Starting phenix.real_space_refine on Mon Aug 25 18:25:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x43_38041/08_2025/8x43_38041_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x43_38041/08_2025/8x43_38041.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x43_38041/08_2025/8x43_38041.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x43_38041/08_2025/8x43_38041.map" model { file = "/net/cci-nas-00/data/ceres_data/8x43_38041/08_2025/8x43_38041_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x43_38041/08_2025/8x43_38041_neut_trim.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 6 Type Number sf(0) Gaussians S 88 5.16 5 C 9804 2.51 5 N 2572 2.21 5 O 2712 1.98 5 F 4 1.80 5 H 14984 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30164 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 5389 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 6, 'TRANS': 320} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2129 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 5389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 5389 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 6, 'TRANS': 320} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2129 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "E" Number of atoms: 5389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 5389 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 6, 'TRANS': 320} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2129 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "G" Number of atoms: 5389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 5389 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 6, 'TRANS': 320} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 2129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2129 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'7Q0': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'7Q0': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'7Q0': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'7Q0': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.06, per 1000 atoms: 0.20 Number of scatterers: 30164 At special positions: 0 Unit cell: (125.55, 125.55, 120.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 88 16.00 F 4 9.00 O 2712 8.00 N 2572 7.00 C 9804 6.00 H 14984 1.00 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: 2.89 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 953.7 nanoseconds 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3496 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 4 sheets defined 83.4% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 70 through 86 Processing helix chain 'A' and resid 91 through 115 removed outlier: 3.896A pdb=" N TYR A 95 " --> pdb=" O TRP A 91 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE A 115 " --> pdb=" O VAL A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 148 removed outlier: 4.016A pdb=" N ILE A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 151 No H-bonds generated for 'chain 'A' and resid 149 through 151' Processing helix chain 'A' and resid 155 through 165 Processing helix chain 'A' and resid 166 through 182 Processing helix chain 'A' and resid 196 through 211 Processing helix chain 'A' and resid 215 through 228 Processing helix chain 'A' and resid 228 through 255 Processing helix chain 'A' and resid 263 through 276 Processing helix chain 'A' and resid 287 through 330 removed outlier: 4.165A pdb=" N ILE A 300 " --> pdb=" O THR A 296 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N SER A 303 " --> pdb=" O LEU A 299 " (cutoff:3.500A) Proline residue: A 308 - end of helix removed outlier: 4.055A pdb=" N HIS A 328 " --> pdb=" O HIS A 324 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N PHE A 329 " --> pdb=" O ARG A 325 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLU A 330 " --> pdb=" O GLN A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 350 removed outlier: 3.645A pdb=" N ALA A 336 " --> pdb=" O ARG A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 560 Processing helix chain 'A' and resid 563 through 595 removed outlier: 4.034A pdb=" N VAL A 567 " --> pdb=" O ASP A 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 21 Processing helix chain 'B' and resid 29 through 41 Processing helix chain 'B' and resid 45 through 57 Processing helix chain 'B' and resid 65 through 75 removed outlier: 3.838A pdb=" N ARG B 75 " --> pdb=" O THR B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'B' and resid 102 through 113 Processing helix chain 'B' and resid 118 through 130 removed outlier: 3.748A pdb=" N VAL B 122 " --> pdb=" O THR B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 148 Processing helix chain 'C' and resid 71 through 86 Processing helix chain 'C' and resid 91 through 115 removed outlier: 3.897A pdb=" N TYR C 95 " --> pdb=" O TRP C 91 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE C 115 " --> pdb=" O VAL C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 148 removed outlier: 4.015A pdb=" N ILE C 128 " --> pdb=" O GLY C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 151 No H-bonds generated for 'chain 'C' and resid 149 through 151' Processing helix chain 'C' and resid 155 through 165 Processing helix chain 'C' and resid 166 through 182 Processing helix chain 'C' and resid 196 through 211 Processing helix chain 'C' and resid 215 through 228 Processing helix chain 'C' and resid 228 through 255 Processing helix chain 'C' and resid 263 through 276 Processing helix chain 'C' and resid 287 through 330 removed outlier: 4.165A pdb=" N ILE C 300 " --> pdb=" O THR C 296 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N SER C 303 " --> pdb=" O LEU C 299 " (cutoff:3.500A) Proline residue: C 308 - end of helix removed outlier: 4.071A pdb=" N HIS C 328 " --> pdb=" O HIS C 324 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N PHE C 329 " --> pdb=" O ARG C 325 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU C 330 " --> pdb=" O GLN C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 350 removed outlier: 3.683A pdb=" N ALA C 336 " --> pdb=" O ARG C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 560 Processing helix chain 'C' and resid 563 through 595 removed outlier: 3.953A pdb=" N VAL C 567 " --> pdb=" O ASP C 563 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 21 Processing helix chain 'D' and resid 29 through 41 Processing helix chain 'D' and resid 45 through 57 Processing helix chain 'D' and resid 65 through 74 Processing helix chain 'D' and resid 82 through 94 Processing helix chain 'D' and resid 