Starting phenix.real_space_refine on Sat Sep 12 09:27:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6o96_0652/09_2026/6o96_0652.cif Found real_map, /net/cci-nas-00/data/ceres_data/6o96_0652/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6o96_0652/09_2026/6o96_0652.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6o96_0652/09_2026/6o96_0652.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6o96_0652/09_2026/6o96_0652.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6o96_0652/09_2026/6o96_0652.map" model { file = "/net/cci-nas-00/data/ceres_data/6o96_0652/09_2026/6o96_0652.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6o96_0652/09_2026/6o96_0652.cif" } 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-2.2.1-6174/lib/python3.11/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: 3.18, per 1000 atoms: 0.21 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: 1.30 Conformation dependent library (CDL) restraints added in 484.7 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: 2.08 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: 3.16 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=" C3' DG J 101 " pdb=" O3' DG J 101 " ideal model delta sigma weight residual 1.435 1.377 0.058 1.30e-02 5.92e+03 1.99e+01 bond pdb=" C3' DC J 142 " pdb=" C2' DC J 142 " ideal model delta sigma weight residual 1.516 1.551 -0.035 8.00e-03 1.56e+04 1.86e+01 bond pdb=" N7 DA I 113 " pdb=" C5 DA I 113 " ideal model delta sigma weight residual 1.388 1.362 0.026 6.00e-03 2.78e+04 1.81e+01 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=" C3' DG J 82 " pdb=" O3' DG J 82 " ideal model delta sigma weight residual 1.435 1.381 0.054 1.30e-02 5.92e+03 1.71e+01 ... (remaining 16070 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 21659 2.25 - 4.50: 1227 4.50 - 6.76: 88 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=" O4' DG J 145 " pdb=" C1' DG J 145 " pdb=" N9 DG J 145 " ideal model delta sigma weight residual 108.00 111.31 -3.31 7.00e-01 2.04e+00 2.24e+01 angle pdb=" N3 DT I 35 " pdb=" C4 DT I 35 " pdb=" O4 DT I 35 " ideal model delta sigma weight residual 119.90 122.73 -2.83 6.00e-01 2.78e+00 2.22e+01 angle pdb=" O5' DC I 110 " pdb=" C5' DC I 110 " pdb=" C4' DC I 110 " ideal model delta sigma weight residual 109.40 113.14 -3.74 8.00e-01 1.56e+00 2.19e+01 angle pdb=" N3 DT I 105 " pdb=" C4 DT I 105 " pdb=" O4 DT I 105 " ideal model delta sigma weight residual 119.90 122.70 -2.80 6.00e-01 2.78e+00 2.18e+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: 1963 0.067 - 0.134: 566 0.134 - 0.201: 74 0.201 - 0.268: 11 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: 2.360 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: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 16.320 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 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= 0.766 Angle : 1.122 11.260 22999 Z= 0.814 Chirality : 0.062 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/Z covalent geometry : bond 0.01138 / 0.77 (16075) covalent geometry : angle 1.12193 / 0.81 (22999) hydrogen bonds : bond 0.10890 / 6.95 ( 887) hydrogen bonds : angle 5.50282 / 3.82 ( 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 : 0.592 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 93 GLN cc_start: 0.7279 (tt0) cc_final: 0.6707 (tt0) REVERT: A 116 ARG cc_start: 0.7277 (mtm110) cc_final: 0.6717 (mtp180) REVERT: A 120 MET cc_start: 0.6506 (mtp) cc_final: 0.5994 (mtm) REVERT: C 57 TYR cc_start: 0.7821 (t80) cc_final: 0.7313 (t80) REVERT: C 94 ASN cc_start: 0.8289 (t0) cc_final: 0.8028 (t0) REVERT: D 68 ASP cc_start: 0.7915 (t0) cc_final: 0.7633 (t0) REVERT: D 89 ILE cc_start: 0.8832 (mm) cc_final: 0.8619 (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: 0.7625 (t80) REVERT: G 57 TYR cc_start: 0.7630 (t80) cc_final: 0.7315 (t80) REVERT: G 100 VAL cc_start: 0.8659 (m) cc_final: 0.8373 (m) REVERT: K 241 ASN cc_start: 0.8129 (t0) cc_final: 0.7502 (t0) REVERT: K 312 TYR cc_start: 0.7937 (m-80) cc_final: 0.7683 (m-80) outliers start: 4 outliers final: 1 residues processed: 613 average time/residue: 0.1668 time to fit residues: 139.5781 Evaluate side-chains 493 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 492 time to evaluate : 0.451 ------------------------------------------------------------------------------- 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: 10.0000 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN C 38 ASN C 89 ASN 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 104 GLN H 84 ASN H 95 GLN K 99 ASN K 113 GLN ** K 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 315 HIS ** K 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 60 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.104519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.064757 restraints weight = 42245.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.066845 restraints weight = 16985.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.068104 restraints weight = 10714.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.068721 restraints weight = 8494.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.069092 restraints weight = 7659.532| |-----------------------------------------------------------------------------| r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3035 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3035 r_free = 0.3035 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3029 r_free = 0.3029 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 8 (13 function evaluations) r_final: 0.3029 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 16075 Z= 0.205 Angle : 0.801 8.190 22999 Z= 0.448 Chirality : 0.050 0.229 2615 Planarity : 0.007 0.064 1909 Dihedral : 30.229 168.912 4480 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 6.63 % Allowed : 24.74 % Favored : 68.63 % 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: -1.85 (0.22), residues: 1139 helix: -0.80 (0.17), residues: 688 sheet: -0.63 (0.56), residues: 75 loop : -1.92 (0.29), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 55 TYR 0.026 0.003 TYR B 88 PHE 0.033 0.003 PHE A 67 TRP 0.011 0.002 TRP K 305 HIS 0.011 0.002 HIS K 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.20 (16075) covalent geometry : angle 0.80150 / 0.45 (22999) hydrogen bonds : bond 0.05679 / 3.63 ( 887) hydrogen bonds : angle 4.23597 / 2.97 ( 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 606 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 542 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8531 (pm20) cc_final: 0.8319 (pm20) REVERT: A 81 ASP cc_start: 0.8379 (t0) cc_final: 0.8073 (t0) REVERT: A 93 GLN cc_start: 0.8829 (tt0) cc_final: 0.7939 (tt0) REVERT: A 94 GLU cc_start: 0.9048 (mm-30) cc_final: 0.8637 (mm-30) REVERT: A 97 GLU cc_start: 0.8281 (mt-10) cc_final: 0.7792 (mp0) REVERT: A 118 THR cc_start: 0.9594 (m) cc_final: 0.9371 (p) REVERT: A 120 MET cc_start: 0.8059 (mtp) cc_final: 0.7700 (mtm) REVERT: A 126 LEU cc_start: 0.9548 (tp) cc_final: 0.9267 (tp) REVERT: B 44 LYS cc_start: 0.9400 (ttpp) cc_final: 0.8673 (mtmt) REVERT: B 71 THR cc_start: 0.9761 (m) cc_final: 0.9489 (p) REVERT: B 74 GLU cc_start: 0.9088 (tt0) cc_final: 0.8839 (tt0) REVERT: B 77 LYS cc_start: 0.9498 (mmtt) cc_final: 0.9104 (mmmt) REVERT: B 79 LYS cc_start: 0.8741 (mtmt) cc_final: 0.8375 (mtmt) REVERT: B 85 ASP cc_start: 0.8918 (m-30) cc_final: 0.8497 (m-30) REVERT: B 88 TYR cc_start: 0.9100 (m-80) cc_final: 0.8589 (m-80) REVERT: B 96 THR cc_start: 0.9365 (p) cc_final: 0.9149 (p) REVERT: B 98 TYR cc_start: 0.9163 (m-80) cc_final: 0.8437 (m-80) REVERT: C 24 GLN cc_start: 0.9030 (mm-40) cc_final: 0.8817 (mm110) REVERT: C 68 ASN cc_start: 0.8903 (m-40) cc_final: 0.8616 (m-40) REVERT: C 72 ASP cc_start: 0.8721 (m-30) cc_final: 0.8491 (m-30) REVERT: C 73 ASN cc_start: 0.9104 (t0) cc_final: 0.8795 (t0) REVERT: C 75 LYS cc_start: 0.9168 (mmtp) cc_final: 0.8933 (mmtp) REVERT: C 82 HIS cc_start: 0.9408 (m170) cc_final: 0.9020 (m90) REVERT: C 104 GLN cc_start: 0.8269 (mm110) cc_final: 0.7960 (mm110) REVERT: D 46 LYS cc_start: 0.9521 (mmtt) cc_final: 0.9292 (mmmt) REVERT: D 48 VAL cc_start: 0.9648 (OUTLIER) cc_final: 0.9447 (p) REVERT: D 56 SER cc_start: 