98 TYR cc_start: 0.9567 (m-10) cc_final: 0.8986 (m-80) REVERT: G 42 ARG cc_start: 0.9197 (ptp-110) cc_final: 0.8760 (ptm160) REVERT: G 50 TYR cc_start: 0.9295 (t80) cc_final: 0.9028 (t80) REVERT: G 57 TYR cc_start: 0.9228 (t80) cc_final: 0.8829 (t80) REVERT: G 71 ARG cc_start: 0.9227 (ttp80) cc_final: 0.8666 (ttp80) REVERT: G 73 ASN cc_start: 0.9040 (t0) cc_final: 0.8810 (t0) REVERT: G 84 GLN cc_start: 0.9440 (tp-100) cc_final: 0.8667 (tp-100) REVERT: G 85 LEU cc_start: 0.9545 (OUTLIER) cc_final: 0.9258 (mp) REVERT: G 89 ASN cc_start: 0.9400 (m-40) cc_final: 0.9061 (m-40) REVERT: G 90 ASP cc_start: 0.8345 (t70) cc_final: 0.8052 (t70) REVERT: G 99 ARG cc_start: 0.8514 (mmm160) cc_final: 0.8203 (mmm-85) REVERT: H 37 TYR cc_start: 0.9462 (m-80) cc_final: 0.8630 (m-80) REVERT: H 47 GLN cc_start: 0.9426 (mt0) cc_final: 0.9169 (tm-30) REVERT: H 64 SER cc_start: 0.9634 (t) cc_final: 0.9334 (t) REVERT: H 68 ASP cc_start: 0.9395 (t0) cc_final: 0.9097 (t0) REVERT: H 86 ARG cc_start: 0.9213 (mmm-85) cc_final: 0.8878 (mmm160) REVERT: K 55 MET cc_start: -0.0566 (mmt) cc_final: -0.1160 (tpp) REVERT: K 101 ARG cc_start: 0.7451 (mmt90) cc_final: 0.5978 (mmp80) REVERT: K 113 GLN cc_start: 0.8202 (pt0) cc_final: 0.7994 (pp30) REVERT: K 243 PHE cc_start: 0.9096 (m-10) cc_final: 0.8840 (m-80) outliers start: 68 outliers final: 44 residues processed: 542 average time/residue: 0.1352 time to fit residues: 103.5723 Evaluate side-chains 540 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 491 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 52 LYS Chi-restraints excluded: chain K residue 60 LEU Chi-restraints excluded: chain K residue 112 GLN Chi-restraints excluded: chain K residue 177 THR Chi-restraints excluded: chain K residue 179 CYS Chi-restraints excluded: chain K residue 190 ILE Chi-restraints excluded: chain K residue 316 THR Chi-restraints excluded: chain K residue 317 ILE Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 68 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 55 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 107 optimal weight: 8.9990 chunk 119 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 70 optimal weight: 0.6980 chunk 63 optimal weight: 0.0980 chunk 113 optimal weight: 2.9990 chunk 132 optimal weight: 20.0000 chunk 43 optimal weight: 0.5980 chunk 73 optimal weight: 6.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 93 GLN A 108 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN L 25 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.104742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.066014 restraints weight = 42417.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.068069 restraints weight = 17121.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.069314 restraints weight = 10732.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.069990 restraints weight = 8463.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.070284 restraints weight = 7559.142| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3050 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3050 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16075 Z= 0.173 Angle : 0.660 10.149 22999 Z= 0.369 Chirality : 0.038 0.180 2615 Planarity : 0.004 0.044 1909 Dihedral : 29.321 174.184 4480 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 6.31 % Allowed : 31.37 % Favored : 62.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.25), residues: 1139 helix: 1.34 (0.19), residues: 692 sheet: -0.30 (0.58), residues: 77 loop : -1.36 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 74 TYR 0.022 0.002 TYR F 51 PHE 0.046 0.002 PHE A 67 TRP 0.008 0.001 TRP K 305 HIS 0.008 0.001 HIS L 68 Details of bonding type rmsd covalent geometry : bond 0.00388 (16075) covalent geometry : angle 0.65975 (22999) hydrogen bonds : bond 0.03703 ( 887) hydrogen bonds : angle 3.57253 ( 2276) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 516 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.9259 (m-80) cc_final: 0.8828 (m-80) REVERT: A 63 ARG cc_start: 0.9098 (mmp-170) cc_final: 0.8379 (mmm-85) REVERT: A 85 GLN cc_start: 0.8580 (mt0) cc_final: 0.8362 (mt0) REVERT: A 92 LEU cc_start: 0.9529 (OUTLIER) cc_final: 0.9267 (tt) REVERT: A 93 GLN cc_start: 0.8885 (tt0) cc_final: 0.8647 (tt0) REVERT: A 97 GLU cc_start: 0.8328 (mt-10) cc_final: 0.7978 (mp0) REVERT: A 120 MET cc_start: 0.8110 (mtp) cc_final: 0.7688 (mtp) REVERT: A 125 GLN cc_start: 0.9271 (mt0) cc_final: 0.8951 (mt0) REVERT: A 126 LEU cc_start: 0.9487 (tp) cc_final: 0.9283 (tp) REVERT: A 129 ARG cc_start: 0.9105 (tpt-90) cc_final: 0.8828 (tpp80) REVERT: B 25 ASN cc_start: 0.8088 (t0) cc_final: 0.7691 (t0) REVERT: B 44 LYS cc_start: 0.9473 (ttpp) cc_final: 0.8737 (mtpt) REVERT: B 51 TYR cc_start: 0.8978 (m-80) cc_final: 0.8449 (m-10) REVERT: B 74 GLU cc_start: 0.9140 (tt0) cc_final: 0.8921 (tt0) REVERT: B 77 LYS cc_start: 0.9445 (mmtt) cc_final: 0.9208 (mmmm) REVERT: B 79 LYS cc_start: 0.8676 (mtmt) cc_final: 0.8314 (mtmm) REVERT: B 82 THR cc_start: 0.9311 (OUTLIER) cc_final: 0.8778 (t) REVERT: B 85 ASP cc_start: 0.8880 (m-30) cc_final: 