102 through 113 Processing helix chain 'D' and resid 118 through 130 removed outlier: 3.751A pdb=" N VAL D 122 " --> pdb=" O THR D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 148 Processing helix chain 'E' and resid 71 through 86 Processing helix chain 'E' and resid 91 through 115 removed outlier: 3.895A pdb=" N TYR E 95 " --> pdb=" O TRP E 91 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE E 115 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 148 removed outlier: 4.018A pdb=" N ILE E 128 " --> pdb=" O GLY E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 151 No H-bonds generated for 'chain 'E' and resid 149 through 151' Processing helix chain 'E' and resid 155 through 165 Processing helix chain 'E' and resid 166 through 182 Processing helix chain 'E' and resid 196 through 211 Processing helix chain 'E' and resid 215 through 228 Processing helix chain 'E' and resid 228 through 255 Processing helix chain 'E' and resid 263 through 276 Processing helix chain 'E' and resid 287 through 327 removed outlier: 4.168A pdb=" N ILE E 300 " --> pdb=" O THR E 296 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N SER E 303 " --> pdb=" O LEU E 299 " (cutoff:3.500A) Proline residue: E 308 - end of helix Processing helix chain 'E' and resid 332 through 350 removed outlier: 3.736A pdb=" N ALA E 336 " --> pdb=" O ARG E 332 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN E 350 " --> pdb=" O PHE E 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 539 through 560 Processing helix chain 'E' and resid 563 through 595 removed outlier: 4.064A pdb=" N VAL E 567 " --> pdb=" O ASP E 563 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 21 Processing helix chain 'F' and resid 29 through 41 Processing helix chain 'F' and resid 45 through 57 Processing helix chain 'F' and resid 65 through 74 Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'F' and resid 102 through 113 Processing helix chain 'F' and resid 118 through 130 removed outlier: 3.704A pdb=" N VAL F 122 " --> pdb=" O THR F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 148 Processing helix chain 'G' and resid 71 through 86 Processing helix chain 'G' and resid 91 through 115 removed outlier: 3.900A pdb=" N TYR G 95 " --> pdb=" O TRP G 91 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE G 115 " --> pdb=" O VAL G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 148 removed outlier: 4.033A pdb=" N ILE G 128 " --> pdb=" O GLY G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 149 through 151 No H-bonds generated for 'chain 'G' and resid 149 through 151' Processing helix chain 'G' and resid 155 through 165 Processing helix chain 'G' and resid 166 through 182 Processing helix chain 'G' and resid 196 through 211 Processing helix chain 'G' and resid 215 through 228 Processing helix chain 'G' and resid 228 through 255 Processing helix chain 'G' and resid 263 through 276 Processing helix chain 'G' and resid 287 through 330 removed outlier: 4.168A pdb=" N ILE G 300 " --> pdb=" O THR G 296 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N SER G 303 " --> pdb=" O LEU G 299 " (cutoff:3.500A) Proline residue: G 308 - end of helix removed outlier: 4.055A pdb=" N HIS G 328 " --> pdb=" O HIS G 324 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N PHE G 329 " --> pdb=" O ARG G 325 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU G 330 " --> pdb=" O GLN G 326 " (cutoff:3.500A) Processing helix chain 'G' and resid 332 through 350 removed outlier: 3.676A pdb=" N ALA G 336 " --> pdb=" O ARG G 332 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN G 350 " --> pdb=" O PHE G 346 " (cutoff:3.500A) Processing helix chain 'G' and resid 539 through 560 Processing helix chain 'G' and resid 563 through 595 removed outlier: 3.965A pdb=" N VAL G 567 " --> pdb=" O ASP G 563 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 21 Processing helix chain 'H' and resid 29 through 41 Processing helix chain 'H' and resid 45 through 57 Processing helix chain 'H' and resid 65 through 75 removed outlier: 3.854A pdb=" N ARG H 75 " --> pdb=" O THR H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 94 Processing helix chain 'H' and resid 102 through 113 removed outlier: 3.543A pdb=" N LEU H 113 " --> pdb=" O VAL H 109 " (cutoff:3.500A) Processing helix chain 'H' and resid 118 through 130 removed outlier: 3.640A pdb=" N VAL H 122 " --> pdb=" O THR H 118 " (cutoff:3.500A) Processing helix chain 'H' and resid 139 through 148 Processing sheet with id=AA1, first strand: chain 'B' and resid 100 through 101 Processing sheet with id=AA2, first strand: chain 'D' and resid 100 through 101 Processing sheet with id=AA3, first strand: chain 'F' and resid 100 through 101 Processing sheet with id=AA4, first strand: chain 'H' and resid 100 through 101 1170 hydrogen bonds defined for protein. 3498 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.64 Time building geometry restraints manager: 3.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 14956 1.03 - 1.23: 39 1.23 - 1.42: 6685 1.42 - 1.62: 8660 1.62 - 1.81: 148 Bond restraints: 30488 Sorted by residual: bond pdb=" C13 7Q0 C 801 " pdb=" N1 7Q0 C 801 " ideal model delta sigma weight residual 1.354 1.443 -0.089 2.00e-02 2.50e+03 1.97e+01 bond pdb=" C13 7Q0 E 801 " pdb=" N1 7Q0 E 801 " ideal model delta sigma weight residual 1.354 1.442 -0.088 2.00e-02 2.50e+03 1.95e+01 bond pdb=" C13 7Q0 G 801 " pdb=" N1 7Q0 G 801 " ideal model delta sigma weight residual 1.354 1.442 -0.088 2.00e-02 2.50e+03 1.95e+01 bond pdb=" C13 7Q0 A 801 " pdb=" N1 7Q0 A 801 " ideal model delta sigma weight residual 1.354 1.442 -0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" C8 7Q0 A 801 " pdb=" N2 7Q0 A 801 " ideal model delta sigma weight residual 1.370 1.447 -0.077 2.00e-02 2.50e+03 1.46e+01 ... (remaining 30483 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 53158 1.37 - 2.74: 1546 2.74 - 4.11: 119 4.11 - 5.47: 8 5.47 - 6.84: 5 Bond angle restraints: 54836 Sorted by residual: angle pdb=" CB MET D 125 " pdb=" CG MET D 125 " pdb=" SD MET D 125 " ideal model delta sigma weight residual 112.70 119.54 -6.84 3.00e+00 1.11e-01 5.20e+00 angle pdb=" CB MET B 125 " pdb=" CG MET B 125 " pdb=" SD MET B 125 " ideal model delta sigma weight residual 112.70 119.49 -6.79 3.00e+00 1.11e-01 5.12e+00 angle pdb=" CB MET H 125 " pdb=" CG MET H 125 " pdb=" SD MET H 125 " ideal model delta sigma weight residual 112.70 119.45 -6.75 3.00e+00 1.11e-01 5.06e+00 angle pdb=" N ARG C 213 " pdb=" CA ARG C 213 " pdb=" CB ARG C 213 " ideal model delta sigma weight residual 113.65 110.47 3.18 