0.9510 (t) cc_final: 0.9279 (p) REVERT: D 68 ASP cc_start: 0.9262 (t0) cc_final: 0.8746 (t0) REVERT: E 68 GLN cc_start: 0.9313 (tt0) cc_final: 0.9082 (tt0) REVERT: E 85 GLN cc_start: 0.9112 (OUTLIER) cc_final: 0.8897 (mt0) REVERT: E 97 GLU cc_start: 0.9019 (pt0) cc_final: 0.8743 (pt0) REVERT: E 125 GLN cc_start: 0.8882 (mt0) cc_final: 0.8605 (mt0) REVERT: F 45 ARG cc_start: 0.8716 (mtp85) cc_final: 0.7645 (mtp85) REVERT: F 77 LYS cc_start: 0.9382 (mmmt) cc_final: 0.8770 (mmtt) REVERT: G 25 PHE cc_start: 0.9254 (m-80) cc_final: 0.8915 (m-80) REVERT: G 35 ARG cc_start: 0.9307 (mtm110) cc_final: 0.8838 (ttp-110) REVERT: G 50 TYR cc_start: 0.9430 (t80) cc_final: 0.8794 (t80) REVERT: G 57 TYR cc_start: 0.9080 (t80) cc_final: 0.8786 (t80) REVERT: G 59 THR cc_start: 0.9725 (m) cc_final: 0.9498 (p) REVERT: G 81 ARG cc_start: 0.9143 (tpt-90) cc_final: 0.8932 (tpt170) REVERT: G 84 GLN cc_start: 0.9444 (tp-100) cc_final: 0.8804 (tp-100) REVERT: G 85 LEU cc_start: 0.9544 (mt) cc_final: 0.9339 (mm) REVERT: G 90 ASP cc_start: 0.8495 (t70) cc_final: 0.8082 (t70) REVERT: H 64 SER cc_start: 0.9665 (t) cc_final: 0.9178 (t) REVERT: H 68 ASP cc_start: 0.9357 (t0) cc_final: 0.9099 (t0) REVERT: H 87 SER cc_start: 0.9390 (OUTLIER) cc_final: 0.8931 (p) REVERT: H 95 GLN cc_start: 0.9411 (tt0) cc_final: 0.8742 (tp40) REVERT: H 111 VAL cc_start: 0.9612 (p) cc_final: 0.9356 (p) REVERT: H 113 GLU cc_start: 0.9031 (OUTLIER) cc_final: 0.8728 (tp30) REVERT: K 198 MET cc_start: 0.8572 (mmt) cc_final: 0.8303 (mmt) REVERT: L 39 ASP cc_start: 0.9107 (p0) cc_final: 0.8782 (p0) REVERT: L 41 GLN cc_start: 0.8364 (pt0) cc_final: 0.8049 (pt0) REVERT: L 42 ARG cc_start: 0.8492 (mtm110) cc_final: 0.8066 (mtm110) REVERT: L 50 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.8765 (tp) outliers start: 64 outliers final: 30 residues processed: 556 average time/residue: 0.1398 time to fit residues: 110.7166 Evaluate side-chains 554 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 519 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 65 LEU 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 71 THR Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 111 ILE 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 106 LEU Chi-restraints excluded: chain H residue 113 GLU 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 286 ASP Chi-restraints excluded: chain K residue 317 ILE Chi-restraints excluded: chain L residue 4 PHE Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 50 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 4 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 79 optimal weight: 10.0000 chunk 111 optimal weight: 20.0000 chunk 67 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 73 optimal weight: 20.0000 chunk 59 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 42 optimal weight: 0.5980 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN D 63 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 113 GLN ** K 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.101848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.063271 restraints weight = 42705.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.065249 restraints weight = 17036.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.066413 restraints weight = 10668.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.067053 restraints weight = 8450.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.067376 restraints weight = 7563.702| |-----------------------------------------------------------------------------| r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2979 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (13 function evaluations) r_final: 0.2979 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 16075 Z= 0.250 Angle : 0.775 12.241 22999 Z= 0.435 Chirality : 0.047 0.234 2615 Planarity : 0.006 0.052 1909 Dihedral : 30.106 167.915 4479 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 7.76 % Allowed : 26.29 % Favored : 65.94 % 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: -0.83 (0.23), residues: 1139 helix: 0.14 (0.18), residues: 694 sheet: -0.75 (0.56), residues: 75 loop : -1.70 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG L 72 TYR 0.022 0.003 TYR D 40 PHE 0.033 0.003 PHE A 67 TRP 0.013 0.002 TRP K 305 HIS 0.009 0.002 HIS K 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.25 (16075) covalent geometry : angle 0.77511 / 0.43 (22999) hydrogen bonds : bond 0.05490 / 3.52 ( 887) hydrogen bonds : angle 4.12723 / 2.89 ( 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 608 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 533 time to evaluate : 0.386 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 42 ARG cc_start: 0.8523 (mtp180) cc_final: 0.8214 (ttm110) REVERT: A 59 GLU cc_start: 0.8562 (pm20) cc_final: 0.8325 (pm20) REVERT: A 73 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7614 (mt-10) REVERT: A 81 ASP cc_start: 0.8550 (t0) cc_final: 0.8210 (t0) REVERT: A 85 GLN cc_start: 0.8673 (mt0) cc_final: 0.8456 (mt0) REVERT: A 87 SER cc_start: 0.9095 (p) cc_final: 0.8871 (p) REVERT: A 93 GLN cc_start: 0.8894 (tt0) cc_final: 0.8212 (tt0) REVERT: A 94 GLU cc_start: 0.9128 (mm-30) cc_final: 0.8645 (mm-30) REVERT: A 97 GLU cc_start: 0.8349 (mt-10) cc_final: 0.7856 (mp0) REVERT: A 118 THR cc_start: 0.9689 (m) cc_final: 0.9439 (p) REVERT: A 120 MET cc_start: 0.8162 (mtp) cc_final: 0.7747 (mtm) REVERT: A 126 LEU cc_start: 0.9542 (tp) cc_final: 0.9302 (tp) REVERT: A 129 ARG cc_start: 0.9106 (tpt-90) cc_final: 0.8901 (tpp80) REVERT: B 44 LYS cc_start: 0.9460 (ttpp) cc_final: 0.8727 (mtmt) REVERT: B 45 ARG cc_start: 0.8462 (mmm-85) cc_final: 0.7920 (mmm-85) REVERT: B 49 LEU cc_start: 0.9313 (mt) cc_final: 0.8830 (mm) REVERT: B 71 THR cc_start: 0.9716 (m) cc_final: 0.9476 (p) REVERT: B 74 GLU cc_start: 0.9163 (tt0) cc_final: 0.8883 (tt0) REVERT: B 77 LYS cc_start: 0.9503 (mmtt) cc_final: 0.9088 (mmmt) REVERT: B 79 LYS cc_start: 0.8649 (mtmt) cc_final: 0.8346 (mtmt) REVERT: B 82 THR cc_start: 0.9251 (OUTLIER) cc_final: 0.8759 (t) REVERT: B 85 ASP cc_start: 0.9093 (m-30) cc_final: 0.8589 (m-30) REVERT: B 88 TYR cc_start: 0.9088 (m-10) cc_final: 0.8509 (m-10) REVERT: B 98 TYR cc_start: 0.9224 (m-10) cc_final: 0.8808 (m-80) REVERT: C 68 ASN cc_start: 0.8993 (m-40) cc_final: 0.8475 (m-40) REVERT: C 72 ASP cc_start: 0.8769 (m-30) cc_final: 0.8344 (m-30) REVERT: C 73 ASN cc_start: 0.9135 (t0) cc_final: 0.8750 (t0) REVERT: C 75 LYS cc_start: 0.9166 (mmtp) cc_final: 0.8854 (mmtp) REVERT: C 104 GLN cc_start: 0.8498 (mm110) cc_final: 0.8010 (mm110) REVERT: D 56 SER cc_start: 0.9464 (t) cc_final: 0.9223 (p) REVERT: D 68 ASP cc_start: 0.9261 (t0) cc_final: 0.8743 (t0) REVERT: D 93 GLU cc_start: 0.9053 (mp0) cc_final: 0.8826 (mp0) REVERT: E 68 GLN cc_start: 0.9326 (tt0) cc_final: 0.9078 (tt0) REVERT: E 85 GLN cc_start: 0.9112 (OUTLIER) cc_final: 0.8894 (mt0) REVERT: E 97 GLU cc_start: 0.9104 (pt0) cc_final: 0.8872 (pt0) REVERT: E 125 GLN cc_start: 0.8936 (mt0) cc_final: 0.8616 (mt0) REVERT: F 45 ARG cc_start: 0.8886 (mtp85) cc_final: 0.7620 (mtp85) REVERT: F 51 TYR cc_start: 0.8679 (m-80) cc_final: 0.8143 (m-10) REVERT: F 55 ARG cc_start: 0.9343 (mtt90) cc_final: 0.8278 (mtt90) REVERT: F 77 LYS cc_start: 0.9392 (mmmt) cc_final: 0.8893 (mmmt) REVERT: F 84 MET cc_start: 0.9068 (mmm) cc_final: 0.8077 (mmm) REVERT: F 98 TYR cc_start: 0.9458 (m-10) cc_final: 0.8984 (m-80) REVERT: G 25 PHE cc_start: 0.9394 (m-80) cc_final: 0.9146 (m-80) REVERT: G 50 TYR cc_start: 0.9441 (t80) cc_final: 0.9086 (t80) REVERT: G 57 TYR cc_start: 0.9213 (t80) cc_final: 0.8847 (t80) REVERT: G 59 THR cc_start: 0.9721 (m) cc_final: 0.9351 (t) REVERT: G 84 GLN cc_start: 0.9370 (tp-100) cc_final: 0.8689 (tp-100) REVERT: G 90 ASP cc_start: 0.8368 (t70) cc_final: 0.8060 (t70) REVERT: H 63 ASN cc_start: 0.9534 (t0) cc_final: 0.9266 (t0) REVERT: H 68 ASP cc_start: 0.9357 (t0) cc_final: 0.9061 (t0) REVERT: H 79 ARG cc_start: 0.9132 (ttm-80) cc_final: 0.8870 (ttp-110) REVERT: H 87 SER cc_start: 0.9382 (OUTLIER) cc_final: 0.8926 (p) REVERT: H 95 GLN cc_start: 0.9445 (tt0) cc_final: 0.8539 (tp40) REVERT: H 111 VAL cc_start: 0.9608 (p) cc_final: 0.9206 (p) REVERT: K 55 MET cc_start: -0.0501 (mmt) cc_final: -0.1085 (tpp) REVERT: K 101 