0.8528 (m-30) REVERT: B 88 TYR cc_start: 0.9023 (m-10) cc_final: 0.8399 (m-10) REVERT: B 98 TYR cc_start: 0.9345 (m-10) cc_final: 0.8583 (m-80) REVERT: C 42 ARG cc_start: 0.9242 (OUTLIER) cc_final: 0.8996 (mtp-110) REVERT: C 72 ASP cc_start: 0.8720 (m-30) cc_final: 0.8497 (m-30) REVERT: C 73 ASN cc_start: 0.9250 (t0) cc_final: 0.8901 (t0) REVERT: D 47 GLN cc_start: 0.9501 (mt0) cc_final: 0.8917 (mt0) REVERT: D 68 ASP cc_start: 0.9260 (t0) cc_final: 0.8720 (t0) REVERT: D 83 TYR cc_start: 0.8490 (m-10) cc_final: 0.6922 (m-10) REVERT: D 108 LYS cc_start: 0.8936 (mtmt) cc_final: 0.8726 (ttmt) REVERT: D 121 TYR cc_start: 0.9512 (t80) cc_final: 0.9272 (t80) REVERT: E 68 GLN cc_start: 0.9286 (tt0) cc_final: 0.9028 (tt0) REVERT: E 73 GLU cc_start: 0.8756 (tt0) cc_final: 0.7872 (tt0) REVERT: E 90 MET cc_start: 0.9127 (mmt) cc_final: 0.8895 (mmp) REVERT: E 120 MET cc_start: 0.8572 (mtp) cc_final: 0.7960 (mtp) REVERT: E 125 GLN cc_start: 0.8948 (mt0) cc_final: 0.8586 (mt0) REVERT: E 133 GLU cc_start: 0.7689 (mp0) cc_final: 0.7451 (mp0) REVERT: F 24 ASP cc_start: 0.8411 (p0) cc_final: 0.8139 (p0) REVERT: F 30 THR cc_start: 0.9145 (p) cc_final: 0.8770 (t) REVERT: F 31 LYS cc_start: 0.9146 (tttm) cc_final: 0.8672 (tptm) REVERT: F 45 ARG cc_start: 0.8846 (mtp85) cc_final: 0.8129 (mtp85) REVERT: F 55 ARG cc_start: 0.9341 (mtt90) cc_final: 0.8301 (mtt90) REVERT: F 77 LYS cc_start: 0.9474 (mmmt) cc_final: 0.9108 (mmtm) REVERT: F 84 MET cc_start: 0.9031 (mmm) cc_final: 0.8455 (tpp) REVERT: F 98 TYR cc_start: 0.9580 (m-10) cc_final: 0.8959 (m-80) REVERT: G 57 TYR cc_start: 0.9144 (t80) cc_final: 0.8631 (t80) REVERT: G 84 GLN cc_start: 0.9441 (tp-100) cc_final: 0.8814 (tp-100) REVERT: G 90 ASP cc_start: 0.8318 (t70) cc_final: 0.8046 (t70) REVERT: G 92 GLU cc_start: 0.8535 (pm20) cc_final: 0.8318 (pm20) REVERT: H 37 TYR cc_start: 0.9409 (m-80) cc_final: 0.8511 (m-80) REVERT: H 47 GLN cc_start: 0.9438 (mt0) cc_final: 0.9157 (tm-30) REVERT: H 52 THR cc_start: 0.9576 (p) cc_final: 0.9338 (t) REVERT: H 64 SER cc_start: 0.9626 (t) cc_final: 0.9193 (t) REVERT: H 68 ASP cc_start: 0.9338 (t0) cc_final: 0.9026 (t0) REVERT: H 86 ARG cc_start: 0.9287 (mmm-85) cc_final: 0.8740 (mmm160) REVERT: H 96 THR cc_start: 0.9654 (m) cc_final: 0.9248 (t) REVERT: K 55 MET cc_start: -0.0768 (mmt) cc_final: -0.1312 (tpp) REVERT: K 101 ARG cc_start: 0.7378 (mmt90) cc_final: 0.5858 (mmp80) REVERT: K 113 GLN cc_start: 0.8309 (pt0) cc_final: 0.8086 (pp30) REVERT: K 198 MET cc_start: 0.8355 (mmt) cc_final: 0.8103 (mmm) REVERT: L 41 GLN cc_start: 0.8756 (pt0) cc_final: 0.7781 (tp40) outliers start: 61 outliers final: 42 residues processed: 538 average time/residue: 0.1422 time to fit residues: 106.8385 Evaluate side-chains 531 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 486 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 52 LYS Chi-restraints excluded: chain K residue 60 LEU Chi-restraints excluded: chain K residue 112 GLN Chi-restraints excluded: chain K residue 190 ILE Chi-restraints excluded: chain K residue 316 THR Chi-restraints excluded: chain K residue 317 ILE Chi-restraints excluded: chain L residue 39 ASP Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 68 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 28 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 138 optimal weight: 7.9990 chunk 98 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 85 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 133 optimal weight: 30.0000 chunk 3 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 108 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN G 73 ASN G 104 GLN H 63 ASN K 30 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.101833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.062061 restraints weight = 43413.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.064027 restraints weight = 18063.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.065225 restraints weight = 11586.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.065854 restraints weight = 9206.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.066156 restraints weight = 8279.937| |-----------------------------------------------------------------------------| r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2979 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2979 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 16075 Z= 0.283 Angle : 0.696 8.586 22999 Z= 0.391 Chirality : 0.041 0.181 2615 Planarity : 0.005 0.041 1909 Dihedral : 29.358 177.793 4480 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 7.76 % Allowed : 29.81 % Favored : 62.42 % 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: 0.46 (0.25), residues: 1139 helix: 1.23 (0.19), residues: 705 sheet: -0.57 (0.55), residues: 79 loop : -1.33 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 45 TYR 0.023 0.002 TYR D 40 PHE 0.035 0.002 PHE E 67 TRP 0.007 0.001 TRP K 89 HIS 0.008 0.001 HIS G 82 Details of bonding type rmsd covalent geometry : bond 0.00629 (16075) covalent geometry : angle 0.69621 (22999) hydrogen bonds : bond 0.04377 ( 887) hydrogen