1.47e+00 4.63e-01 4.68e+00 angle pdb=" N ARG G 213 " pdb=" CA ARG G 213 " pdb=" CB ARG G 213 " ideal model delta sigma weight residual 113.65 110.48 3.17 1.47e+00 4.63e-01 4.66e+00 ... (remaining 54831 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 12358 17.90 - 35.81: 1303 35.81 - 53.71: 402 53.71 - 71.61: 91 71.61 - 89.52: 18 Dihedral angle restraints: 14172 sinusoidal: 7544 harmonic: 6628 Sorted by residual: dihedral pdb=" CA THR B 111 " pdb=" C THR B 111 " pdb=" N ASN B 112 " pdb=" CA ASN B 112 " ideal model delta harmonic sigma weight residual -180.00 -161.49 -18.51 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA THR D 111 " pdb=" C THR D 111 " pdb=" N ASN D 112 " pdb=" CA ASN D 112 " ideal model delta harmonic sigma weight residual -180.00 -161.65 -18.35 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA THR F 111 " pdb=" C THR F 111 " pdb=" N ASN F 112 " pdb=" CA ASN F 112 " ideal model delta harmonic sigma weight residual -180.00 -161.76 -18.24 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 14169 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1629 0.032 - 0.064: 491 0.064 - 0.096: 138 0.096 - 0.129: 29 0.129 - 0.161: 1 Chirality restraints: 2288 Sorted by residual: chirality pdb=" CA ILE F 101 " pdb=" N ILE F 101 " pdb=" C ILE F 101 " pdb=" CB ILE F 101 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.46e-01 chirality pdb=" CB THR G 296 " pdb=" CA THR G 296 " pdb=" OG1 THR G 296 " pdb=" CG2 THR G 296 " both_signs ideal model delta sigma weight residual False 2.55 2.43 0.12 2.00e-01 2.50e+01 3.75e-01 chirality pdb=" CB THR A 296 " pdb=" CA THR A 296 " pdb=" OG1 THR A 296 " pdb=" CG2 THR A 296 " both_signs ideal model delta sigma weight residual False 2.55 2.43 0.12 2.00e-01 2.50e+01 3.63e-01 ... (remaining 2285 not shown) Planarity restraints: 4468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG E 560 " -0.033 5.00e-02 4.00e+02 4.95e-02 3.92e+00 pdb=" N PRO E 561 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO E 561 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 561 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG G 560 " 0.032 5.00e-02 4.00e+02 4.90e-02 3.84e+00 pdb=" N PRO G 561 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO G 561 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO G 561 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR G 298 " -0.007 2.00e-02 2.50e+03 1.31e-02 1.72e+00 pdb=" C THR G 298 " 0.023 2.00e-02 2.50e+03 pdb=" O THR G 298 " -0.008 2.00e-02 2.50e+03 pdb=" N LEU G 299 " -0.008 2.00e-02 2.50e+03 ... (remaining 4465 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 1956 2.18 - 2.79: 61777 2.79 - 3.39: 89225 3.39 - 4.00: 107061 4.00 - 4.60: 168885 Nonbonded interactions: 428904 Sorted by model distance: nonbonded pdb=" O ARG B 91 " pdb="HH11 ARG B 91 " model vdw 1.580 2.450 nonbonded pdb=" O ARG H 91 " pdb="HH11 ARG H 91 " model vdw 1.580 2.450 nonbonded pdb=" HH TYR A 95 " pdb=" OE1 GLU A 140 " model vdw 1.582 2.450 nonbonded pdb=" HH TYR G 95 " pdb=" OE1 GLU G 140 " model vdw 1.585 2.450 nonbonded pdb=" HH TYR E 95 " pdb=" OE1 GLU E 140 " model vdw 1.586 2.450 ... (remaining 428899 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 0.860 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: 0.190 Extract box with map and model: 0.430 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 29.740 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6808 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 15504 Z= 0.240 Angle : 0.564 6.842 20912 Z= 0.313 Chirality : 0.034 0.161 2288 Planarity : 0.003 0.050 2636 Dihedral : 17.005 89.519 5604 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.38 % Allowed : 23.36 % Favored : 76.26 % 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 aren not related in a simple way. whole: 2.23 (0.20), residues: 1848 helix: 2.03 (0.13), residues: 1468 sheet: None (None), residues: 0 loop : -0.70 (0.36), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 581 TYR 0.010 0.001 TYR G 74 PHE 0.017 0.001 PHE C 329 TRP 0.008 0.001 TRP G 91 HIS 0.003 0.001 HIS C 228 Details of bonding type rmsd covalent geometry : bond 0.00494 (15504) covalent geometry : angle 0.56355 (20912) hydrogen bonds : bond 0.09558 ( 1170) hydrogen bonds : angle 5.22496 ( 3498) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 315 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 309 time to evaluate : 0.900 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ARG cc_start: 0.6289 (ptp90) cc_final: 0.5819 (ptm-80) REVERT: A 123 GLU cc_start: 0.7050 (tp30) cc_final: 0.6217 (tt0) REVERT: A 322 GLU cc_start: 0.7715 (tp30) cc_final: 0.7082 (mt-10) REVERT: A 334 ASN cc_start: 0.8055 (m-40) cc_final: 0.7816 (m110) REVERT: A 342 SER cc_start: 0.6464 (OUTLIER) cc_final: 0.6034 (m) REVERT: A 553 ARG cc_start: 0.7602 (mpt180) cc_final: 0.7180 (tpt-90) REVERT: A 578 MET cc_start: 0.7306 (ptt) cc_final: 0.6969 (mmm) REVERT: B 73 MET cc_start: -0.1826 (mmm) cc_final: -0.2348 (ttm) REVERT: B 87 ARG cc_start: 0.5032 (tpp80) cc_final: 0.4823 (tmt-80) REVERT: B 106 LEU cc_start: 0.7011 (tp) cc_final: 0.6774 (tm) REVERT: B 107 ARG cc_start: 0.3520 (mtt90) cc_final: 0.3270 (tpp-160) REVERT: B 134 ASP cc_start: 0.5168 (p0) cc_final: 0.4149 (m-30) REVERT: C 89 ARG cc_start: 0.6196 (ptp90) cc_final: 0.5809 (ptm-80) REVERT: C 123 GLU cc_start: 0.7047 (tp30) cc_final: 0.6209 (tt0) REVERT: C 322 GLU cc_start: 0.7743 (tp30) cc_final: 0.7124 (mt-10) REVERT: C 334 ASN cc_start: 0.8006 (m-40) cc_final: 0.7788 (m110) REVERT: C 342 SER cc_start: 0.6421 (OUTLIER) cc_final: 0.5993 (m) REVERT: D 73 MET cc_start: -0.2785 (mmt) cc_final: -0.3317 (ttm) REVERT: D 106 LEU cc_start: 0.6998 (tp) cc_final: 0.6789 (tm) REVERT: D 134 ASP cc_start: 0.5189 (p0) cc_final: 0.4157 (m-30) REVERT: D 142 PHE cc_start: 0.6645 (t80) cc_final: 0.6220 (t80) REVERT: D 146 MET cc_start: 0.6280 (mmm) cc_final: 0.5629 (mmm) REVERT: E 89 ARG cc_start: 0.6189 (ptp90) cc_final: 0.5769 (ptm-80) REVERT: E 123 GLU cc_start: 0.7109 (tp30) cc_final: 0.6259 (tt0) REVERT: E 152 CYS cc_start: 0.7820 (m) cc_final: 0.7378 (t) REVERT: E 322 GLU cc_start: 0.7714 (tp30) cc_final: 0.7054 (mt-10) REVERT: E 334 ASN cc_start: 0.8013 (m-40) cc_final: 0.7752 (m110) REVERT: E 342 SER cc_start: 0.6372 (OUTLIER) cc_final: 0.5951 (m) REVERT: F 72 MET cc_start: -0.0260 (ptt) cc_final: -0.0462 (tmm) REVERT: F 73 MET cc_start: -0.1943 (mmm) cc_final: -0.2449 (ttm) REVERT: F 134 ASP cc_start: 0.5021 (p0) cc_final: 0.4005 (m-30) REVERT: F 142 PHE cc_start: 0.6706 (t80) cc_final: 0.6354 (t80) REVERT: F 146 MET cc_start: 0.6143 (mmm) cc_final: 0.5491 (mmm) REVERT: G 89 ARG cc_start: 0.6246 (ptp90) cc_final: 0.5680 (ptm-80) REVERT: G 123 GLU cc_start: 0.7091 (tp30) cc_final: 0.6250 (tt0) REVERT: G 152 CYS cc_start: 0.7893 (m) cc_final: 0.7408 (t) REVERT: G 322 GLU cc_start: 0.7697 (tp30) cc_final: 0.7225 (mt-10) REVERT: G 334 ASN cc_start: 0.7985 (m-40) cc_final: 0.7698 (m110) REVERT: G 342 SER cc_start: 0.6355 (OUTLIER) cc_final: 0.5946 (m) REVERT: G 553 ARG cc_start: 0.7587 (mpt180) cc_final: 0.7038 (tpp80) REVERT: G 578 MET cc_start: 0.6921 (ptt) cc_final: 0.6586 (mmm) REVERT: H 72 MET cc_start: -0.0290 (ptt) cc_final: -0.0716 (tmm) REVERT: H 73 MET cc_start: -0.1817 (tpt) cc_final: -0.2833 (ttm) REVERT: H 87 ARG cc_start: 0.5257 (tpp80) cc_final: 0.4956 (tmt-80) REVERT: H 134 ASP cc_start: 0.5129 (p0) cc_final: 0.4089 (m-30) REVERT: H 142 PHE cc_start: 0.6759 (t80) cc_final: 0.6537 (t80) outliers start: 6 outliers final: 4 residues processed: 314 average time/residue: 1.4829 time to fit residues: 510.3985 Evaluate side-chains 252 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 244 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain C residue 577 ASP Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain G residue 342 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.0370 chunk 130 optimal weight: 50.0000 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 0.0770 overall best weight: 0.9820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 144 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4795 r_free = 0.4795 target = 0.228790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.129797 restraints weight = 55921.330| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.31 r_work: 0.3452 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15504 Z= 0.130 Angle : 0.500 5.310 20912 Z= 0.269 Chirality : 0.033 0.119 2288 Planarity : 0.003 0.032 2636 Dihedral : 4.340 50.594 2084 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.96 % Allowed : 23.11 % Favored : 74.94 % 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 aren not related in a simple way. whole: 2.33 (0.20), residues: 1848 helix: 2.14 (0.13), residues: 1480 sheet: None (None), residues: 0 loop : -1.00 (0.34), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 144 TYR 0.008 0.001 TYR G 74 PHE 0.010 0.001 PHE E 329 TRP 0.006 0.001 TRP E 270 HIS 0.004 0.001 HIS H 108 Details of bonding type rmsd covalent geometry : bond 0.00279 (15504) covalent geometry : angle 0.49979 (20912) hydrogen bonds : bond 0.03981 ( 1170) hydrogen bonds : angle 4.42462 ( 3498) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 292 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 261 time to evaluate : 0.841 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: 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: 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 89 ARG cc_start: 0.6273 (ptp90) cc_final: 0.5895 (ptm-80) REVERT: A 123 GLU cc_start: 0.7116 (tp30) cc_final: 0.6523 (tt0) REVERT: A 322 GLU cc_start: 0.7796 (tp30) cc_final: 0.7523 (mt-10) REVERT: A 334 ASN cc_start: 0.7913 (m-40) cc_final: 0.7646 (m110) REVERT: A 342 SER cc_start: 0.6185 (OUTLIER) cc_final: 0.5610 (m) REVERT: A 544 CYS cc_start: 0.5282 (OUTLIER) cc_final: 0.3944 (m) REVERT: A 553 ARG cc_start: 0.7659 (mpt180) cc_final: 0.7098 (tpt-90) REVERT: A 578 MET cc_start: 0.7472 (ptt) cc_final: 0.6971 (mmm) REVERT: B 72 MET cc_start: 0.1692 (tmm) cc_final: 0.1308 (tmm) REVERT: B 107 ARG cc_start: 0.3331 (mtt90) cc_final: 0.3111 (tpp-160) REVERT: B 134 ASP cc_start: 0.4829 (p0) cc_final: 0.3663 (t0) REVERT: C 89 ARG cc_start: 0.6268 (ptp90) cc_final: 0.5923 (ptm-80) REVERT: C 123 GLU cc_start: 0.7130 (tp30) cc_final: 0.6536 (tt0) REVERT: C 214 ARG cc_start: 0.6452 (OUTLIER) cc_final: 0.6097 (ptt180) REVERT: C 322 GLU cc_start: 0.7840 (tp30) cc_final: 0.7610 (mt-10) REVERT: C 334 ASN cc_start: 0.7891 (m-40) cc_final: 0.7617 (m110) REVERT: C 342 SER cc_start: 0.6234 (OUTLIER) cc_final: 0.5681 (m) REVERT: C 544 CYS cc_start: 0.4917 (OUTLIER) cc_final: 0.3622 (m) REVERT: C 553 ARG cc_start: 0.7642 (mpt180) cc_final: 0.7074 (tpt-90) REVERT: D 72 MET cc_start: 0.1581 (tmm) cc_final: 0.1253 (tmm) REVERT: D 73 MET cc_start: -0.2867 (mmt) cc_final: -0.3213 (ttm) REVERT: D 77 MET cc_start: 0.1476 (OUTLIER) cc_final: 0.1115 (mmt) REVERT: D 106 LEU cc_start: 0.7084 (OUTLIER) cc_final: 0.6792 (tm) REVERT: D 134 ASP cc_start: 0.4873 (p0) cc_final: 0.3669 (t0) REVERT: D 142 PHE cc_start: 0.6927 (t80) cc_final: 0.6628 (t80) REVERT: D 146 MET cc_start: 0.6333 (mmm) cc_final: 0.6003 (mmm) REVERT: E 123 GLU cc_start: 0.7140 (tp30) cc_final: 0.6548 (tt0) REVERT: E 152 CYS cc_start: 0.7833 (m) cc_final: 0.7289 (t) REVERT: E 176 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.7144 (mp) REVERT: E 214 ARG cc_start: 0.6657 (OUTLIER) cc_final: 0.6403 (ptt180) REVERT: E 322 GLU cc_start: 0.7817 (tp30) cc_final: 0.7610 (mt-10) REVERT: E 334 ASN cc_start: 0.7977 (m-40) cc_final: 0.7690 (m110) REVERT: E 342 SER cc_start: 0.6162 (OUTLIER) cc_final: 0.5702 (m) REVERT: E 544 CYS cc_start: 0.5057 (OUTLIER) cc_final: 0.3644 (m) REVERT: E 553 ARG cc_start: 0.7675 (mpt180) cc_final: 0.7143 (tpt-90) REVERT: E 570 GLN cc_start: 0.7985 (tm-30) cc_final: 0.7583 (tm-30) REVERT: F 72 MET cc_start: 0.0153 (ptt) cc_final: -0.0185 (tmm) REVERT: F 73 MET cc_start: -0.1957 (mmm) cc_final: -0.2474 (ttm) REVERT: F 77 MET cc_start: 0.0868 (OUTLIER) cc_final: 0.0505 (mtt) REVERT: F 134 ASP cc_start: 0.4799 (p0) cc_final: 0.3647 (t0) REVERT: F 142 PHE cc_start: 0.6923 (t80) cc_final: 0.6512 (t80) REVERT: F 145 MET cc_start: 0.5356 (ttp) cc_final: 0.5151 (ttp) REVERT: F 146 MET cc_start: 0.6444 (mmm) cc_final: 0.5922 (mmm) REVERT: G 89 ARG cc_start: 0.6400 (ptp90) cc_final: 0.5999 (ptm-80) REVERT: G 123 GLU cc_start: 0.7123 (tp30) cc_final: 0.6531 (tt0) REVERT: G 152 CYS cc_start: 0.7995 (m) cc_final: 0.7445 (t) REVERT: G 214 ARG cc_start: 0.6636 (OUTLIER) cc_final: 0.6235 (ptt180) REVERT: G 322 GLU cc_start: 0.7992 (tp30) cc_final: 0.7679 (mt-10) REVERT: G 334 ASN cc_start: 0.7924 (m-40) cc_final: 0.7640 (m110) REVERT: G 342 SER cc_start: 0.6324 (OUTLIER) cc_final: 0.5821 (m) REVERT: G 544 CYS cc_start: 0.5096 (OUTLIER) cc_final: 0.3858 (m) REVERT: G 553 ARG cc_start: 0.7650 (mpt180) cc_final: 0.7125 (tpt-90) REVERT: H 72 MET cc_start: -0.0255 (OUTLIER) cc_final: -0.0705 (tmm) REVERT: H 73 MET cc_start: -0.1665 (tpt) cc_final: -0.2637 (ttm) REVERT: H 134 ASP cc_start: 0.4844 (p0) cc_final: 0.3712 (t0) outliers start: 31 outliers final: 4 residues processed: 279 average time/residue: 1.2818 time to