ARG cc_start: 0.7212 (mmt90) cc_final: 0.5597 (mmp80) REVERT: K 278 ARG cc_start: 0.8305 (mmt180) cc_final: 0.8099 (mmt180) REVERT: L 50 LEU cc_start: 0.9283 (mm) cc_final: 0.8784 (tp) outliers start: 75 outliers final: 47 residues processed: 553 average time/residue: 0.1387 time to fit residues: 109.2168 Evaluate side-chains 557 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 507 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 60 VAL 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 C residue 16 THR Chi-restraints excluded: chain C residue 30 VAL 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 102 ILE Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 74 ILE 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 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 H residue 54 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 88 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 63 TYR Chi-restraints excluded: chain K residue 86 HIS Chi-restraints excluded: chain K residue 119 VAL 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 26 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 31 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 126 optimal weight: 0.0870 chunk 117 optimal weight: 8.9990 chunk 42 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 83 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN K 116 ASN ** K 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.104134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.065369 restraints weight = 41710.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.067428 restraints weight = 16511.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.068655 restraints weight = 10292.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.069310 restraints weight = 8085.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.069605 restraints weight = 7232.462| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3032 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3032 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16075 Z= 0.159 Angle : 0.711 10.464 22999 Z= 0.402 Chirality : 0.046 0.253 2615 Planarity : 0.005 0.049 1909 Dihedral : 29.958 167.971 4479 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 6.73 % Allowed : 27.54 % Favored : 65.73 % 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: -0.33 (0.24), residues: 1139 helix: 0.56 (0.19), residues: 698 sheet: -0.86 (0.56), residues: 77 loop : -1.49 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 36 TYR 0.027 0.002 TYR H 40 PHE 0.033 0.002 PHE A 67 TRP 0.011 0.001 TRP K 305 HIS 0.012 0.001 HIS L 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.16 (16075) covalent geometry : angle 0.71056 / 0.40 (22999) hydrogen bonds : bond 0.04689 / 3.02 ( 887) hydrogen bonds : angle 3.83964 / 2.70 ( 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 596 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 531 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.9070 (m-80) cc_final: 0.8520 (m-80) REVERT: A 42 ARG cc_start: 0.8558 (mtp180) cc_final: 0.8221 (ttm110) REVERT: A 59 GLU cc_start: 0.8325 (pm20) cc_final: 0.8089 (pm20) REVERT: A 73 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7882 (mt-10) REVERT: A 81 ASP cc_start: 0.8572 (t0) cc_final: 0.8231 (t0) REVERT: A 85 GLN cc_start: 0.8667 (mt0) cc_final: 0.8461 (mt0) REVERT: A 87 SER cc_start: 0.9069 (OUTLIER) cc_final: 0.8854 (p) REVERT: A 93 GLN cc_start: 0.8866 (tt0) cc_final: 0.8237 (tt0) REVERT: A 94 GLU cc_start: 0.9107 (mm-30) cc_final: 0.8535 (mm-30) REVERT: A 97 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7753 (mp0) REVERT: A 120 MET cc_start: 0.8110 (mtp) cc_final: 0.7652 (mtp) REVERT: A 125 GLN cc_start: 0.9323 (mt0) cc_final: 0.8899 (mt0) REVERT: A 126 LEU cc_start: 0.9532 (tp) cc_final: 0.9272 (tp) REVERT: A 129 ARG cc_start: 0.9105 (tpt-90) cc_final: 0.8861 (tpp80) REVERT: B 44 LYS cc_start: 0.9407 (ttpp) cc_final: 0.8827 (mtpt) REVERT: B 45 ARG cc_start: 0.8443 (mmm-85) cc_final: 0.8216 (mmm-85) REVERT: B 49 LEU cc_start: 0.9182 (mt) cc_final: 0.8800 (mm) REVERT: B 51 TYR cc_start: 0.8707 (m-80) cc_final: 0.8132 (m-10) REVERT: B 74 GLU cc_start: 0.9153 (tt0) cc_final: 0.8863 (tt0) REVERT: B 77 LYS cc_start: 0.9483 (mmtt) cc_final: 0.9264 (mmmm) REVERT: B 79 LYS cc_start: 0.8552 (mtmt) cc_final: 0.8218 (mtmt) REVERT: B 88 TYR cc_start: 0.9089 (m-10) cc_final: 0.8545 (m-10) REVERT: B 98 TYR cc_start: 0.9241 (m-10) cc_final: 0.8951 (m-80) REVERT: C 24 GLN cc_start: 0.8649 (mm-40) cc_final: 0.8433 (mm-40) REVERT: C 68 ASN cc_start: 0.8927 (m-40) cc_final: 0.8495 (m-40) REVERT: C 72 ASP cc_start: 0.8664 (m-30) cc_final: 0.8427 (m-30) REVERT: C 73 ASN cc_start: 0.9189 (t0) cc_final: 0.8882 (t0) REVERT: C 82 HIS cc_start: 0.9428 (m170) cc_final: 0.8997 (m90) REVERT: C 104 GLN cc_start: 0.8538 (mm110) cc_final: 0.8141 (mm110) REVERT: D 47 GLN cc_start: 0.9490 (mt0) cc_final: 0.9090 (mt0) REVERT: D 68 ASP cc_start: 0.9219 (t0) cc_final: 0.8611 (t0) REVERT: E 60 LEU cc_start: 0.9432 (mm) cc_final: 0.9053 (mm) REVERT: E 68 GLN cc_start: 0.9282 (tt0) cc_final: 0.9018 (tt0) REVERT: E 97 GLU cc_start: 0.9078 (pt0) cc_final: 0.8806 (pt0) REVERT: E 125 GLN cc_start: 0.8939 (mt0) cc_final: 0.8561 (mt0) REVERT: F 30 THR cc_start: 0.9082 (p) cc_final: 0.8519 (t) REVERT: F 36 ARG cc_start: 0.8720 (mtm-85) cc_final: 0.7351 (mtm-85) REVERT: F 45 ARG cc_start: 0.8983 (mtp85) cc_final: 0.8108 (mtp85) REVERT: F 51 TYR cc_start: 0.8582 (m-80) cc_final: 0.8027 (m-80) REVERT: F 55 ARG cc_start: 0.9368 (mtt90) cc_final: 0.8295 (mtt90) REVERT: F 77 LYS cc_start: 0.9404 (mmmt) cc_final: 0.8906 (mmmt) REVERT: F 84 MET cc_start: 0.9074 (mmm) cc_final: 0.8328 (mmm) REVERT: F 98 TYR cc_start: 0.9507 (m-10) cc_final: 0.8807 (m-80) REVERT: G 25 PHE cc_start: 0.9323 (m-80) cc_final: 0.9014 (m-80) REVERT: G 50 TYR cc_start: 0.9354 (t80) cc_final: 0.9072 (t80) REVERT: G 57 TYR cc_start: 0.9209 (t80) cc_final: 0.8901 (t80) REVERT: G 71 ARG cc_start: 0.9146 (ttp80) cc_final: 0.8545 (ttp80) REVERT: G 88 ARG cc_start: 0.9139 (mmt180) cc_final: 0.8916 (mmt180) REVERT: G 90 ASP cc_start: 0.8323 (t70) cc_final: 0.8086 (t70) REVERT: H 37 TYR cc_start: 0.9414 (m-80) cc_final: 0.9127 (m-80) REVERT: H 64 SER cc_start: 0.9634 (t) cc_final: 0.9353 (t) REVERT: H 68 ASP cc_start: 0.9390 (t0) cc_final: 0.9117 (t0) REVERT: H 79 ARG cc_start: 0.9095 (ttm-80) cc_final: 0.8795 (ttp-110) REVERT: H 87 SER cc_start: 0.9357 (OUTLIER) cc_final: 0.8914 (p) REVERT: K 55 MET cc_start: -0.0267 (mmt) cc_final: -0.0755 (tpp) REVERT: K 101 ARG cc_start: 0.7400 (mmt90) cc_final: 0.5665 (mmp80) outliers start: 65 outliers final: 39 residues processed: 551 average time/residue: 0.1364 time to fit residues: 107.4974 Evaluate side-chains 544 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 503 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER 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 92 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain E residue 46 VAL 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 G residue 43 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 73 ASN 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 K residue 9 LEU Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 60 LEU Chi-restraints excluded: chain K residue 63 TYR Chi-restraints excluded: chain K residue 86 HIS Chi-restraints excluded: chain K residue 119 VAL 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 26 VAL 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: 2.9990 chunk 29 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 70 optimal weight: 0.0970 chunk 63 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 73 optimal weight: 20.0000 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN H 49 HIS H 63 ASN ** K 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.103663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.065127 restraints weight = 42087.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.067140 restraints weight = 16811.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.068361 restraints weight = 10536.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.068991 restraints weight = 8266.