bonds : angle 3.76169 ( 2276) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 495 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.9259 (m-80) cc_final: 0.8815 (m-80) REVERT: A 63 ARG cc_start: 0.9127 (mmp-170) cc_final: 0.8389 (mmm-85) REVERT: A 93 GLN cc_start: 0.8899 (tt0) cc_final: 0.8552 (tt0) REVERT: A 97 GLU cc_start: 0.8425 (mt-10) cc_final: 0.7990 (mp0) REVERT: A 120 MET cc_start: 0.8233 (mtp) cc_final: 0.7762 (mtp) REVERT: A 129 ARG cc_start: 0.9129 (tpt-90) cc_final: 0.8598 (mmm160) REVERT: B 25 ASN cc_start: 0.8180 (t0) cc_final: 0.7673 (t0) REVERT: B 44 LYS cc_start: 0.9477 (ttpp) cc_final: 0.8864 (mtpt) REVERT: B 51 TYR cc_start: 0.9024 (m-80) cc_final: 0.8448 (m-10) REVERT: B 74 GLU cc_start: 0.9152 (tt0) cc_final: 0.8920 (tt0) REVERT: B 77 LYS cc_start: 0.9464 (mmtt) cc_final: 0.9226 (mmmm) REVERT: B 79 LYS cc_start: 0.8766 (mtmt) cc_final: 0.8362 (mtmm) REVERT: B 88 TYR cc_start: 0.9161 (m-10) cc_final: 0.8741 (m-80) REVERT: B 98 TYR cc_start: 0.9368 (m-10) cc_final: 0.9012 (m-80) REVERT: C 24 GLN cc_start: 0.8966 (mm-40) cc_final: 0.8614 (mp10) REVERT: C 42 ARG cc_start: 0.9288 (OUTLIER) cc_final: 0.8886 (mtp85) REVERT: C 72 ASP cc_start: 0.8826 (m-30) cc_final: 0.8513 (m-30) REVERT: C 73 ASN cc_start: 0.9283 (t0) cc_final: 0.8780 (t0) REVERT: D 46 LYS cc_start: 0.9476 (mmmt) cc_final: 0.9194 (mmmt) REVERT: D 68 ASP cc_start: 0.9303 (t0) cc_final: 0.8804 (t0) REVERT: D 83 TYR cc_start: 0.8617 (m-10) cc_final: 0.6952 (m-10) REVERT: D 108 LYS cc_start: 0.8983 (mttt) cc_final: 0.8761 (mtpt) REVERT: E 68 GLN cc_start: 0.9319 (tt0) cc_final: 0.9065 (tt0) REVERT: E 90 MET cc_start: 0.9116 (mmt) cc_final: 0.8906 (mmp) REVERT: E 120 MET cc_start: 0.8689 (mtp) cc_final: 0.8056 (mtp) REVERT: E 125 GLN cc_start: 0.8967 (mt0) cc_final: 0.8584 (mt0) REVERT: E 133 GLU cc_start: 0.7897 (mp0) cc_final: 0.7605 (mp0) REVERT: F 27 GLN cc_start: 0.9289 (mm-40) cc_final: 0.8795 (pm20) REVERT: F 30 THR cc_start: 0.9267 (p) cc_final: 0.8811 (t) REVERT: F 31 LYS cc_start: 0.9164 (tttm) cc_final: 0.8886 (tttm) REVERT: F 36 ARG cc_start: 0.8902 (mtm-85) cc_final: 0.7428 (mtm-85) REVERT: F 45 ARG cc_start: 0.8881 (mtp85) cc_final: 0.8375 (mmm-85) REVERT: F 51 TYR cc_start: 0.9088 (m-80) cc_final: 0.8328 (m-80) REVERT: F 55 ARG cc_start: 0.9419 (mtt90) cc_final: 0.8269 (mtt90) REVERT: F 77 LYS cc_start: 0.9475 (mmmt) cc_final: 0.9222 (mmtm) REVERT: F 84 MET cc_start: 0.9096 (mmm) cc_final: 0.8187 (mmm) REVERT: F 98 TYR cc_start: 0.9567 (m-10) cc_final: 0.9049 (m-80) REVERT: G 38 ASN cc_start: 0.9049 (m-40) cc_final: 0.8829 (m-40) REVERT: G 42 ARG cc_start: 0.9217 (ptm-80) cc_final: 0.8852 (ptm-80) REVERT: G 57 TYR cc_start: 0.9147 (t80) cc_final: 0.8510 (t80) REVERT: G 84 GLN cc_start: 0.9546 (tp-100) cc_final: 0.8657 (tp-100) REVERT: G 89 ASN cc_start: 0.9453 (m-40) cc_final: 0.8984 (m-40) REVERT: H 37 TYR cc_start: 0.9386 (m-80) cc_final: 0.8519 (m-80) REVERT: H 52 THR cc_start: 0.9601 (OUTLIER) cc_final: 0.9350 (t) REVERT: H 64 SER cc_start: 0.9642 (t) cc_final: 0.9346 (t) REVERT: H 68 ASP cc_start: 0.9349 (t0) cc_final: 0.9049 (t0) REVERT: H 86 ARG cc_start: 0.9333 (mmm-85) cc_final: 0.8980 (mmm160) REVERT: K 55 MET cc_start: -0.0548 (mmt) cc_final: -0.1174 (tpp) REVERT: K 101 ARG cc_start: 0.7442 (mmt90) cc_final: 0.5963 (mmp80) REVERT: K 198 MET cc_start: 0.8515 (mmt) cc_final: 0.8261 (mmm) REVERT: K 243 PHE cc_start: 0.9202 (m-10) cc_final: 0.8889 (m-80) REVERT: L 3 ILE cc_start: 0.8632 (pt) cc_final: 0.8211 (pt) REVERT: L 54 ARG cc_start: 0.8764 (mmt-90) cc_final: 0.8519 (mmp80) outliers start: 75 outliers final: 54 residues processed: 520 average time/residue: 0.1336 time to fit residues: 98.0930 Evaluate side-chains 530 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 474 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 52 LYS Chi-restraints excluded: chain K residue 60 LEU Chi-restraints excluded: chain K residue 63 TYR Chi-restraints excluded: chain K residue 112 GLN Chi-restraints excluded: chain K residue 190 ILE Chi-restraints excluded: chain K residue 316 THR Chi-restraints excluded: chain K residue 317 ILE Chi-restraints excluded: chain L residue 39 ASP Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 68 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 79 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 chunk 101 optimal weight: 6.9990 chunk 134 optimal weight: 4.9990 chunk 137 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 76 optimal weight: 3.9990 chunk 34 optimal weight: 0.3980 chunk 118 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 108 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 82 HIS G 104 GLN H 63 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.104012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.065733 restraints weight = 41845.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.067783 restraints weight = 17059.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.069065 restraints weight = 10701.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.069773 restraints weight = 8349.