fit residues: 398.2848 Evaluate side-chains 263 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 243 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain C residue 544 CYS Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 214 ARG Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain E residue 544 CYS Chi-restraints excluded: chain E residue 579 LEU Chi-restraints excluded: chain F residue 77 MET Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain G residue 214 ARG Chi-restraints excluded: chain G residue 342 SER Chi-restraints excluded: chain G residue 544 CYS Chi-restraints excluded: chain H residue 72 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 19 optimal weight: 1.9990 chunk 76 optimal weight: 20.0000 chunk 31 optimal weight: 9.9990 chunk 41 optimal weight: 9.9990 chunk 114 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 119 optimal weight: 20.0000 chunk 110 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 83 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4802 r_free = 0.4802 target = 0.228237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.130534 restraints weight = 56207.933| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 2.10 r_work: 0.3400 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15504 Z= 0.189 Angle : 0.509 5.622 20912 Z= 0.276 Chirality : 0.034 0.128 2288 Planarity : 0.004 0.042 2636 Dihedral : 4.205 50.847 2078 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.83 % Allowed : 23.86 % Favored : 74.31 % 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 aren not related in a simple way. whole: 2.32 (0.19), residues: 1848 helix: 2.14 (0.13), residues: 1480 sheet: None (None), residues: 0 loop : -1.01 (0.34), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 87 TYR 0.013 0.001 TYR A 74 PHE 0.013 0.001 PHE E 100 TRP 0.007 0.001 TRP A 91 HIS 0.003 0.001 HIS H 108 Details of bonding type rmsd covalent geometry : bond 0.00421 (15504) covalent geometry : angle 0.50875 (20912) hydrogen bonds : bond 0.04039 ( 1170) hydrogen bonds : angle 4.35994 ( 3498) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 258 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 229 time to evaluate : 0.839 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: 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: 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 89 ARG cc_start: 0.6479 (ptp90) cc_final: 0.6046 (ptm-80) REVERT: A 123 GLU cc_start: 0.7069 (tp30) cc_final: 0.6433 (tt0) REVERT: A 322 GLU cc_start: 0.7868 (tp30) cc_final: 0.7598 (mt-10) REVERT: A 334 ASN cc_start: 0.7975 (m-40) cc_final: 0.7722 (m110) REVERT: A 342 SER cc_start: 0.6141 (OUTLIER) cc_final: 0.5556 (m) REVERT: A 544 CYS cc_start: 0.5314 (OUTLIER) cc_final: 0.3849 (m) REVERT: A 553 ARG cc_start: 0.7587 (mpt180) cc_final: 0.6985 (tpt-90) REVERT: A 578 MET cc_start: 0.7032 (ptt) cc_final: 0.6815 (mmm) REVERT: B 91 ARG cc_start: 0.8434 (ptm160) cc_final: 0.8229 (ptm160) REVERT: B 107 ARG cc_start: 0.3445 (mtt90) cc_final: 0.3149 (tpp-160) REVERT: B 134 ASP cc_start: 0.4857 (p0) cc_final: 0.3650 (t0) REVERT: C 89 ARG cc_start: 0.6377 (ptp90) cc_final: 0.5963 (ptm-80) REVERT: C 123 GLU cc_start: 0.7105 (tp30) cc_final: 0.6471 (tt0) REVERT: C 214 ARG cc_start: 0.6452 (OUTLIER) cc_final: 0.6244 (ptt180) REVERT: C 322 GLU cc_start: 0.7970 (tp30) cc_final: 0.7659 (mt-10) REVERT: C 334 ASN cc_start: 0.7942 (m-40) cc_final: 0.7705 (m110) REVERT: C 342 SER cc_start: 0.6187 (OUTLIER) cc_final: 0.5637 (m) REVERT: C 544 CYS cc_start: 0.4674 (OUTLIER) cc_final: 0.3393 (m) REVERT: C 553 ARG cc_start: 0.7696 (mpt180) cc_final: 0.7110 (tpt-90) REVERT: D 72 MET cc_start: 0.1469 (tmm) cc_final: 0.1228 (tmm) REVERT: D 73 MET cc_start: -0.2953 (mmt) cc_final: -0.3157 (ttm) REVERT: D 134 ASP cc_start: 0.4867 (p0) cc_final: 0.3676 (t0) REVERT: D 142 PHE cc_start: 0.6938 (t80) cc_final: 0.6613 (t80) REVERT: D 146 MET cc_start: 0.6425 (mmm) cc_final: 0.6217 (mmm) REVERT: E 123 GLU cc_start: 0.7088 (tp30) cc_final: 0.6452 (tt0) REVERT: E 176 LEU cc_start: 0.7480 (OUTLIER) cc_final: 0.7264 (mp) REVERT: E 322 GLU cc_start: 0.7862 (tp30) cc_final: 0.7532 (mt-10) REVERT: E 334 ASN cc_start: 0.7996 (m-40) cc_final: 0.7710 (m110) REVERT: E 342 SER cc_start: 0.6059 (OUTLIER) cc_final: 0.5582 (m) REVERT: E 544 CYS cc_start: 0.5198 (OUTLIER) cc_final: 0.3784 (m) REVERT: E 553 ARG cc_start: 0.7708 (mpt180) cc_final: 0.7137 (tpt-90) REVERT: F 72 MET cc_start: -0.0027 (ptt) cc_final: -0.0397 (tmm) REVERT: F 73 MET cc_start: -0.2253 (mmm) cc_final: -0.2499 (ttm) REVERT: F 134 ASP cc_start: 0.4843 (p0) cc_final: 0.3672 (t0) REVERT: F 142 PHE cc_start: 0.6971 (t80) cc_final: 0.6628 (t80) REVERT: F 145 MET cc_start: 0.5317 (ttp) cc_final: 0.5115 (ttp) REVERT: F 146 MET cc_start: 0.6320 (mmm) cc_final: 0.5809 (mmm) REVERT: G 89 ARG cc_start: 0.6557 (ptp90) cc_final: 0.6129 (ptm-80) REVERT: G 123 GLU cc_start: 0.7080 (tp30) cc_final: 0.6448 (tt0) REVERT: G 214 ARG cc_start: 0.6414 (OUTLIER) cc_final: 0.6185 (ptt180) REVERT: G 322 GLU cc_start: 0.8034 (tp30) cc_final: 0.7702 (mt-10) REVERT: G 334 ASN cc_start: 0.7967 (m-40) cc_final: 0.7685 (m110) REVERT: G 342 SER cc_start: 0.6274 (OUTLIER) cc_final: 0.5756 (m) REVERT: G 544 CYS cc_start: 0.5103 (OUTLIER) cc_final: 0.3955 (m) REVERT: G 553 ARG cc_start: 0.7642 (mpt180) cc_final: 0.7110 (tpt-90) REVERT: H 72 MET cc_start: -0.0457 (OUTLIER) cc_final: -0.0799 (tmm) REVERT: H 73 MET cc_start: -0.1821 (tpt) cc_final: -0.2860 (ttm) REVERT: H 134 ASP cc_start: 0.4870 (p0) cc_final: 0.3688 (t0) outliers start: 29 outliers final: 5 residues processed: 246 average time/residue: 1.2902 time to fit residues: 352.6783 Evaluate side-chains 233 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 216 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain C residue 544 CYS Chi-restraints excluded: chain C residue 577 ASP Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain E residue 544 CYS Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain G residue 214 ARG Chi-restraints excluded: chain G residue 342 SER Chi-restraints excluded: chain G residue 544 CYS Chi-restraints excluded: chain H residue 72 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 1 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 179 optimal weight: 8.9990 chunk 86 optimal weight: 20.0000 chunk 46 optimal weight: 10.0000 chunk 174 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 44 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4752 r_free = 0.4752 target = 0.224626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.135598 restraints weight = 54018.117| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 3.46 r_work: 0.3367 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 15504 Z= 0.193 Angle : 0.510 5.811 20912 Z= 0.275 Chirality : 0.034 0.130 2288 Planarity : 0.004 0.034 2636 Dihedral : 4.321 51.013 2078 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.27 % Allowed : 23.42 % Favored : 74.31 % 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 aren not related in a simple way. whole: 2.45 (0.19), residues: 1848 helix: 2.22 (0.13), residues: 1480 sheet: None (None), residues: 0 loop : -0.93 (0.34), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 158 TYR 0.012 0.001 TYR A 74 PHE 0.016 0.001 PHE E 329 TRP 0.007 0.001 TRP G 91 HIS 0.003 0.001 HIS G 96 Details of bonding type rmsd covalent geometry : bond 0.00427 (15504) covalent geometry : angle 0.50965 (20912) hydrogen bonds : bond 0.03986 ( 1170) hydrogen bonds : angle 4.28543 ( 3498) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 265 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 229 time to evaluate : 0.850 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: 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 89 ARG cc_start: 0.6540 (ptp90) cc_final: 0.6092 (ptm-80) REVERT: A 123 GLU cc_start: 0.7148 (tp30) cc_final: 0.6127 (tm-30) REVERT: A 176 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7546 (tt) REVERT: A 322 GLU cc_start: 0.7911 (tp30) cc_final: 0.7655 (mt-10) REVERT: A 334 ASN cc_start: 0.7916 (m-40) cc_final: 0.7683 (m110) REVERT: A 342 SER cc_start: 0.6150 (OUTLIER) cc_final: 0.5589 (m) REVERT: A 544 CYS cc_start: 0.5263 (OUTLIER) cc_final: 0.3850 (m) REVERT: A 553 ARG cc_start: 0.7641 (mpt180) cc_final: 0.7019 (tpt-90) REVERT: A 578 MET cc_start: 0.6959 (ptt) cc_final: 0.6686 (mmm) REVERT: B 77 MET cc_start: 0.2168 (OUTLIER) cc_final: 0.1792 (mmt) REVERT: B 91 ARG cc_start: 0.8385 (ptm160) cc_final: 0.8159 (ptm-80) REVERT: B 107 ARG cc_start: 0.3446 (mtt90) cc_final: 0.3153 (tpp-160) REVERT: B 134 ASP cc_start: 0.5012 (p0) cc_final: 0.3744 (t0) REVERT: C 89 ARG cc_start: 0.6573 (ptp90) cc_final: 0.6078 (ptm-80) REVERT: C 123 GLU cc_start: 0.7183 (tp30) cc_final: 0.6167 (tm-30) REVERT: C 322 GLU cc_start: 0.8045 (tp30) cc_final: 0.7714 (mt-10) REVERT: C 334 ASN cc_start: 0.7914 (m-40) cc_final: 0.7680 (m110) REVERT: C 342 SER cc_start: 0.6280 (OUTLIER) cc_final: 0.5753 (m) REVERT: C 544 CYS cc_start: 0.4695 (OUTLIER) cc_final: 0.3430 (m) REVERT: C 553 ARG cc_start: 0.7680 (mpt180) cc_final: 0.7126 (tpt-90) REVERT: D 72 MET cc_start: 0.1672 (tmm) cc_final: 0.1270 (tmm) REVERT: D 73 MET cc_start: -0.2697 (mmt) cc_final: -0.2967 (ttt) REVERT: D 134 ASP cc_start: 0.5168 (p0) cc_final: 0.3841 (t0) REVERT: D 142 PHE cc_start: 0.6948 (t80) cc_final: 0.6571 (t80) REVERT: D 146 MET cc_start: 0.6444 (mmm) cc_final: 0.6210 (mmm) REVERT: E 89 ARG cc_start: 0.6535 (ptp90) cc_final: 0.6079 (ptm-80) REVERT: E 123 GLU cc_start: 0.7161 (tp30) cc_final: 0.6155 (tm-30) REVERT: E 176 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.7226 (mp) REVERT: E 322 GLU cc_start: 0.7921 (tp30) cc_final: 0.7606 (mt-10) REVERT: E 334 ASN cc_start: 0.7977 (m-40) cc_final: 0.7685 (m110) REVERT: E 342 SER cc_start: 0.6035 (OUTLIER) cc_final: 0.5525 (m) REVERT: E 544 CYS cc_start: 0.5068 (OUTLIER) cc_final: 0.3889 (m) REVERT: E 553 ARG cc_start: 0.7679 (mpt180) cc_final: 0.7089 (tpt-90) REVERT: E 570 GLN cc_start: 0.7781 (tm-30) cc_final: 0.7477 (tm-30) REVERT: F 72 MET cc_start: 0.0115 (ptt) cc_final: -0.0282 (tmm) REVERT: F 73 MET cc_start: -0.2173 (mmm) cc_final: -0.2482 (ttm) REVERT: F 134 ASP cc_start: 0.4910 (p0) cc_final: 0.3698 (t0) REVERT: F 142 PHE cc_start: 0.6925 (t80) cc_final: 0.6647 (t80) REVERT: F 145 MET cc_start: 0.5284 (ttp) cc_final: 0.5066 (ttp) REVERT: F 146 MET cc_start: 0.6349 (mmm) cc_final: 0.5972 (mmm) REVERT: G 83 ASN cc_start: 0.7680 (t0) cc_final: 0.7468 (m-40) REVERT: G 89 ARG cc_start: 0.6593 (ptp90) cc_final: 0.6095 (ptm-80) REVERT: G 123 GLU cc_start: 0.7156 (tp30) cc_final: 0.6155 (tm-30) REVERT: G 322 GLU cc_start: 0.8078 (tp30) cc_final: 0.7739 (mt-10) REVERT: G 334 ASN cc_start: 0.7971 (m-40) cc_final: 0.7691 (m110) REVERT: G 342 SER cc_start: 0.6194 (OUTLIER) cc_final: 0.5637 (m) REVERT: G 544 CYS cc_start: 0.5086 (OUTLIER) cc_final: 0.3970 (m) REVERT: G 546 MET cc_start: 0.5484 (OUTLIER) cc_final: 0.5233 (mmp) REVERT: G 553 ARG cc_start: 0.7647 (mpt180) cc_final: 0.7152 (tpt-90) REVERT: H 72 MET cc_start: -0.0420 (OUTLIER) cc_final: -0.0772 (tmm) REVERT: H 73 MET cc_start: -0.1796 (tpt) cc_final: -0.2828 (ttm) REVERT: H 134 ASP cc_start: 0.5090 (p0) cc_final: 0.3772 (t0) outliers start: 36 outliers final: 8 residues processed: 254 average time/residue: 1.2896 time to fit residues: 364.7480 Evaluate side-chains 234 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 213 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain B residue 77 MET Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain C residue 544 CYS Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain E residue 544 CYS Chi-restraints excluded: chain E residue 577 ASP Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain G residue 342 SER Chi-restraints excluded: chain G residue 544 CYS Chi-restraints excluded: chain G residue 546 MET Chi-restraints excluded: chain H residue 72 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 120 optimal weight: 10.0000 chunk 127 optimal weight: 10.0000 chunk 144 optimal weight: 0.7980 chunk 73 optimal weight: 20.0000 chunk 138 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 153 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 36 optimal weight: 30.0000 chunk 109 optimal weight: 0.5980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4789 r_free = 0.4789 target = 0.228424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.128460 restraints weight = 56301.531| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.31 r_work: 0.3420 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15504 Z= 0.130 Angle : 0.488 6.644 20912 Z= 0.258 Chirality : 0.033 0.123 2288 Planarity : 0.003 0.032 2636 Dihedral : 4.247 50.639 2078 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.40 % Allowed : 23.36 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.66 (0.19), residues: 1848 helix: 2.41 (0.13), residues: 1476 sheet: None (None), residues: 0 loop : -1.03 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 91 TYR 0.009 0.001 TYR A 74 PHE 0.012 0.001 PHE C 168 TRP 0.013 0.001 TRP A 344 HIS 0.003 0.001 HIS C 575 Details of bonding type rmsd covalent geometry : bond 0.00281 (15504) covalent geometry : angle 0.48763 (20912) hydrogen bonds : bond 0.03680 ( 1170) hydrogen bonds : angle 4.16010 ( 3498) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 269 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 231 time to evaluate : 0.866 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: 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 123 GLU cc_start: 0.7046 (tp30) cc_final: 0.6036 (tm-30) REVERT: A 176 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7521 (tt) REVERT: A 322 GLU cc_start: 0.7766 (tp30) cc_final: 0.7513 (mt-10) REVERT: A 334 ASN cc_start: 0.7933 (m-40) cc_final: 0.7705 (m110) REVERT: A 342 SER cc_start: 0.6086 (OUTLIER) cc_final: 0.5504 (m) REVERT: A 544 CYS cc_start: 0.5269 (OUTLIER) cc_final: 0.3752 (m) REVERT: A 553 ARG cc_start: 0.7585 (mpt180) cc_final: 0.6982 (tpt-90) REVERT: A 578 MET cc_start: 0.6872 (ptt) cc_final: 0.6619 (mmm) REVERT: B 107 ARG cc_start: 0.3481 (mtt90) cc_final: 0.3279 (tpp-160) REVERT: B 134 ASP cc_start: 0.4878 (p0) cc_final: 0.3541 (t0) REVERT: C 123 GLU cc_start: 0.7065 (tp30) cc_final: 0.6059 (tm-30) REVERT: C 322 GLU cc_start: 0.7925 (tp30) cc_final: 0.7613 (mt-10) REVERT: C 334 ASN cc_start: 0.7902 (m-40) cc_final: 0.7669 (m110) REVERT: C 342 SER cc_start: 0.6276 (OUTLIER) cc_final: 0.5752 (m) REVERT: C 544 CYS cc_start: 0.4735 (OUTLIER) cc_final: 0.3494 (m) REVERT: C 553 ARG cc_start: 0.7673 (mpt180) cc_final: 0.7086 (tpt-90) REVERT: D 72 MET cc_start: 0.1359 (tmm) cc_final: 0.1041 (tmm) REVERT: D 73 MET cc_start: -0.2765 (mmt) cc_final: -0.2992 (ttt) REVERT: D 134 ASP cc_start: 0.4933 (p0) cc_final: 0.3596 (t0) REVERT: D 142 PHE cc_start: 0.6941 (t80) cc_final: 0.6587 (t80) REVERT: E 123 GLU cc_start: 0.7065 (tp30) cc_final: 0.6048 (tm-30) REVERT: E 176 LEU cc_start: 0.7422 (OUTLIER) cc_final: 0.7190 (mp) REVERT: E 322 GLU cc_start: 0.7789 (tp30) cc_final: 0.7516 (mt-10) REVERT: E 334 ASN cc_start: 0.7952 (m-40) cc_final: 0.7650 (m110) REVERT: E 342 SER cc_start: 0.6172 (OUTLIER) cc_final: 0.5634 (m) REVERT: E 544 CYS cc_start: 0.4981 (OUTLIER) cc_final: 0.3803 (m) REVERT: E 553 ARG cc_start: 0.7617 (mpt180) cc_final: 0.7044 (tpt-90) REVERT: E 570 GLN cc_start: 0.7636 (tm-30) cc_final: 0.7434 (tm-30) REVERT: F 72 MET cc_start: 0.0091 (ptt) cc_final: -0.0231 (tmm) REVERT: F 73 MET cc_start: -0.2107 (mmm) cc_final: -0.2409 (ttm) REVERT: F 91 ARG cc_start: 0.8563 (ptm160) cc_final: 0.8064 (ptm160) REVERT: F 134 ASP cc_start: 0.4789 (p0) cc_final: 0.3494 (t0) REVERT: F 142 PHE cc_start: 0.6953 (t80) cc_final: 0.6682 (t80) REVERT: F 146 MET cc_start: 0.6307 (mmm) cc_final: 0.5964 (mmm) REVERT: G 83 ASN cc_start: 0.7688 (t0) cc_final: 0.7447 (m-40) REVERT: G 89 ARG cc_start: 0.6520 (ptp90) cc_final: 0.6125 (ptm-80) REVERT: G 123 GLU cc_start: 0.7042 (tp30) cc_final: 0.6042 (tm-30) REVERT: G 322 GLU cc_start: 0.7969 (tp30) cc_final: 0.7637 (mt-10) REVERT: G 334 ASN cc_start: 0.7960 (m-40) cc_final: 0.7677 (m110) REVERT: G 342 SER cc_start: 0.6175 (OUTLIER) cc_final: 0.5601 (m) REVERT: G 544 CYS cc_start: 0.5041 (OUTLIER) cc_final: 0.3926 (m) REVERT: G 546 MET cc_start: 0.5499 (OUTLIER) cc_final: 0.5257 (mmp) REVERT: G 553 ARG cc_start: 0.7651 (mpt180) cc_final: 0.7121 (tpt-90) REVERT: H 72 MET cc_start: -0.0532 (OUTLIER) cc_final: -0.0863 (tmm) REVERT: H 73 MET cc_start: -0.1858 (tpt) cc_final: -0.2865 (ttm) REVERT: H 91 ARG cc_start: 0.8500 (ptm160) cc_final: 0.8215 (ptp-170) REVERT: H 134 ASP cc_start: 0.4815 (p0) cc_final: 0.3522 (t0) outliers start: 38 outliers final: 9 residues processed: 259 average time/residue: 1.1678 time to fit residues: 340.9931 Evaluate side-chains 241 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 220 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain B residue 77 MET Chi-restraints excluded: chain B residue 112 ASN Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain C residue 544 CYS Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain E residue 544 CYS Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain G residue 342 SER Chi-restraints excluded: chain G residue 544 CYS Chi-restraints excluded: chain G residue 546 MET Chi-restraints excluded: chain H residue 72 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 50 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 90 optimal weight: 8.9990 chunk 118 optimal weight: 30.0000 chunk 83 optimal weight: 30.0000 chunk 100 optimal weight: 9.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4766 r_free = 0.4766 target = 0.225839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.124471 restraints weight = 56133.093| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.46 r_work: 0.3364 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 15504 Z= 0.220 Angle : 0.533 6.656 20912 Z= 0.286 Chirality : 0.035 0.134 2288 Planarity : 0.004 0.033 2636 Dihedral : 4.335 51.391 2078 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.34 % Allowed : 24.24 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.58 (0.19), residues: 1848 helix: 2.32 (0.13), residues: 1484 sheet: None (None), residues: 0 loop : -0.98 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 588 TYR 0.014 0.001 TYR A 74 PHE 0.017 0.001 PHE A 329 TRP 0.009 0.001 TRP A 91 HIS 0.004 0.001 HIS G 96 Details of bonding type rmsd covalent geometry : bond 0.00494 (15504) covalent geometry : angle 0.53292 (20912) hydrogen bonds : bond 0.04030 ( 1170) hydrogen bonds : angle 4.26946 ( 3498) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 266 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 229 time to evaluate : 0.888 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: 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 89 ARG cc_start: 0.6613 (ptp90) cc_final: 0.6175 (ptm-80) REVERT: A 123 GLU cc_start: 0.7132 (tp30) cc_final: 0.6141 (tm-30) REVERT: A 322 GLU cc_start: 0.7820 (tp30) cc_final: 0.7551 (mt-10) REVERT: A 334 ASN cc_start: 0.7988 (m-40) cc_final: 0.7770 (m110) REVERT: A 342 SER cc_start: 0.6050 (OUTLIER) cc_final: 0.5498 (m) REVERT: A 544 CYS cc_start: 0.5042 (OUTLIER) cc_final: 0.3690 (m) REVERT: A 553 ARG cc_start: 0.7555 (mpt180) cc_final: 0.6804 (tpp80) REVERT: A 578 MET cc_start: 0.6983 (ptt) cc_final: 0.6646 (mmm) REVERT: B 107 ARG cc_start: 0.3479 (mtt90) cc_final: 0.3150 (tpp-160) REVERT: B 134 ASP cc_start: 0.4873 (p0) cc_final: 0.3469 (t0) REVERT: C 89 ARG cc_start: 0.6614 (ptp90) cc_final: 0.6115 (ptm-80) REVERT: C 123 GLU cc_start: 0.7178 (tp30) cc_final: 0.6207 (tm-30) REVERT: C 322 GLU cc_start: 0.7965 (tp30) cc_final: 0.7646 (mt-10) REVERT: C 334 ASN cc_start: 0.7951 (m-40) cc_final: 