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.069381 restraints weight = 7409.505| |-----------------------------------------------------------------------------| r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3045 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3045 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 16075 Z= 0.183 Angle : 0.726 9.802 22999 Z= 0.405 Chirality : 0.046 0.259 2615 Planarity : 0.005 0.046 1909 Dihedral : 29.895 168.176 4479 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 6.21 % Allowed : 31.57 % Favored : 62.22 % 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: -0.04 (0.24), residues: 1139 helix: 0.88 (0.19), residues: 686 sheet: -0.64 (0.60), residues: 75 loop : -1.53 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 74 TYR 0.021 0.002 TYR H 40 PHE 0.032 0.002 PHE E 67 TRP 0.013 0.001 TRP K 205 HIS 0.012 0.001 HIS L 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.18 (16075) covalent geometry : angle 0.72641 / 0.41 (22999) hydrogen bonds : bond 0.04681 / 3.02 ( 887) hydrogen bonds : angle 3.85511 / 2.70 ( 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 575 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 515 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.9101 (m-80) cc_final: 0.8597 (m-80) REVERT: A 42 ARG cc_start: 0.8526 (mtp180) cc_final: 0.8193 (ttm110) REVERT: A 73 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7938 (mt-10) REVERT: A 81 ASP cc_start: 0.8625 (t0) cc_final: 0.8339 (t0) REVERT: A 85 GLN cc_start: 0.8720 (mt0) cc_final: 0.8323 (mt0) REVERT: A 93 GLN cc_start: 0.8902 (tt0) cc_final: 0.8258 (tt0) REVERT: A 94 GLU cc_start: 0.9111 (mm-30) cc_final: 0.8560 (mm-30) REVERT: A 97 GLU cc_start: 0.8275 (mt-10) cc_final: 0.7732 (mp0) REVERT: A 120 MET cc_start: 0.8172 (mtp) cc_final: 0.7700 (mtp) REVERT: A 125 GLN cc_start: 0.9320 (mt0) cc_final: 0.8930 (mt0) REVERT: A 126 LEU cc_start: 0.9515 (tp) cc_final: 0.9190 (tp) REVERT: A 129 ARG cc_start: 0.9141 (tpt-90) cc_final: 0.8876 (tpp80) REVERT: B 25 ASN cc_start: 0.8854 (t0) cc_final: 0.7945 (t0) REVERT: B 36 ARG cc_start: 0.8677 (mtm-85) cc_final: 0.7872 (mtm-85) REVERT: B 44 LYS cc_start: 0.9409 (ttpp) cc_final: 0.8678 (mtmt) REVERT: B 51 TYR cc_start: 0.8752 (m-80) cc_final: 0.8270 (m-10) REVERT: B 74 GLU cc_start: 0.9155 (tt0) cc_final: 0.8855 (tt0) REVERT: B 77 LYS cc_start: 0.9493 (mmtt) cc_final: 0.9266 (mmmm) REVERT: B 79 LYS cc_start: 0.8526 (mtmt) cc_final: 0.8226 (mtmt) REVERT: B 88 TYR cc_start: 0.8940 (m-10) cc_final: 0.8276 (m-10) REVERT: B 98 TYR cc_start: 0.9321 (m-10) cc_final: 0.8816 (m-80) REVERT: C 72 ASP cc_start: 0.8733 (m-30) cc_final: 0.8422 (m-30) REVERT: C 73 ASN cc_start: 0.9261 (t0) cc_final: 0.8793 (t0) REVERT: C 104 GLN cc_start: 0.8699 (mm110) cc_final: 0.8282 (mm110) REVERT: D 46 LYS cc_start: 0.9536 (mmmt) cc_final: 0.9293 (mmmt) REVERT: D 47 GLN cc_start: 0.9496 (mt0) cc_final: 0.9104 (mt0) REVERT: D 68 ASP cc_start: 0.9180 (t0) cc_final: 0.8630 (t0) REVERT: D 83 TYR cc_start: 0.8339 (m-10) cc_final: 0.7425 (m-10) REVERT: D 108 LYS cc_start: 0.8940 (mtmt) cc_final: 0.8740 (ttmt) REVERT: E 60 LEU cc_start: 0.9452 (mm) cc_final: 0.9165 (mm) REVERT: E 68 GLN cc_start: 0.9296 (tt0) cc_final: 0.8994 (tt0) REVERT: E 120 MET cc_start: 0.8238 (mtp) cc_final: 0.7815 (mtp) REVERT: E 125 GLN cc_start: 0.8951 (mt0) cc_final: 0.8557 (mt0) REVERT: F 30 THR cc_start: 0.9133 (p) cc_final: 0.8601 (t) REVERT: F 36 ARG cc_start: 0.8739 (mtm-85) cc_final: 0.7283 (mtm-85) REVERT: F 45 ARG cc_start: 0.8938 (mtp85) cc_final: 0.7826 (mtp85) REVERT: F 51 TYR cc_start: 0.8658 (m-80) cc_final: 0.8172 (m-10) REVERT: F 55 ARG cc_start: 0.9402 (mtt90) cc_final: 0.8321 (mtt90) REVERT: F 84 MET cc_start: 0.9108 (mmm) cc_final: 0.8379 (mmm) REVERT: F 98 TYR cc_start: 0.9497 (m-10) cc_final: 0.8933 (m-80) REVERT: G 25 PHE cc_start: 0.9378 (m-80) cc_final: 0.9076 (m-80) REVERT: G 29 ARG cc_start: 0.9383 (tpp80) cc_final: 0.9105 (ttm-80) REVERT: G 56 GLU cc_start: 0.8844 (tm-30) cc_final: 0.8394 (tt0) REVERT: G 57 TYR cc_start: 0.9225 (t80) cc_final: 0.8788 (t80) REVERT: G 71 ARG cc_start: 0.9129 (ttp80) cc_final: 0.8575 (ttp80) REVERT: G 73 ASN cc_start: 0.9292 (OUTLIER) cc_final: 0.8527 (t0) REVERT: G 75 LYS cc_start: 0.8730 (mmtp) cc_final: 0.8495 (mmtp) REVERT: G 90 ASP cc_start: 0.8366 (t70) cc_final: 0.8102 (t70) REVERT: G 104 GLN cc_start: 0.8842 (mt0) cc_final: 0.8542 (mt0) REVERT: H 37 TYR cc_start: 0.9377 (m-80) cc_final: 0.8889 (m-80) REVERT: H 64 SER cc_start: 0.9654 (t) cc_final: 0.9303 (t) REVERT: H 68 ASP cc_start: 0.9407 (t0) cc_final: 0.9105 (t0) REVERT: H 79 ARG cc_start: 0.9134 (ttm-80) cc_final: 0.8855 (ttp-110) REVERT: H 87 SER cc_start: 0.9354 (OUTLIER) cc_final: 0.8936 (p) REVERT: H 96 THR cc_start: 0.9629 (m) cc_final: 0.9202 (t) REVERT: K 55 MET cc_start: -0.0698 (mmt) cc_final: -0.1172 (tpp) REVERT: K 101 ARG cc_start: 0.7399 (mmt90) cc_final: 0.5666 (mmp80) outliers start: 60 outliers final: 43 residues processed: 533 average time/residue: 0.1381 time to fit residues: 104.5135 Evaluate side-chains 541 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 496 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 74 ILE 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 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 43 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 74 ILE 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 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 73 ASN Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 60 LEU Chi-restraints excluded: chain K residue 63 TYR Chi-restraints excluded: chain K residue 86 HIS Chi-restraints excluded: chain K residue 112 GLN Chi-restraints excluded: chain K residue 119 VAL 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 26 VAL 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: 0.9980 chunk 66 optimal weight: 0.9990 chunk 82 optimal weight: 10.0000 chunk 138 optimal weight: 1.9990 chunk 98 optimal weight: 9.9990 chunk 61 optimal weight: 0.7980 chunk 85 optimal weight: 20.0000 chunk 7 optimal weight: 0.0870 chunk 9 optimal weight: 0.0970 chunk 133 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 108 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN ** K 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 2 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.104499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.065622 restraints weight = 41964.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.067699 restraints weight = 16809.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.068945 restraints weight = 10503.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.069622 restraints weight = 8269.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.069951 restraints weight = 7388.649| |-----------------------------------------------------------------------------| r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3069 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3069 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 16075 Z= 0.158 Angle : 0.718 10.372 22999 Z= 0.400 Chirality : 0.045 0.262 2615 Planarity : 0.005 0.052 1909 Dihedral : 29.817 168.400 4479 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 6.83 % Allowed : 32.40 % Favored : 60.