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.070092 restraints weight = 7399.064| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3071 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3071 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.4249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 16075 Z= 0.199 Angle : 0.691 9.239 22999 Z= 0.384 Chirality : 0.040 0.182 2615 Planarity : 0.005 0.049 1909 Dihedral : 29.333 179.220 4480 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 5.49 % Allowed : 32.92 % Favored : 61.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.25), residues: 1139 helix: 1.39 (0.19), residues: 690 sheet: -0.38 (0.57), residues: 76 loop : -1.27 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 81 TYR 0.030 0.002 TYR C 57 PHE 0.036 0.002 PHE A 67 TRP 0.010 0.001 TRP K 205 HIS 0.008 0.001 HIS L 68 Details of bonding type rmsd covalent geometry : bond 0.00452 (16075) covalent geometry : angle 0.69134 (22999) hydrogen bonds : bond 0.03797 ( 887) hydrogen bonds : angle 3.67252 ( 2276) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 493 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.9262 (m-80) cc_final: 0.8879 (m-80) REVERT: A 63 ARG cc_start: 0.9106 (mmp-170) cc_final: 0.8377 (mmm-85) REVERT: A 97 GLU cc_start: 0.8465 (mt-10) cc_final: 0.7938 (mt-10) REVERT: A 120 MET cc_start: 0.8217 (mtp) cc_final: 0.7974 (mtp) REVERT: A 129 ARG cc_start: 0.9017 (tpt-90) cc_final: 0.8531 (mmm160) REVERT: B 25 ASN cc_start: 0.8153 (t0) cc_final: 0.7695 (t0) REVERT: B 44 LYS cc_start: 0.9430 (ttpp) cc_final: 0.8782 (mtpt) REVERT: B 51 TYR cc_start: 0.8936 (m-80) cc_final: 0.8565 (m-10) REVERT: B 74 GLU cc_start: 0.9121 (tt0) cc_final: 0.8915 (tt0) REVERT: B 77 LYS cc_start: 0.9452 (mmtt) cc_final: 0.9209 (mmmm) REVERT: B 79 LYS cc_start: 0.8719 (mtmt) cc_final: 0.8332 (mtmm) REVERT: B 88 TYR cc_start: 0.9140 (m-10) cc_final: 0.8693 (m-80) REVERT: B 98 TYR cc_start: 0.9416 (m-10) cc_final: 0.9213 (m-80) REVERT: C 42 ARG cc_start: 0.9295 (OUTLIER) cc_final: 0.8962 (mtp85) REVERT: C 56 GLU cc_start: 0.8658 (tt0) cc_final: 0.8426 (mt-10) REVERT: C 63 LEU cc_start: 0.9717 (mt) cc_final: 0.9454 (mt) REVERT: C 72 ASP cc_start: 0.8802 (m-30) cc_final: 0.8492 (m-30) REVERT: C 73 ASN cc_start: 0.9312 (t0) cc_final: 0.8815 (t0) REVERT: C 84 GLN cc_start: 0.9528 (tp-100) cc_final: 0.9220 (tp-100) REVERT: D 47 GLN cc_start: 0.9477 (mt0) cc_final: 0.9264 (mt0) REVERT: D 68 ASP cc_start: 0.9279 (t0) cc_final: 0.8741 (t0) REVERT: D 83 TYR cc_start: 0.8441 (m-10) cc_final: 0.7209 (m-10) REVERT: E 41 TYR cc_start: 0.8863 (m-80) cc_final: 0.8601 (m-80) REVERT: E 52 ARG cc_start: 0.9214 (mtt90) cc_final: 0.8901 (ttm110) REVERT: E 59 GLU cc_start: 0.8736 (tp30) cc_final: 0.8507 (tp30) REVERT: E 68 GLN cc_start: 0.9291 (tt0) cc_final: 0.9020 (tt0) REVERT: E 90 MET cc_start: 0.9091 (mmt) cc_final: 0.8886 (mmp) REVERT: E 120 MET cc_start: 0.8657 (mtp) cc_final: 0.8032 (mtp) REVERT: E 125 GLN cc_start: 0.8971 (mt0) cc_final: 0.8585 (mt0) REVERT: E 133 GLU cc_start: 0.7921 (mp0) cc_final: 0.7599 (mp0) REVERT: F 30 THR cc_start: 0.9163 (p) cc_final: 0.8880 (t) REVERT: F 31 LYS cc_start: 0.9161 (tttm) cc_final: 0.8831 (tttm) REVERT: F 45 ARG cc_start: 0.8929 (mtp85) cc_final: 0.8145 (mtm-85) REVERT: F 51 TYR cc_start: 0.9034 (m-80) cc_final: 0.8587 (m-80) REVERT: F 77 LYS cc_start: 0.9472 (mmmt) cc_final: 0.9000 (mmtm) REVERT: F 84 MET cc_start: 0.8952 (mmm) cc_final: 0.8376 (tpp) REVERT: F 92 ARG cc_start: 0.9280 (OUTLIER) cc_final: 0.7728 (tmm-80) REVERT: F 98 TYR cc_start: 0.9585 (m-10) cc_final: 0.9037 (m-80) REVERT: G 42 ARG cc_start: 0.9198 (ptm-80) cc_final: 0.8795 (ptm-80) REVERT: G 84 GLN cc_start: 0.9522 (tp-100) cc_final: 0.8453 (tp-100) REVERT: G 89 ASN cc_start: 0.9474 (m-40) cc_final: 0.9020 (m-40) REVERT: H 37 TYR cc_start: 0.9330 (m-80) cc_final: 0.8479 (m-80) REVERT: H 52 THR cc_start: 0.9612 (p) cc_final: 0.9357 (t) REVERT: H 64 SER cc_start: 0.9646 (t) cc_final: 0.9399 (t) REVERT: H 68 ASP cc_start: 0.9325 (t0) cc_final: 0.9050 (t0) REVERT: H 86 ARG cc_start: 0.9311 (mmm-85) cc_final: 0.8790 (mmm160) REVERT: H 96 THR cc_start: 0.9704 (m) cc_final: 0.9282 (t) REVERT: K 55 MET cc_start: -0.0661 (mmt) cc_final: -0.1329 (tpp) REVERT: K 101 ARG cc_start: 0.7407 (mmt90) cc_final: 0.5901 (mmp80) REVERT: K 198 MET cc_start: 0.8522 (mmt) cc_final: 0.8284 (mmm) REVERT: L 51 GLU cc_start: 0.8886 (mm-30) cc_final: 0.8559 (tp30) REVERT: L 74 ARG cc_start: 0.8988 (ttp-110) cc_final: 0.8491 (mtm110) outliers start: 53 outliers final: 39 residues processed: 513 average time/residue: 0.1362 time to fit residues: 97.8170 Evaluate side-chains 520 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 479 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 52 LYS Chi-restraints excluded: chain K residue 60 LEU Chi-restraints excluded: chain K residue 112 GLN Chi-restraints excluded: chain K residue 190 ILE Chi-restraints excluded: chain K residue 316 THR Chi-restraints excluded: chain K residue 317 ILE Chi-restraints excluded: chain L residue 39 ASP Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 68 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 52 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 110 optimal weight: 9.