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.24), residues: 1139 helix: 1.01 (0.19), residues: 684 sheet: -0.70 (0.59), residues: 76 loop : -1.51 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 74 TYR 0.025 0.002 TYR C 57 PHE 0.031 0.002 PHE A 67 TRP 0.015 0.001 TRP K 205 HIS 0.020 0.001 HIS L 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.16 (16075) covalent geometry : angle 0.71850 / 0.40 (22999) hydrogen bonds : bond 0.04455 / 2.89 ( 887) hydrogen bonds : angle 3.75398 / 2.63 ( 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 583 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 517 time to evaluate : 0.436 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: 0.9091 (m-80) cc_final: 0.8618 (m-80) REVERT: A 42 ARG cc_start: 0.8514 (mtp180) cc_final: 0.8238 (ttm110) REVERT: A 67 PHE cc_start: 0.9089 (t80) cc_final: 0.8747 (t80) REVERT: A 73 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7996 (mt-10) REVERT: A 81 ASP cc_start: 0.8612 (t0) cc_final: 0.8345 (t0) REVERT: A 85 GLN cc_start: 0.8634 (mt0) cc_final: 0.8266 (mt0) REVERT: A 94 GLU cc_start: 0.9082 (mm-30) cc_final: 0.8487 (mm-30) REVERT: A 97 GLU cc_start: 0.8341 (mt-10) cc_final: 0.7809 (mt-10) REVERT: A 115 LYS cc_start: 0.9463 (mmmm) cc_final: 0.9256 (mmtm) REVERT: A 120 MET cc_start: 0.8162 (mtp) cc_final: 0.7918 (mtp) REVERT: A 125 GLN cc_start: 0.9316 (mt0) cc_final: 0.8863 (mt0) REVERT: A 129 ARG cc_start: 0.9070 (tpt-90) cc_final: 0.8570 (mmm160) REVERT: B 25 ASN cc_start: 0.8868 (t0) cc_final: 0.7959 (t0) REVERT: B 30 THR cc_start: 0.9332 (p) cc_final: 0.9110 (t) REVERT: B 35 ARG cc_start: 0.9320 (ttm-80) cc_final: 0.9045 (ttm-80) REVERT: B 36 ARG cc_start: 0.8634 (mtm-85) cc_final: 0.7925 (mtm-85) REVERT: B 40 ARG cc_start: 0.9114 (tpp80) cc_final: 0.8913 (tpp80) REVERT: B 44 LYS cc_start: 0.9406 (ttpp) cc_final: 0.8740 (mtpt) REVERT: B 51 TYR cc_start: 0.8783 (m-80) cc_final: 0.8434 (m-10) REVERT: B 74 GLU cc_start: 0.9090 (tt0) cc_final: 0.8797 (tt0) REVERT: B 77 LYS cc_start: 0.9466 (mmtt) cc_final: 0.9228 (mmmm) REVERT: B 79 LYS cc_start: 0.8530 (mtmt) cc_final: 0.8183 (mtmm) REVERT: B 88 TYR cc_start: 0.9066 (m-10) cc_final: 0.8414 (m-10) REVERT: B 98 TYR cc_start: 0.9316 (m-10) cc_final: 0.9023 (m-80) REVERT: C 17 ARG cc_start: 0.9503 (ttp-170) cc_final: 0.9183 (ttm170) REVERT: C 73 ASN cc_start: 0.9284 (t0) cc_final: 0.8819 (t0) REVERT: C 84 GLN cc_start: 0.9575 (tp-100) cc_final: 0.9343 (tp-100) REVERT: C 85 LEU cc_start: 0.9651 (mt) cc_final: 0.9315 (mt) REVERT: C 104 GLN cc_start: 0.8750 (mm110) cc_final: 0.8372 (mm110) REVERT: D 37 TYR cc_start: 0.9375 (OUTLIER) cc_final: 0.9135 (m-10) REVERT: D 46 LYS cc_start: 0.9490 (mmmt) cc_final: 0.9191 (mmmt) REVERT: D 47 GLN cc_start: 0.9424 (mt0) cc_final: 0.8856 (mt0) REVERT: D 68 ASP cc_start: 0.9129 (t0) cc_final: 0.8620 (t0) REVERT: D 83 TYR cc_start: 0.8355 (m-10) cc_final: 0.7451 (m-10) REVERT: E 68 GLN cc_start: 0.9275 (tt0) cc_final: 0.8990 (tt0) REVERT: E 120 MET cc_start: 0.8195 (mtp) cc_final: 0.7809 (mtp) REVERT: E 125 GLN cc_start: 0.8946 (mt0) cc_final: 0.8530 (mt0) REVERT: F 30 THR cc_start: 0.9188 (p) cc_final: 0.8878 (t) REVERT: F 31 LYS cc_start: 0.9136 (ttpp) cc_final: 0.8877 (tttp) REVERT: F 45 ARG cc_start: 0.8940 (mtp85) cc_final: 0.8201 (mtp85) REVERT: F 55 ARG cc_start: 0.9412 (mtt90) cc_final: 0.8358 (mtt90) REVERT: F 84 MET cc_start: 0.9076 (mmm) cc_final: 0.8369 (mmm) REVERT: F 98 TYR cc_start: 0.9491 (m-10) cc_final: 0.8851 (m-80) REVERT: G 25 PHE cc_start: 0.9330 (m-80) cc_final: 0.9084 (m-80) REVERT: G 29 ARG cc_start: 0.9326 (tpp80) cc_final: 0.9029 (ttm-80) REVERT: G 57 TYR cc_start: 0.9229 (t80) cc_final: 0.8883 (t80) REVERT: G 71 ARG cc_start: 0.9155 (ttp80) cc_final: 0.8614 (ttp80) REVERT: G 73 ASN cc_start: 0.9391 (OUTLIER) cc_final: 0.8732 (t0) REVERT: G 75 LYS cc_start: 0.8608 (mmtp) cc_final: 0.8392 (mmtp) REVERT: G 84 GLN cc_start: 0.9499 (tp-100) cc_final: 0.8605 (tp40) REVERT: G 90 ASP cc_start: 0.8392 (t70) cc_final: 0.8125 (t70) REVERT: G 104 GLN cc_start: 0.8779 (mt0) cc_final: 0.8490 (mt0) REVERT: H 37 TYR cc_start: 0.9420 (m-80) cc_final: 0.8832 (m-80) REVERT: H 64 SER cc_start: 0.9651 (t) cc_final: 0.9372 (t) REVERT: H 68 ASP cc_start: 0.9341 (t0) cc_final: 0.9090 (t0) REVERT: H 79 ARG cc_start: 0.9186 (ttm-80) cc_final: 0.8964 (ttp-110) REVERT: H 87 SER cc_start: 0.9327 (OUTLIER) cc_final: 0.8896 (p) REVERT: H 96 THR cc_start: 0.9640 (m) cc_final: 0.9224 (t) REVERT: K 55 MET cc_start: -0.0718 (mmt) cc_final: -0.1207 (tpp) REVERT: K 101 ARG cc_start: 0.7394 (mmt90) cc_final: 0.5660 (mmp80) REVERT: K 198 MET cc_start: 0.8274 (mmt) cc_final: 0.7963 (mmm) REVERT: L 74 ARG cc_start: 0.8674 (ttp-110) cc_final: 0.8013 (ptt180) outliers start: 66 outliers final: 45 residues processed: 541 average time/residue: 0.1421 time to fit residues: 109.4081 Evaluate side-chains 558 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 510 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 49 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 43 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 87 SER 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 34 ILE 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 73 ASN Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 90 THR 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 86 HIS Chi-restraints excluded: chain K residue 112 GLN Chi-restraints excluded: chain K residue 119 VAL 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 39 ASP Chi-restraints excluded: chain L residue 57 SER 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: 9.9990 chunk 75 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 chunk 93 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 chunk 134 optimal weight: 5.9990 chunk 137 optimal weight: 9.9990 chunk 18 optimal weight: 0.5980 chunk 76 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 30 HIS ** 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 = 0.3736 r_free = 0.3736 target = 0.102162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.062721 restraints weight = 43117.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.064640 restraints weight = 18008.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.065809 restraints weight = 11537.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.066443 restraints weight = 9213.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.066729 restraints weight = 8279.172| |-----------------------------------------------------------------------------| r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2999 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (16 function evaluations) r_final: 0.2999 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 16075 Z= 0.264 Angle : 0.764 9.961 22999 Z= 0.422 Chirality : 0.047 0.261 2615 Planarity : 0.005 0.048 1909 Dihedral : 29.832 168.954 4479 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 7.25 % Allowed : 31.68 % Favored : 61.08 % 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: 0.15 (0.25), residues: 1139 helix: 1.04 (0.19), residues: 686 sheet: -0.92 (0.56), residues: 78 loop : -1.38 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG C 81 TYR 0.023 0.002 TYR C 57 PHE 0.040 0.002 PHE A 67 TRP 0.020 0.001 TRP K 205 HIS 0.010 0.001 HIS L 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.26 (16075) covalent geometry : angle 0.76408 / 0.42 (22999) hydrogen bonds : bond 0.04947 / 3.20 ( 887) hydrogen bonds : angle 3.97692 / 2.76 ( 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 563 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 493 time to evaluate : 0.455 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: 0.9127 (m-80) cc_final: 0.8684 (m-80) REVERT: A 73 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7960 (mt-10) REVERT: A 81 ASP cc_start: 0.8719 (t0) cc_final: 0.8468 (t0) REVERT: A 85 GLN cc_start: 0.8787 (mt0) cc_final: 0.8549 (mt0) REVERT: A 90 MET cc_start: 0.9211 (tpp) cc_final: 0.8989 (mmm) REVERT: A 93 GLN cc_start: 0.8682 (mt0) cc_final: 0.8387 (mt0) REVERT: A 97 GLU cc_start: 0.8217 (mt-10) cc_final: 0.8008 (mp0) REVERT: A 120 MET cc_start: 0.8232 (mtp) cc_final: 0.8003 (mtp) REVERT: A 129 ARG cc_start: 0.9058 (tpt-90) cc_final: 0.8572 (mmm160) REVERT: B 25 ASN cc_start: 0.8873 (t0) cc_final: 0.7825 (t0) REVERT: B 44 LYS cc_start: 0.9427 (ttpp) cc_final: 0.8748 (mtmt) REVERT: B 51 TYR cc_start: 0.8897 (m-80) cc_final: 0.8555 (m-10) REVERT: B 74 GLU cc_start: 0.9118 (tt0) cc_final: 0.8895 (tt0) REVERT: B 77 LYS cc_start: 0.9497 (mmtt) cc_final: 0.9266 (mmmm) REVERT: B 79 LYS cc_start: 0.8571 (mtmt) cc_final: 0.8242 (mtmm) REVERT: B 88 TYR cc_start: 0.9087 (m-10) cc_final: 0.8637 (m-10) REVERT: B 98 TYR cc_start: 0.9368 (m-10) cc_final: 0.8750 (m-80) REVERT: C 24 GLN cc_start: 0.8930 (mt0) cc_final: 0.8644 (mt0) REVERT: C 38 ASN cc_start: 0.8766 (p0) cc_final: 0.8411 (p0) REVERT: C 72 ASP cc_start: 0.8770 (m-30) cc_final: 0.8450 (m-30) REVERT: C 73 ASN cc_start: 0.9305 (t0) cc_final: 0.8891 (t0) REVERT: C 85 LEU cc_start: 0.9702 (mt) cc_final: 0.9478 (mt) REVERT: C 104 GLN cc_start: 0.8933 (mm110) cc_final: 0.8480 (mm110) REVERT: D 46 LYS cc_start: 0.9439 (mmmt) cc_final: 0.9116 (mmmt) REVERT: D 47 GLN cc_start: 0.9389 (mt0) cc_final: 0.9026 (mt0) REVERT: D 68 ASP cc_start: 0.9216 (t0) cc_final: 0.8656 (t0) REVERT: D 83 TYR cc_start: 0.8433 (m-10) cc_final: 0.7459 (m-10) REVERT: E 68 GLN cc_start: 0.9308 (tt0) cc_final: 0.9046 (tt0) REVERT: E 120 MET cc_start: 0.8389 (mtp) cc_final: 0.7891 (mtp) REVERT: E 125 GLN cc_start: 0.8964 (mt0) cc_final: 0.8539 (mt0) REVERT: F 31 LYS cc_start: 0.9182 (ttpp) cc_final: 0.8938 (tttm) REVERT: F 44 LYS cc_start: 0.9006 (mtmm) cc_final: 0.8612 (mtmm) REVERT: F 51 TYR cc_start: 0.8975 (m-80) cc_final: 0.8358 (m-10) REVERT: F 55 ARG cc_start: 0.9417 (mtt90) cc_final: 0.8308 (mtt90) REVERT: F 84 MET cc_start: 0.9153 (mmm) cc_final: 0.8460 (mmm) REVERT: F 98 TYR cc_start: 0.9471 (m-10) cc_final: 0.9093 (m-10) REVERT: G 25 PHE cc_start: 0.9456 (m-80) cc_final: 0.9204 (m-10) REVERT: G 29 ARG cc_start: 0.9402 (tpp80) cc_final: 0.9106 (ttm-80) REVERT: G 35 ARG cc_start: 0.9400 (mtm110) cc_final: 0.8699 (mtm110) REVERT: G 56 GLU cc_start: 0.8831 (tm-30) cc_final: 0.8440 (tt0) REVERT: G 57 TYR cc_start: 0.9302 (t80) cc_final: 0.8838 (t80) REVERT: G 71 ARG cc_start: 0.9153 (ttp80) cc_final: 0.8649 (ttp80) REVERT: G 73 ASN cc_start: 0.9438 (t0) cc_final: 0.8735 (t0) REVERT: G 75 LYS cc_start: 0.8641 (mmtp) cc_final: 0.8367 (mmtp) REVERT: G 84 GLN cc_start: 0.9539 (tp-100) cc_final: 0.8801 (tp-100) REVERT: G 90 ASP cc_start: 0.8361 (t70) cc_final: 0.8045 (t70) REVERT: G 99 ARG cc_start: 0.8668 (mmm160) cc_final: 0.8377 (mmm-85) REVERT: H 37 TYR cc_start: 0.9484 (m-80) cc_final: 0.8664 (m-80) REVERT: H 64 SER cc_start: 0.9684 (t) cc_final: 0.9293 (t) REVERT: H 68 ASP cc_start: 0.9351 (t0) cc_final: 0.9054 (t0) REVERT: H 79 ARG cc_start: 0.9197 (ttm-80) cc_final: 0.8843 (ttp-110) REVERT: H 87 SER cc_start: 0.9316 (OUTLIER) cc_final: 0.8923 (p) REVERT: K 55 MET cc_start: -0.0742 (mmt) cc_final: -0.1222 (tpp) REVERT: K 101 ARG cc_start: 0.7392 (mmt90) cc_final: 0.5756 (mmp80) REVERT: K 198 MET cc_start: 0.8286 (mmt) cc_final: 0.7768 (mmt) outliers start: 70 outliers final: 53 residues processed: 520 average time/residue: 0.1374 time to fit residues: 101.5068 Evaluate side-chains 538 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 484 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 74 ILE 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 34 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 65 VAL 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 43 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 66 VAL 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 87 SER 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 G residue 43 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 88 THR 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 63 TYR Chi-restraints excluded: chain K residue 86 HIS Chi-restraints excluded: chain K residue 112 GLN Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 177 THR Chi-restraints excluded: chain K residue 190 ILE Chi-restraints excluded: chain K residue 293 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 52 optimal weight: 0.7980 chunk 94 optimal weight: 8.9990 chunk 4 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 76 optimal weight: 9.9990 chunk 119 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 110 optimal weight: 8.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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** G 104 GLN ** K 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.104451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.065922 restraints weight = 42400.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.067960 restraints weight = 17121.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.069186 restraints weight = 10724.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.069867 restraints weight = 8418.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.070234 restraints weight = 7498.612| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- 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 = 0.49 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 = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3071 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 16075 Z= 0.164 Angle : 0.724 9.816 22999 Z= 0.403 Chirality : 0.046 0.263 2615 Planarity : 0.005 0.044 1909 Dihedral : 29.748 169.011 4479 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 5.18 % Allowed : 34.16 % Favored : 60.66 % 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: 0.32 (0.25), residues: 1139 helix: 1.14 (0.19), residues: 686 sheet: -0.83 (0.57), residues: 76 loop : -1.25 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 92 TYR 0.028 0.002 TYR H 40 PHE 0.029 0.002 PHE E 67 TRP 0.008 0.001 TRP K 205 HIS 0.008 0.001 HIS L 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.16 (16075) covalent geometry : angle 0.72446 / 0.40 (22999) hydrogen bonds : bond 0.04362 / 2.85 ( 887) hydrogen bonds : angle 3.75285 / 2.60 ( 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 570 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 520 time to evaluate : 0.450 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 73 GLU cc_start: 0.8275 (mt-10) cc_final: 0.7989 (mt-10) REVERT: A 81 ASP cc_start: 0.8705 (t0) cc_final: 0.8407 (t0) REVERT: A 85 GLN cc_start: 0.8895 (mt0) cc_final: 0.8478 (mt0) REVERT: A 90 MET cc_start: 0.9138 (tpp) cc_final: 0.8937 (mmm) REVERT: A 97 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7906 (mp0) REVERT: A 115 LYS cc_start: 0.9559 (mmmm) cc_final: 0.9330 (mmmm) REVERT: A 120 MET cc_start: 0.8164 (mtp) cc_final: 0.7713 (mtp) REVERT: A 125 GLN cc_start: 0.9293 (mt0) cc_final: 0.8881 (mt0) REVERT: A 129 ARG cc_start: 0.9016 (tpt-90) cc_final: 0.8548 (mmm160) REVERT: B 25 ASN cc_start: 0.8899 (t0) cc_final: 0.7928 (t0) REVERT: B 30 THR cc_start: 0.9327 (p) cc_final: 0.9012 (t) REVERT: B 36 ARG cc_start: 0.8497 (mtm-85) cc_final: 0.7848 (mtm-85) REVERT: B 44 LYS cc_start: 0.9381 (ttpp) cc_final: 0.8675 (mtmt) REVERT: B 49 LEU cc_start: 0.9372 (mm) cc_final: 0.9145 (mm) REVERT: B 51 TYR cc_start: 0.8895 (m-80) cc_final: 0.8508 (m-10) REVERT: B 68 ASP cc_start: 0.9151 (m-30) cc_final: 0.8942 (m-30) REVERT: B 74 GLU cc_start: 0.9095 (tt0) cc_final: 0.8843 (tt0) REVERT: B 77 LYS cc_start: 0.9477 (mmtt) cc_final: 0.9232 (mmmm) REVERT: B 79 LYS cc_start: 0.8536 (mtmt) cc_final: 0.8212 (mtmt) REVERT: B 88 TYR cc_start: 0.8912 (m-10) cc_final: 0.8634 (m-10) REVERT: B 98 TYR cc_start: 0.9300 (m-10) cc_final: 0.8685 (m-80) REVERT: C 17 ARG cc_start: 0.9464 (ttp-170) cc_final: 0.9225 (ttm170) REVERT: C 24 GLN cc_start: 0.8704 (mt0) cc_final: 0.8496 (mp10) REVERT: C 38 ASN cc_start: 0.8622 (p0) cc_final: 0.8235 (p0) REVERT: C 72 ASP cc_start: 0.8737 (m-30) cc_final: 0.8498 (m-30) REVERT: C 73 ASN cc_start: 0.9357 (t0) cc_final: 0.8815 (t0) REVERT: C 82 HIS cc_start: 0.9433 (m170) cc_final: 0.8918 (m90) REVERT: C 104 GLN cc_start: 0.8895 (mm110) cc_final: 0.8429 (mm110) REVERT: D 46 LYS cc_start: 0.9448 (mmmt) cc_final: 0.9106 (mmmt) REVERT: D 68 ASP cc_start: 0.9216 (t0) cc_final: 0.8681 (t0) REVERT: D 83 TYR cc_start: 0.8398 (m-10) cc_final: 0.7390 (m-10) REVERT: E 68 GLN cc_start: 0.9256 (tt0) cc_final: 0.9018 (tt0) REVERT: E 85 GLN cc_start: 0.8961 (mt0) cc_final: 0.8594 (mt0) REVERT: E 120 MET cc_start: 0.8328 (mtp) cc_final: 0.7851 (mtp) REVERT: E 125 GLN cc_start: 0.8929 (mt0) cc_final: 0.8499 (mt0) REVERT: F 31 LYS cc_start: 0.9175 (ttpp) cc_final: 0.8892 (tttm) REVERT: F 51 TYR cc_start: 0.8932 (m-80) cc_final: 0.8320 (m-10) REVERT: F 55 ARG cc_start: 0.9379 (mtt90) cc_final: 0.8358 (mtt90) REVERT: F 84 MET cc_start: 0.9032 (mmm) cc_final: 0.8339 (mmm) REVERT: F 98 TYR cc_start: 0.9521 (m-10) cc_final: 0.9186 (m-10) REVERT: G 25 PHE cc_start: 0.9349 (m-80) cc_final: 0.9115 (m-80) REVERT: G 29 ARG cc_start: 0.9279 (tpp80) cc_final: 0.8949 (ttm-80) REVERT: G 42 ARG cc_start: 0.9219 (ptp90) cc_final: 0.8053 (ptm-80) REVERT: G 56 GLU cc_start: 0.8882 (tm-30) cc_final: 0.8437 (tt0) REVERT: G 57 TYR cc_start: 0.9266 (t80) cc_final: 0.8745 (t80) REVERT: G 68 ASN cc_start: 0.9280 (m-40) cc_final: 0.8864 (m-40) REVERT: G 71 ARG cc_start: 0.9178 (ttp80) cc_final: 0.8680 (ttp80) REVERT: G 73 ASN cc_start: 0.9467 (t0) cc_final: 0.8902 (t0) REVERT: G 84 GLN cc_start: 0.9493 (tp-100) cc_final: 0.8764 (tp-100) REVERT: G 90 ASP cc_start: 0.8310 (t70) cc_final: 0.7478 (t70) REVERT: G 92 GLU cc_start: 0.8518 (pm20) cc_final: 0.8107 (pm20) REVERT: G 99 ARG cc_start: 0.8638 (mmm160) cc_final: 0.8325 (mmm-85) REVERT: H 37 TYR cc_start: 0.9430 (m-80) cc_final: 0.8605 (m-80) REVERT: H 64 SER cc_start: 0.9641 (t) cc_final: 0.9253 (t) REVERT: H 68 ASP cc_start: 0.9333 (t0) cc_final: 0.9068 (t0) REVERT: H 87 SER cc_start: 0.9301 (OUTLIER) cc_final: 0.8788 (p) REVERT: H 96 THR cc_start: 0.9619 (m) cc_final: 0.9254 (t) REVERT: K 55 MET cc_start: -0.0865 (mmt) cc_final: -0.1396 (tpp) REVERT: K 101 ARG cc_start: 0.7376 (mmt90) cc_final: 0.5700 (mmp80) REVERT: K 198 MET cc_start: 0.8330 (mmt) cc_final: 0.8094 (mmm) REVERT: K 278 ARG cc_start: 0.7843 (mmp80) cc_final: 0.7574 (mmt-90) REVERT: L 74 ARG cc_start: 0.8853 (ttp-110) cc_final: 0.8234 (ttm110) outliers start: 50 outliers final: 39 residues processed: 537 average time/residue: 0.1389 time to fit residues: 106.5939 Evaluate side-chains 545 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 505 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 34 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 43 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 74 ILE 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 30 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 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 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 36 ILE Chi-restraints excluded: chain L residue 39 ASP Chi-restraints excluded: chain L residue 57 SER 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: 0.8980 chunk 4 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 115 optimal weight: 40.0000 chunk 62 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 chunk 78 optimal weight: 9.9990 chunk 76 optimal weight: 10.0000 chunk 33 optimal weight: 0.6980 chunk 86 optimal weight: 20.0000 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 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 ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN ** 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 = 0.3764 r_free = 0.3764 target = 0.103805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.065224 restraints weight = 42620.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.067254 restraints weight = 17403.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.068475 restraints weight = 10940.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.069136 restraints weight = 8592.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.069450 restraints weight = 7663.464| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3054 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3054 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 16075 Z= 0.193 Angle : 0.762 11.732 22999 Z= 0.417 Chirality : 0.047 0.268 2615 Planarity : 0.005 0.042 1909 Dihedral : 29.750 169.116 4479 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 5.28 % Allowed : 35.92 % Favored : 58.80 % 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: 0.28 (0.25), residues: 1139 helix: 1.08 (0.19), residues: 686 sheet: -0.98 (0.56), residues: 78 loop : -1.16 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 81 TYR 0.043 0.002 TYR H 83 PHE 0.032 0.002 PHE K 257 TRP 0.024 0.001 TRP K 205 HIS 0.012 0.001 HIS L 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.19 (16075) covalent geometry : angle 0.76211 / 0.42 (22999) hydrogen bonds : bond 0.04545 / 2.93 ( 887) hydrogen bonds : angle 3.86445 / 2.69 ( 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 560 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 509 time to evaluate : 0.441 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 73 GLU cc_start: 0.8295 (mt-10) cc_final: 0.8050 (mt-10) REVERT: A 85 GLN cc_start: 0.8909 (mt0) cc_final: 0.8518 (mt0) REVERT: A 90 MET cc_start: 0.9167 (tpp) cc_final: 0.8928 (mmm) REVERT: A 97 GLU cc_start: 0.8283 (mt-10) cc_final: 0.7975 (mp0) REVERT: A 115 LYS cc_start: 0.9574 (mmmm) cc_final: 0.9354 (mmmm) REVERT: A 125 GLN cc_start: 0.9298 (mt0) cc_final: 0.8884 (mt0) REVERT: A 129 ARG cc_start: 0.9012 (tpt-90) cc_final: 0.8548 (mmm160) REVERT: B 25 ASN cc_start: 0.8861 (t0) cc_final: 0.8262 (t0) REVERT: B 30 THR cc_start: 0.9371 (p) cc_final: 0.9074 (t) REVERT: B 36 ARG cc_start: 0.8632 (mtm-85) cc_final: 0.7906 (mtm-85) REVERT: B 44 LYS cc_start: 0.9417 (ttpp) cc_final: 0.8713 (mtmt) REVERT: B 49 LEU cc_start: 0.9377 (mm) cc_final: 0.9165 (mm) REVERT: B 51 TYR cc_start: 0.8941 (m-80) cc_final: 0.8682 (m-10) REVERT: B 68 ASP cc_start: 0.9167 (m-30) cc_final: 0.8957 (m-30) REVERT: B 77 LYS cc_start: 0.9479 (mmtt) cc_final: 0.9241 (mmmm) REVERT: B 79 LYS cc_start: 0.8644 (mtmt) cc_final: 0.8338 (mtmm) REVERT: B 88 TYR cc_start: 0.8966 (m-10) cc_final: 0.8739 (m-80) REVERT: B 98 TYR cc_start: 0.9387 (m-10) cc_final: 0.8853 (m-80) REVERT: C 17 ARG cc_start: 0.9483 (ttp-170) cc_final: 0.9216 (ttm170) REVERT: C 38 ASN cc_start: 0.8723 (p0) cc_final: 0.8394 (p0) REVERT: C 56 GLU cc_start: 0.8751 (tt0) cc_final: 0.8199 (tt0) REVERT: C 63 LEU cc_start: 0.9717 (mt) cc_final: 0.9471 (mt) REVERT: C 72 ASP cc_start: 0.8836 (m-30) cc_final: 0.8503 (m-30) REVERT: C 73 ASN cc_start: 0.9374 (t0) cc_final: 0.8768 (t0) REVERT: C 89 ASN cc_start: 0.9465 (m-40) cc_final: 0.9191 (m110) REVERT: C 104 GLN cc_start: 0.8938 (mm110) cc_final: 0.8461 (mm110) REVERT: D 46 LYS cc_start: 0.9447 (mmmt) cc_final: 0.9076 (mmmt) REVERT: D 68 ASP cc_start: 0.9207 (t0) cc_final: 0.8690 (t0) REVERT: D 83 TYR cc_start: 0.8452 (m-10) cc_final: 0.7105 (m-10) REVERT: E 68 GLN cc_start: 0.9265 (tt0) cc_final: 0.9039 (tt0) REVERT: E 120 MET cc_start: 0.8397 (mtp) cc_final: 0.7902 (mtp) REVERT: E 125 GLN cc_start: 0.8954 (mt0) cc_final: 0.8728 (mt0) REVERT: F 31 LYS cc_start: 0.9207 (ttpp) cc_final: 0.8929 (tttm) REVERT: F 51 TYR cc_start: 0.8980 (m-80) cc_final: 0.8349 (m-10) REVERT: F 55 ARG cc_start: 0.9371 (mtt90) cc_final: 0.8329 (mtt90) REVERT: F 98 TYR cc_start: 0.9497 (m-10) cc_final: 0.8934 (m-80) REVERT: G 25 PHE cc_start: 0.9394 (m-80) cc_final: 0.9172 (m-10) REVERT: G 29 ARG cc_start: 0.9302 (tpp80) cc_final: 0.8997 (ttm-80) REVERT: G 56 GLU cc_start: 0.8873 (tm-30) cc_final: 0.8467 (tt0) REVERT: G 57 TYR cc_start: 0.9237 (t80) cc_final: 0.8784 (t80) REVERT: G 68 ASN cc_start: 0.9264 (m-40) cc_final: 0.8832 (m-40) REVERT: G 71 ARG cc_start: 0.9190 (ttp80) cc_final: 0.8715 (ttp80) REVERT: G 73 ASN cc_start: 0.9445 (t0) cc_final: 0.8992 (t0) REVERT: G 90 ASP cc_start: 0.8393 (t70) cc_final: 0.7782 (t70) REVERT: G 99 ARG cc_start: 0.8644 (mmm160) cc_final: 0.8335 (mmm-85) REVERT: H 37 TYR cc_start: 0.9445 (m-80) cc_final: 0.8576 (m-80) REVERT: H 64 SER cc_start: 0.9659 (t) cc_final: 0.9284 (t) REVERT: H 68 ASP cc_start: 0.9329 (t0) cc_final: 0.9065 (t0) REVERT: H 87 SER cc_start: 0.9421 (OUTLIER) cc_final: 0.9016 (p) REVERT: H 96 THR cc_start: 0.9674 (m) cc_final: 0.9314 (t) REVERT: K 55 MET cc_start: -0.0881 (mmt) cc_final: -0.1408 (tpp) REVERT: K 101 ARG cc_start: 0.7367 (mmt90) cc_final: 0.5706 (mmp80) REVERT: K 198 MET cc_start: 0.8342 (mmt) cc_final: 0.8023 (mmm) outliers start: 51 outliers final: 42 residues processed: 525 average time/residue: 0.1314 time to fit residues: 98.7241 Evaluate side-chains 541 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 498 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 34 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 43 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain E residue 124 ILE 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 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 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 63 TYR Chi-restraints excluded: chain K residue 112 GLN 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 36 ILE Chi-restraints excluded: chain L residue 39 ASP Chi-restraints excluded: chain L residue 57 SER 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: 0.9980 chunk 62 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 78 optimal weight: 8.9990 chunk 44 optimal weight: 0.8980 chunk 134 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 110 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 79 optimal weight: 10.0000 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 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** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN G 82 HIS G 104 GLN ** K 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.104242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.064639 restraints weight = 42858.