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 108 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.105046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.066113 restraints weight = 42666.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.068177 restraints weight = 17577.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.069441 restraints weight = 11100.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.070118 restraints weight = 8757.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.070460 restraints weight = 7822.863| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3089 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3089 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.4515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 16075 Z= 0.183 Angle : 0.707 11.066 22999 Z= 0.389 Chirality : 0.040 0.183 2615 Planarity : 0.004 0.044 1909 Dihedral : 29.235 178.482 4480 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 5.28 % Allowed : 35.30 % Favored : 59.42 % 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: 0.63 (0.25), residues: 1139 helix: 1.37 (0.19), residues: 689 sheet: -0.54 (0.56), residues: 79 loop : -1.15 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 71 TYR 0.046 0.002 TYR H 83 PHE 0.013 0.002 PHE A 84 TRP 0.010 0.001 TRP K 205 HIS 0.007 0.001 HIS L 68 Details of bonding type rmsd covalent geometry : bond 0.00416 (16075) covalent geometry : angle 0.70672 (22999) hydrogen bonds : bond 0.03805 ( 887) hydrogen bonds : angle 3.64254 ( 2276) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 504 time to evaluate : 0.395 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 41 TYR cc_start: 0.9241 (m-80) cc_final: 0.8887 (m-80) REVERT: A 63 ARG cc_start: 0.9062 (mmp-170) cc_final: 0.8322 (mmm-85) REVERT: A 94 GLU cc_start: 0.9114 (mm-30) cc_final: 0.8452 (mm-30) REVERT: A 97 GLU cc_start: 0.8505 (mt-10) cc_final: 0.8024 (mt-10) REVERT: A 120 MET cc_start: 0.8218 (mtp) cc_final: 0.7737 (mtp) REVERT: A 125 GLN cc_start: 0.9261 (mt0) cc_final: 0.8877 (mt0) REVERT: A 129 ARG cc_start: 0.8985 (tpt-90) cc_final: 0.8517 (mmm160) REVERT: B 25 ASN cc_start: 0.8147 (t0) cc_final: 0.7699 (t0) REVERT: B 44 LYS cc_start: 0.9404 (ttpp) cc_final: 0.8746 (mtpt) REVERT: B 51 TYR cc_start: 0.8924 (m-80) cc_final: 0.8703 (m-10) REVERT: B 77 LYS cc_start: 0.9451 (mmtt) cc_final: 0.9208 (mmmm) REVERT: B 79 LYS cc_start: 0.8744 (mtmt) cc_final: 0.8394 (mtmm) REVERT: B 98 TYR cc_start: 0.9438 (m-10) cc_final: 0.9213 (m-80) REVERT: C 42 ARG cc_start: 0.9296 (OUTLIER) cc_final: 0.8970 (mtp85) REVERT: C 63 LEU cc_start: 0.9695 (mt) cc_final: 0.9450 (mt) REVERT: C 72 ASP cc_start: 0.8719 (m-30) cc_final: 0.8421 (m-30) REVERT: C 73 ASN cc_start: 0.9365 (t0) cc_final: 0.8844 (t0) REVERT: C 81 ARG cc_start: 0.9268 (OUTLIER) cc_final: 0.8975 (tpt170) REVERT: C 84 GLN cc_start: 0.9515 (tp-100) cc_final: 0.9215 (tp-100) REVERT: C 89 ASN cc_start: 0.9456 (m-40) cc_final: 0.9128 (m110) REVERT: D 68 ASP cc_start: 0.9280 (t0) cc_final: 0.8763 (t0) REVERT: D 83 TYR cc_start: 0.8538 (m-10) cc_final: 0.6858 (m-10) REVERT: E 41 TYR cc_start: 0.8832 (m-80) cc_final: 0.8564 (m-80) REVERT: E 52 ARG cc_start: 0.9204 (mtt90) cc_final: 0.8895 (ttm110) REVERT: E 68 GLN cc_start: 0.9286 (tt0) cc_final: 0.9035 (tt0) REVERT: E 93 GLN cc_start: 0.9322 (tt0) cc_final: 0.9003 (tp40) REVERT: E 115 LYS cc_start: 0.9471 (mmmm) cc_final: 0.9135 (mmmm) REVERT: E 120 MET cc_start: 0.8665 (mtp) cc_final: 0.8035 (mtp) REVERT: E 125 GLN cc_start: 0.8970 (mt0) cc_final: 0.8601 (mt0) REVERT: E 133 GLU cc_start: 0.7971 (mp0) cc_final: 0.7624 (mp0) REVERT: F 30 THR cc_start: 0.9140 (p) cc_final: 0.8803 (t) REVERT: F 31 LYS cc_start: 0.9163 (tttm) cc_final: 0.8344 (tttm) REVERT: F 45 ARG cc_start: 0.8954 (mtp85) cc_final: 0.8194 (mtm-85) REVERT: F 51 TYR cc_start: 0.8936 (m-80) cc_final: 0.7879 (m-80) REVERT: F 55 ARG cc_start: 0.9362 (mtt90) cc_final: 0.8475 (mtt90) REVERT: F 77 LYS cc_start: 0.9491 (mmmt) cc_final: 0.9248 (mmtm) REVERT: F 84 MET cc_start: 0.8770 (mmm) cc_final: 0.8514 (tpp) REVERT: F 92 ARG cc_start: 0.9234 (OUTLIER) cc_final: 0.7564 (tmm-80) REVERT: F 98 TYR cc_start: 0.9605 (m-10) cc_final: 0.9107 (m-80) REVERT: G 25 PHE cc_start: 0.8866 (m-80) cc_final: 0.8518 (m-80) REVERT: G 42 ARG cc_start: 0.9226 (ptm-80) cc_final: 0.8802 (ptm-80) REVERT: G 84 GLN cc_start: 0.9520 (tp-100) cc_final: 0.8609 (tp-100) REVERT: G 104 GLN cc_start: 0.8809 (mt0) cc_final: 0.8371 (mt0) REVERT: H 37 TYR cc_start: 0.9363 (m-80) cc_final: 0.8487 (m-80) REVERT: H 47 GLN cc_start: 0.9406 (tt0) cc_final: 0.9194 (tt0) REVERT: H 52 THR cc_start: 0.9594 (p) cc_final: 0.9375 (t) REVERT: H 64 SER cc_start: 0.9662 (t) cc_final: 0.9407 (t) REVERT: H 68 ASP cc_start: 0.9348 (t0) cc_final: 0.9059 (t0) REVERT: H 86 ARG cc_start: 0.9280 (mmm-85) cc_final: 0.8765 (mmm160) REVERT: H 96 THR cc_start: 0.9710 (m) cc_final: 0.9296 (t) REVERT: K 55 MET cc_start: -0.0691 (mmt) cc_final: -0.1327 (tpp) REVERT: K 101 ARG cc_start: 0.7420 (mmt90) cc_final: 0.5990 (mmp80) REVERT: K 153 MET cc_start: 0.7565 (pmm) cc_final: 0.5157 (ptp) REVERT: K 198 MET cc_start: 0.8562 (mmt) cc_final: 0.8340 (mmm) REVERT: K 239 PHE cc_start: 0.9186 (t80) cc_final: 0.8976 (t80) REVERT: K 291 MET cc_start: 0.8996 (tmm) cc_final: 0.8605 (tmm) REVERT: L 51 GLU cc_start: 0.8858 (mm-30) cc_final: 0.8649 (mm-30) REVERT: L 74 ARG cc_start: 0.9020 (ttp-110) cc_final: 0.8416 (mtm110) outliers start: 51 outliers final: 35 residues processed: 521 average time/residue: 0.1394 time to fit residues: 101.4182 Evaluate side-chains 526 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 488 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 81 ARG Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain K residue 52 LYS Chi-restraints excluded: chain K residue 60 LEU Chi-restraints excluded: chain K residue 112 GLN Chi-restraints excluded: chain K residue 190 ILE Chi-restraints excluded: chain K residue 316 THR Chi-restraints excluded: chain K residue 317 ILE Chi-restraints excluded: chain L residue 39 ASP Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 68 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 8 optimal weight: 0.0000 chunk 4 optimal weight: 0.4980 chunk 29 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 115 optimal weight: 5.9990 chunk 62 optimal weight: 0.0470 chunk 80 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 86 optimal weight: 10.0000 overall best weight: 0.6684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 108 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.105989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.068365 restraints weight = 41934.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.070476 restraints weight = 17023.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.071784 restraints weight = 10589.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.072504 restraints weight = 8227.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.072857 restraints weight = 7267.016| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3151 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3151 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.4727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 16075 Z= 0.173 Angle : 0.730 13.415 22999 Z= 0.395 Chirality : 0.040 0.299 2615 Planarity : 0.005 0.045 1909 Dihedral : 29.168 176.453 4480 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 4.55 % Allowed : 36.75 % Favored : 58.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.25), residues: 1139 helix: 1.23 (0.19), residues: 690 sheet: -0.58 (0.56), residues: 78 loop : -1.03 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 71 TYR 0.037 0.002 TYR H 83 PHE 0.033 0.002 PHE A 67 TRP 0.012 0.001 TRP K 205 HIS 0.006 0.001 HIS L 68 Details of bonding type rmsd covalent geometry : bond 0.00395 (16075) covalent geometry : angle 0.72953 (22999) hydrogen bonds : bond 0.03753 ( 887) hydrogen bonds : angle 3.70754 ( 2276) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 487 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.9282 (m-80) cc_final: 0.8927 (m-80) REVERT: A 67 PHE cc_start: 0.9315 (t80) cc_final: 0.8897 (t80) REVERT: A 94 GLU cc_start: 0.9014 (mm-30) cc_final: 0.8457 (mm-30) REVERT: A 97 GLU cc_start: 0.8426 (mt-10) cc_final: 0.7962 (mt-10) REVERT: A 120 MET cc_start: 0.8183 (mtp) cc_final: 0.7983 (mtp) REVERT: A 125 GLN cc_start: 0.9243 (mt0) cc_final: 0.8842 (mt0) REVERT: A 129 ARG cc_start: 0.8925 (tpt-90) cc_final: 0.8484 (mmm160) REVERT: B 25 ASN cc_start: 0.8130 (t0) cc_final: 0.7697 (t0) REVERT: B 44 LYS cc_start: 0.9358 (ttpp) cc_final: 0.8788 (mtpt) REVERT: B 51 TYR cc_start: 0.8864 (m-80) cc_final: 0.8652 (m-10) REVERT: B 77 LYS cc_start: 0.9445 (mmtt) cc_final: 0.9201 (mmmm) REVERT: B 79 LYS cc_start: 0.8776 (mtmt) cc_final: 0.8430 (mtmm) REVERT: B 88 TYR cc_start: 0.8608 (m-80) cc_final: 0.8204 (m-80) REVERT: C 35 ARG cc_start: 0.9433 (ttm110) cc_final: 0.8827 (mtm110) REVERT: C 42 ARG cc_start: 0.9340 (OUTLIER) cc_final: 0.8994 (mtp85) REVERT: C 63 LEU cc_start: 0.9698 (mt) cc_final: 0.9462 (mt) REVERT: C 72 ASP cc_start: 0.8703 (m-30) cc_final: 0.8398 (m-30) REVERT: C 73 ASN cc_start: 0.9392 (t0) cc_final: 0.8884 (t0) REVERT: C 81 ARG cc_start: 0.9271 (OUTLIER) cc_final: 0.8879 (tpt170) REVERT: C 84 GLN cc_start: 0.9514 (tp-100) cc_final: 0.9208 (tp-100) REVERT: C 85 LEU cc_start: 0.9648 (mt) cc_final: 0.9431 (mm) REVERT: C 89 ASN cc_start: 0.9431 (m-40) cc_final: 0.9147 (m-40) REVERT: D 68 ASP cc_start: 0.9256 (t0) cc_final: 0.8767 (t0) REVERT: E 52 ARG cc_start: 0.9201 (mtt90) cc_final: 0.8875 (ttm110) REVERT: E 59 GLU cc_start: 0.8429 (tp30) cc_final: 0.7868 (tp30) REVERT: E 68 GLN cc_start: 0.9276 (tt0) cc_final: 0.9036 (tt0) REVERT: E 120 MET cc_start: 0.8635 (mtp) cc_final: 0.8224 (mtp) REVERT: E 125 GLN cc_start: 0.9007 (mt0) cc_final: 0.8612 (mt0) REVERT: F 30 THR cc_start: 0.9130 (p) cc_final: 0.8789 (t) REVERT: F 31 LYS cc_start: 0.9161 (tttm) cc_final: 0.8311 (tttm) REVERT: F 45 ARG cc_start: 0.8923 (mtp85) cc_final: 0.8625 (mmm-85) REVERT: F 51 TYR cc_start: 0.8897 (m-80) cc_final: 0.8026 (m-80) REVERT: F 77 LYS cc_start: 0.9484 (mmmt) cc_final: 0.9241 (mmtm) REVERT: F 92 ARG cc_start: 0.9231 (OUTLIER) cc_final: 0.7538 (tmm-80) REVERT: G 25 PHE cc_start: 0.8906 (m-80) cc_final: 0.8568 (m-80) REVERT: G 42 ARG cc_start: 0.9232 (ptm-80) cc_final: 0.8819 (ptm-80) REVERT: G 50 TYR cc_start: 0.9114 (t80) cc_final: 0.8790 (t80) REVERT: G 75 LYS cc_start: 0.8762 (mmtp) cc_final: 0.8544 (mmtp) REVERT: G 84 GLN cc_start: 0.9567 (tp-100) cc_final: 0.8872 (tp-100) REVERT: G 90 ASP cc_start: 0.8269 (t0) cc_final: 0.7863 (t70) REVERT: G 104 GLN cc_start: 0.8812 (mt0) cc_final: 0.8354 (mt0) REVERT: H 37 TYR cc_start: 0.9284 (m-80) cc_final: 0.8412 (m-80) REVERT: H 52 THR cc_start: 0.9560 (p) cc_final: 0.9352 (t) REVERT: H 64 SER cc_start: 0.9638 (t) cc_final: 0.9396 (t) REVERT: H 68 ASP cc_start: 0.9330 (t0) cc_final: 0.9093 (t0) REVERT: H 86 ARG cc_start: 0.9253 (mmm-85) cc_final: 0.8727 (mmm160) REVERT: K 55 MET cc_start: -0.0647 (mmt) cc_final: -0.1307 (tpp) REVERT: K 101 ARG cc_start: 0.7350 (mmt90) cc_final: 0.5898 (mmp80) REVERT: K 153 MET cc_start: 0.7602 (pmm) cc_final: 0.5163 (ptp) REVERT: K 198 MET cc_start: 0.8548 (mmt) cc_final: 0.8326 (mmm) REVERT: K 239 PHE cc_start: 0.9109 (t80) cc_final: 0.8575 (t80) REVERT: L 51 GLU cc_start: 0.8961 (mm-30) cc_final: 0.8558 (tp30) REVERT: L 74 ARG cc_start: 0.8962 (ttp-110) cc_final: 0.8362 (mtm110) outliers start: 44 outliers final: 33 residues processed: 501 average time/residue: 0.1436 time to fit residues: 100.1468 Evaluate side-chains 515 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 479 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 81 ARG Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 93 GLN Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain K residue 52 LYS Chi-restraints excluded: chain K residue 60 LEU Chi-restraints excluded: chain K residue 112 GLN Chi-restraints excluded: chain K residue 190 ILE Chi-restraints excluded: chain K residue 316 THR Chi-restraints excluded: chain K residue 317 ILE Chi-restraints excluded: chain L residue 39 ASP Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 68 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 7 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 44 optimal weight: 0.0970 chunk 134 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 112 optimal weight: 7.9990 chunk 79 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN G 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.104310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.065357 restraints weight = 43115.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.067379 restraints weight = 18113.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.068593 restraints weight = 11515.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.069237 restraints weight = 9130.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.069604 restraints weight = 8189.587| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3070 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3070 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.4783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 16075 Z= 0.233 Angle : 0.742 10.236 22999 Z= 0.405 Chirality : 0.042 0.274 2615 Planarity : 0.005 0.050 1909 Dihedral : 29.183 173.439 4480 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 17.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.66 % Allowed : 37.58 % Favored : 57.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.25), residues: 1139 helix: 1.18 (0.19), residues: 691 sheet: -0.64 (0.55), residues: 79 loop : -0.99 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 35 TYR 0.052 0.002 TYR H 83 PHE 0.035 0.002 PHE A 67 TRP 0.010 0.001 TRP K 205 HIS 0.006 0.001 HIS L 68 Details of bonding type rmsd covalent geometry : bond 0.00537 (16075) covalent geometry : angle 0.74221 (22999) hydrogen bonds : bond 0.04041 ( 887) hydrogen bonds : angle 3.81492 ( 2276) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 480 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.9285 (m-80) cc_final: 0.8871 (m-80) REVERT: A 79 LYS cc_start: 0.8850 (tppp) cc_final: 0.8630 (mtpt) REVERT: A 93 GLN cc_start: 0.8722 (tt0) cc_final: 0.8397 (tt0) REVERT: A 97 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8123 (mt-10) REVERT: A 120 MET cc_start: 0.8220 (mtp) cc_final: 0.8012 (mtp) REVERT: A 125 GLN cc_start: 0.9263 (mt0) cc_final: 0.8885 (mt0) REVERT: A 129 ARG cc_start: 0.8964 (tpt-90) cc_final: 0.8506 (mmm160) REVERT: B 25 ASN cc_start: 0.8111 (t0) cc_final: 0.7610 (t0) REVERT: B 44 LYS cc_start: 0.9398 (ttpp) cc_final: 0.8730 (mtpt) REVERT: B 51 TYR cc_start: 0.8943 (m-80) cc_final: 0.8666 (m-10) REVERT: B 77 LYS cc_start: 0.9467 (mmtt) cc_final: 0.9225 (mmmm) REVERT: B 79 LYS cc_start: 0.8831 (mtmt) cc_final: 0.8456 (mtmm) REVERT: B 88 TYR cc_start: 0.8773 (m-80) cc_final: 0.8297 (m-80) REVERT: C 35 ARG cc_start: 0.9436 (ttm110) cc_final: 0.8836 (mtm110) REVERT: C 42 ARG cc_start: 0.9333 (OUTLIER) cc_final: 0.8936 (mtp85) REVERT: C 63 LEU cc_start: 0.9688 (mt) cc_final: 0.9455 (mt) REVERT: C 72 ASP cc_start: 0.8733 (m-30) cc_final: 0.8430 (m-30) REVERT: C 73 ASN cc_start: 0.9394 (t0) cc_final: 0.8892 (t0) REVERT: C 81 ARG cc_start: 0.9282 (OUTLIER) cc_final: 0.8888 (tpt170) REVERT: C 85 LEU cc_start: 0.9638 (mt) cc_final: 0.9408 (mm) REVERT: C 89 ASN cc_start: 0.9461 (m-40) cc_final: 0.9186 (m-40) REVERT: D 68 ASP cc_start: 0.9284 (t0) cc_final: 0.8841 (t0) REVERT: E 52 ARG cc_start: 0.9223 (mtt90) cc_final: 0.8896 (ttm110) REVERT: E 68 GLN cc_start: 0.9315 (tt0) cc_final: 0.9076 (tt0) REVERT: E 94 GLU cc_start: 0.9066 (tp30) cc_final: 0.8818 (tp30) REVERT: E 120 MET cc_start: 0.8662 (mtp) cc_final: 0.8256 (mtp) REVERT: E 125 GLN cc_start: 0.8945 (mt0) cc_final: 0.8528 (mt0) REVERT: F 30 THR cc_start: 0.9151 (p) cc_final: 0.8835 (t) REVERT: F 31 LYS cc_start: 0.9182 (tttm) cc_final: 0.8849 (tttm) REVERT: F 45 ARG cc_start: 0.8899 (mtp85) cc_final: 0.8576 (mmm-85) REVERT: F 51 TYR cc_start: 0.8979 (m-80) cc_final: 0.8704 (m-80) REVERT: F 77 LYS cc_start: 0.9457 (mmmt) cc_final: 0.9194 (mmtm) REVERT: F 92 ARG cc_start: 0.9280 (OUTLIER) cc_final: 0.7628 (tmm-80) REVERT: G 25 PHE cc_start: 0.9203 (m-80) cc_final: 0.8926 (m-80) REVERT: G 42 ARG cc_start: 0.9245 (ptm-80) cc_final: 0.8821 (ptm-80) REVERT: G 50 TYR cc_start: 0.9143 (t80) cc_final: 0.8808 (t80) REVERT: G 75 LYS cc_start: 0.8854 (mmtp) cc_final: 0.8646 (mmtp) REVERT: G 84 GLN cc_start: 0.9562 (tp-100) cc_final: 0.8889 (tp-100) REVERT: G 90 ASP cc_start: 0.8152 (t0) cc_final: 0.7481 (t70) REVERT: G 92 GLU cc_start: 0.8720 (pm20) cc_final: 0.8422 (pm20) REVERT: H 37 TYR cc_start: 0.9362 (m-80) cc_final: 0.8562 (m-80) REVERT: H 47 GLN cc_start: 0.9271 (tt0) cc_final: 0.8759 (tm-30) REVERT: H 52 THR cc_start: 0.9612 (p) cc_final: 0.9372 (t) REVERT: H 68 ASP cc_start: 0.9347 (t0) cc_final: 0.9125 (t0) REVERT: H 86 ARG cc_start: 0.9273 (mmm-85) cc_final: 0.8910 (mmm160) REVERT: H 95 GLN cc_start: 0.9448 (tt0) cc_final: 0.8894 (tp40) REVERT: H 109 HIS cc_start: 0.9256 (m170) cc_final: 0.8718 (m170) REVERT: K 55 MET cc_start: -0.0561 (mmt) cc_final: -0.1193 (tpp) REVERT: K 101 ARG cc_start: 0.7410 (mmt90) cc_final: 0.5960 (mmp80) REVERT: K 198 MET cc_start: 0.8627 (mmt) cc_final: 0.8393 (mmm) REVERT: K 239 PHE cc_start: 0.9158 (t80) cc_final: 0.8619 (t80) REVERT: L 51 GLU cc_start: 0.8958 (mm-30) cc_final: 0.8695 (tp30) REVERT: L 74 ARG cc_start: 0.9031 (ttp-110) cc_final: 0.8452 (mtm110) outliers start: 45 outliers final: 37 residues processed: 495 average time/residue: 0.1404 time to fit residues: 96.9519 Evaluate side-chains 514 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 474 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 81 ARG Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 93 GLN Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain K residue 52 LYS Chi-restraints excluded: chain K residue 60 LEU Chi-restraints excluded: chain K residue 112 GLN Chi-restraints excluded: chain K residue 190 ILE Chi-restraints excluded: chain K residue 316 THR Chi-restraints excluded: chain K residue 317 ILE Chi-restraints excluded: chain L residue 39 ASP Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 68 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 47 optimal weight: 2.9990 chunk 134 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 126 optimal weight: 0.0980 chunk 119 optimal weight: 4.9990 chunk 7 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 109 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 108 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.106918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.069404 restraints weight = 41782.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.071563 restraints weight = 16994.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.072899 restraints weight = 10485.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.073615 restraints weight = 8109.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.073965 restraints weight = 7161.333| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3160 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3160 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.5011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 16075 Z= 0.172 Angle : 0.736 12.144 22999 Z= 0.397 Chirality : 0.040 0.307 2615 Planarity : 0.005 0.043 1909 Dihedral : 29.160 173.086 4480 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 4.24 % Allowed : 37.78 % Favored : 57.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.25), residues: 1139 helix: 1.18 (0.19), residues: 690 sheet: -0.58 (0.55), residues: 78 loop : -1.00 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 35 TYR 0.038 0.002 TYR H 83 PHE 0.011 0.002 PHE F 100 TRP 0.009 0.001 TRP K 89 HIS 0.005 0.001 HIS L 68 Details of bonding type rmsd covalent geometry : bond 0.00396 (16075) covalent geometry : angle 0.73597 (22999) hydrogen bonds : bond 0.03716 ( 887) hydrogen bonds : angle 3.74648 ( 2276) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3541.03 seconds wall clock time: 61 minutes 13.09 seconds (3673.09 seconds total)