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.066663 restraints weight = 17778.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.067866 restraints weight = 11311.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.068560 restraints weight = 9004.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.068868 restraints weight = 8046.368| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3053 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3053 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 16075 Z= 0.188 Angle : 0.777 11.413 22999 Z= 0.423 Chirality : 0.047 0.339 2615 Planarity : 0.005 0.045 1909 Dihedral : 29.738 169.326 4479 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 4.97 % Allowed : 37.16 % Favored : 57.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.25), residues: 1139 helix: 1.04 (0.19), residues: 686 sheet: -1.09 (0.54), residues: 80 loop : -1.08 (0.33), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 81 TYR 0.069 0.002 TYR H 83 PHE 0.027 0.002 PHE K 257 TRP 0.007 0.001 TRP K 305 HIS 0.008 0.001 HIS L 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.19 (16075) covalent geometry : angle 0.77699 / 0.42 (22999) hydrogen bonds : bond 0.04469 / 2.87 ( 887) hydrogen bonds : angle 3.87295 / 2.68 ( 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 545 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 497 time to evaluate : 0.357 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 73 GLU cc_start: 0.8317 (mt-10) cc_final: 0.8013 (mt-10) REVERT: A 85 GLN cc_start: 0.8914 (mt0) cc_final: 0.8507 (mt0) REVERT: A 90 MET cc_start: 0.9130 (tpp) cc_final: 0.8873 (mmm) REVERT: A 97 GLU cc_start: 0.8303 (mt-10) cc_final: 0.7982 (mp0) REVERT: A 115 LYS cc_start: 0.9579 (mmmm) cc_final: 0.9364 (mmmm) REVERT: A 120 MET cc_start: 0.8255 (mtp) cc_final: 0.7632 (mtp) REVERT: A 125 GLN cc_start: 0.9308 (mt0) cc_final: 0.8893 (mt0) REVERT: A 129 ARG cc_start: 0.9011 (tpt-90) cc_final: 0.8545 (mmm160) REVERT: B 25 ASN cc_start: 0.8833 (t0) cc_final: 0.7892 (t0) REVERT: B 36 ARG cc_start: 0.8615 (mtm-85) cc_final: 0.7949 (mtm-85) REVERT: B 44 LYS cc_start: 0.9407 (ttpp) cc_final: 0.8726 (mtmt) REVERT: B 49 LEU cc_start: 0.9374 (mm) cc_final: 0.9157 (mm) REVERT: B 68 ASP cc_start: 0.9145 (m-30) cc_final: 0.8930 (m-30) REVERT: B 77 LYS cc_start: 0.9474 (mmtt) cc_final: 0.9229 (mmmm) REVERT: B 79 LYS cc_start: 0.8711 (mtmt) cc_final: 0.8313 (mtmm) REVERT: B 88 TYR cc_start: 0.8962 (m-10) cc_final: 0.8751 (m-80) REVERT: B 98 TYR cc_start: 0.9393 (m-10) cc_final: 0.8834 (m-80) REVERT: C 17 ARG cc_start: 0.9474 (ttp-170) cc_final: 0.9191 (ttm170) REVERT: C 38 ASN cc_start: 0.8738 (p0) cc_final: 0.8407 (p0) REVERT: C 63 LEU cc_start: 0.9706 (mt) cc_final: 0.9462 (mt) REVERT: C 72 ASP cc_start: 0.8828 (m-30) cc_final: 0.8493 (m-30) REVERT: C 73 ASN cc_start: 0.9379 (t0) cc_final: 0.8799 (t0) REVERT: C 89 ASN cc_start: 0.9460 (m-40) cc_final: 0.9164 (m110) REVERT: C 104 GLN cc_start: 0.8991 (mm110) cc_final: 0.8541 (mm110) REVERT: D 46 LYS cc_start: 0.9476 (mmmt) cc_final: 0.9108 (mmmt) REVERT: D 68 ASP cc_start: 0.9220 (t0) cc_final: 0.8701 (t0) REVERT: D 83 TYR cc_start: 0.8459 (m-10) cc_final: 0.7169 (m-10) REVERT: E 68 GLN cc_start: 0.9269 (tt0) cc_final: 0.9066 (tt0) REVERT: E 85 GLN cc_start: 0.8921 (mt0) cc_final: 0.8595 (mt0) REVERT: E 120 MET cc_start: 0.8383 (mtp) cc_final: 0.7880 (mtp) REVERT: E 125 GLN cc_start: 0.8944 (mt0) cc_final: 0.8716 (mt0) REVERT: F 30 THR cc_start: 0.9157 (p) cc_final: 0.8846 (t) REVERT: F 31 LYS cc_start: 0.9206 (ttpp) cc_final: 0.8950 (tttm) REVERT: F 45 ARG cc_start: 0.8926 (mtp85) cc_final: 0.8163 (mtm-85) REVERT: F 51 TYR cc_start: 0.8981 (m-80) cc_final: 0.8373 (m-80) REVERT: F 55 ARG cc_start: 0.9367 (mtt90) cc_final: 0.8389 (mtt90) REVERT: F 98 TYR cc_start: 0.9499 (m-10) cc_final: 0.8933 (m-80) REVERT: G 29 ARG cc_start: 0.9273 (tpp80) cc_final: 0.8970 (ttm-80) REVERT: G 42 ARG cc_start: 0.9172 (ptm-80) cc_final: 0.8916 (ptm-80) REVERT: G 56 GLU cc_start: 0.8882 (tm-30) cc_final: 0.8410 (tt0) REVERT: G 57 TYR cc_start: 0.9278 (t80) cc_final: 0.8819 (t80) REVERT: G 59 THR cc_start: 0.9730 (m) cc_final: 0.9399 (t) REVERT: G 68 ASN cc_start: 0.9237 (m-40) cc_final: 0.8822 (m-40) REVERT: G 71 ARG cc_start: 0.9194 (ttp80) cc_final: 0.8711 (ttp80) REVERT: G 73 ASN cc_start: 0.9514 (OUTLIER) cc_final: 0.9312 (t0) REVERT: G 84 GLN cc_start: 0.9539 (tp-100) cc_final: 0.8799 (tp-100) REVERT: G 89 ASN cc_start: 0.9342 (m-40) cc_final: 0.8844 (m110) REVERT: G 90 ASP cc_start: 0.8168 (t70) cc_final: 0.7924 (t0) REVERT: G 99 ARG cc_start: 0.8629 (mmm160) cc_final: 0.8323 (mmm-85) REVERT: H 37 TYR cc_start: 0.9423 (m-80) cc_final: 0.8615 (m-80) REVERT: H 64 SER cc_start: 0.9659 (t) cc_final: 0.9285 (t) REVERT: H 68 ASP cc_start: 0.9346 (t0) cc_final: 0.9091 (t0) REVERT: H 87 SER cc_start: 0.9346 (OUTLIER) cc_final: 0.8969 (p) REVERT: H 96 THR cc_start: 0.9683 (m) cc_final: 0.9317 (t) REVERT: K 55 MET cc_start: -0.0887 (mmt) cc_final: -0.1370 (tpp) REVERT: K 101 ARG cc_start: 0.7353 (mmt90) cc_final: 0.5728 (mmp80) REVERT: K 177 THR cc_start: 0.6912 (OUTLIER) cc_final: 0.6531 (p) REVERT: K 198 MET cc_start: 0.8338 (mmt) cc_final: 0.8007 (mmm) REVERT: L 54 ARG cc_start: 0.8777 (mmt-90) cc_final: 0.8560 (mmp80) outliers start: 48 outliers final: 40 residues processed: 512 average time/residue: 0.1418 time to fit residues: 103.1827 Evaluate side-chains 533 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 490 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 124 ILE 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 G residue 73 ASN 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 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 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 39 ASP Chi-restraints excluded: chain L residue 57 SER 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: 4.9990 chunk 12 optimal weight: 0.5980 chunk 126 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 109 optimal weight: 40.0000 chunk 95 optimal weight: 10.0000 chunk 21 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN G 104 GLN H 63 ASN ** K 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 25 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.105320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.066231 restraints weight = 42234.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.068299 restraints weight = 17336.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.069547 restraints weight = 10939.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.070227 restraints weight = 8612.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.070565 restraints weight = 7679.620| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3083 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3083 r_free = 0.3083 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3083 r_free = 0.3083 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3083 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.4178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 16075 Z= 0.166 Angle : 0.766 9.943 22999 Z= 0.419 Chirality : 0.047 0.340 2615 Planarity : 0.005 0.043 1909 Dihedral : 29.713 169.300 4479 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 5.07 % Allowed : 37.78 % Favored : 57.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.24), residues: 1139 helix: 0.87 (0.19), residues: 690 sheet: -1.06 (0.55), residues: 80 loop : -1.15 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 74 TYR 0.053 0.002 TYR H 83 PHE 0.020 0.002 PHE K 257 TRP 0.008 0.001 TRP K 89 HIS 0.009 0.001 HIS L 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.17 (16075) covalent geometry : angle 0.76579 / 0.42 (22999) hydrogen bonds : bond 0.04339 / 2.80 ( 887) hydrogen bonds : angle 3.91335 / 2.71 ( 2276) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3747.87 seconds wall clock time: 64 minutes 59.51 seconds (3899.51 seconds total)