0.7707 (m110) REVERT: C 342 SER cc_start: 0.6224 (OUTLIER) cc_final: 0.5713 (m) REVERT: C 544 CYS cc_start: 0.4837 (OUTLIER) cc_final: 0.3575 (m) REVERT: C 553 ARG cc_start: 0.7568 (mpt180) cc_final: 0.7000 (tpt-90) REVERT: D 72 MET cc_start: 0.1437 (tmm) cc_final: 0.1127 (tmm) REVERT: D 77 MET cc_start: 0.1312 (OUTLIER) cc_final: 0.0773 (mtt) REVERT: D 134 ASP cc_start: 0.5197 (p0) cc_final: 0.3678 (t0) REVERT: E 89 ARG cc_start: 0.6614 (ptp90) cc_final: 0.6169 (ptm-80) REVERT: E 123 GLU cc_start: 0.7144 (tp30) cc_final: 0.6156 (tm-30) REVERT: E 176 LEU cc_start: 0.7466 (OUTLIER) cc_final: 0.7217 (mp) REVERT: E 322 GLU cc_start: 0.7871 (tp30) cc_final: 0.7581 (mt-10) REVERT: E 334 ASN cc_start: 0.7989 (m-40) cc_final: 0.7721 (m110) REVERT: E 342 SER cc_start: 0.6276 (OUTLIER) cc_final: 0.5769 (m) REVERT: E 544 CYS cc_start: 0.4930 (OUTLIER) cc_final: 0.3899 (m) REVERT: E 553 ARG cc_start: 0.7578 (mpt180) cc_final: 0.7007 (tpt-90) REVERT: F 72 MET cc_start: -0.0073 (ptt) cc_final: -0.0430 (tmm) REVERT: F 73 MET cc_start: -0.2027 (mmm) cc_final: -0.2382 (ttm) REVERT: F 91 ARG cc_start: 0.8526 (ptm160) cc_final: 0.8084 (ptm160) REVERT: F 134 ASP cc_start: 0.4987 (p0) cc_final: 0.3609 (t0) REVERT: F 142 PHE cc_start: 0.7017 (t80) cc_final: 0.6657 (t80) REVERT: F 146 MET cc_start: 0.6381 (mmm) cc_final: 0.6108 (mmm) REVERT: G 83 ASN cc_start: 0.7738 (t0) cc_final: 0.7526 (m-40) REVERT: G 89 ARG cc_start: 0.6590 (ptp90) cc_final: 0.6110 (ptm-80) REVERT: G 123 GLU cc_start: 0.7121 (tp30) cc_final: 0.6134 (tm-30) REVERT: G 322 GLU cc_start: 0.7990 (tp30) cc_final: 0.7661 (mt-10) REVERT: G 334 ASN cc_start: 0.7954 (m-40) cc_final: 0.7706 (m110) REVERT: G 342 SER cc_start: 0.6251 (OUTLIER) cc_final: 0.5712 (m) REVERT: G 544 CYS cc_start: 0.5024 (OUTLIER) cc_final: 0.3956 (m) REVERT: G 546 MET cc_start: 0.5421 (OUTLIER) cc_final: 0.5176 (mmp) REVERT: G 553 ARG cc_start: 0.7517 (mpt180) cc_final: 0.7024 (tpt-90) REVERT: H 72 MET cc_start: -0.0533 (OUTLIER) cc_final: -0.0868 (tmm) REVERT: H 73 MET cc_start: -0.1789 (tpt) cc_final: -0.2817 (ttm) REVERT: H 90 PHE cc_start: 0.7702 (OUTLIER) cc_final: 0.7276 (t80) REVERT: H 134 ASP cc_start: 0.5008 (p0) cc_final: 0.3614 (t0) outliers start: 37 outliers final: 11 residues processed: 253 average time/residue: 1.0291 time to fit residues: 291.6533 Evaluate side-chains 244 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 220 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain A residue 563 ASP Chi-restraints excluded: chain B residue 77 MET Chi-restraints excluded: chain B residue 112 ASN Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain C residue 544 CYS Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 112 ASN Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain E residue 544 CYS Chi-restraints excluded: chain E residue 563 ASP Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain G residue 342 SER Chi-restraints excluded: chain G residue 544 CYS Chi-restraints excluded: chain G residue 546 MET Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain H residue 90 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 156 optimal weight: 0.8980 chunk 92 optimal weight: 10.0000 chunk 1 optimal weight: 0.9990 chunk 132 optimal weight: 10.0000 chunk 30 optimal weight: 8.9990 chunk 114 optimal weight: 0.8980 chunk 152 optimal weight: 0.7980 chunk 154 optimal weight: 0.5980 chunk 123 optimal weight: 7.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4796 r_free = 0.4796 target = 0.229068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.129618 restraints weight = 56004.955| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.44 r_work: 0.3438 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15504 Z= 0.116 Angle : 0.499 7.855 20912 Z= 0.259 Chirality : 0.033 0.162 2288 Planarity : 0.003 0.031 2636 Dihedral : 4.211 50.650 2078 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.96 % Allowed : 25.13 % Favored : 72.92 % 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 aren not related in a simple way. whole: 2.86 (0.19), residues: 1848 helix: 2.54 (0.13), residues: 1484 sheet: None (None), residues: 0 loop : -0.97 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 588 TYR 0.007 0.001 TYR E 562 PHE 0.009 0.001 PHE B 142 TRP 0.006 0.001 TRP G 270 HIS 0.003 0.001 HIS C 575 Details of bonding type rmsd covalent geometry : bond 0.00251 (15504) covalent geometry : angle 0.49851 (20912) hydrogen bonds : bond 0.03544 ( 1170) hydrogen bonds : angle 4.07435 ( 3498) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 259 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 228 time to evaluate : 0.975 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: 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 123 GLU cc_start: 0.7035 (tp30) cc_final: 0.6025 (tm-30) REVERT: A 322 GLU cc_start: 0.7772 (tp30) cc_final: 0.7525 (mt-10) REVERT: A 334 ASN cc_start: 0.7914 (m-40) cc_final: 0.7710 (m110) REVERT: A 342 SER cc_start: 0.6072 (OUTLIER) cc_final: 0.5485 (m) REVERT: A 544 CYS cc_start: 0.5144 (OUTLIER) cc_final: 0.3776 (m) REVERT: A 553 ARG cc_start: 0.7576 (mpt180) cc_final: 0.6805 (tpp80) REVERT: A 570 GLN cc_start: 0.7881 (tm-30) cc_final: 0.7434 (tm-30) REVERT: A 578 MET cc_start: 0.6892 (ptt) cc_final: 0.6594 (mmm) REVERT: B 32 GLU cc_start: 0.5540 (mt-10) cc_final: 0.5113 (mm-30) REVERT: B 134 ASP cc_start: 0.4572 (p0) cc_final: 0.3131 (t0) REVERT: C 89 ARG cc_start: 0.6518 (ptp90) cc_final: 0.6026 (ptm-80) REVERT: C 123 GLU cc_start: 0.7040 (tp30) cc_final: 0.6056 (tm-30) REVERT: C 334 ASN cc_start: 0.7904 (m-40) cc_final: 0.7663 (m110) REVERT: C 342 SER cc_start: 0.6230 (OUTLIER) cc_final: 0.5704 (m) REVERT: C 544 CYS cc_start: 0.4788 (OUTLIER) cc_final: 0.3493 (m) REVERT: C 553 ARG cc_start: 0.7544 (mpt180) cc_final: 0.6965 (tpt-90) REVERT: D 73 MET cc_start: -0.2444 (ttt) cc_final: -0.2660 (ttm) REVERT: D 90 PHE cc_start: 0.7693 (OUTLIER) cc_final: 0.7251 (t80) REVERT: D 134 ASP cc_start: 0.4799 (p0) cc_final: 0.3357 (t0) REVERT: E 123 GLU cc_start: 0.7059 (tp30) cc_final: 0.6055 (tm-30) REVERT: E 176 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.7191 (mp) REVERT: E 322 GLU cc_start: 0.7797 (tp30) cc_final: 0.7576 (mt-10) REVERT: E 334 ASN cc_start: 0.7934 (m-40) cc_final: 0.7616 (m110) REVERT: E 342 SER cc_start: 0.6223 (OUTLIER) cc_final: 0.5640 (m) REVERT: E 544 CYS cc_start: 0.5002 (OUTLIER) cc_final: 0.3938 (m) REVERT: E 553 ARG cc_start: 0.7594 (mpt180) cc_final: 0.6909 (tmm-80) REVERT: F 72 MET cc_start: 0.0096 (ptt) cc_final: -0.0202 (tmm) REVERT: F 73 MET cc_start: -0.2075 (mmm) cc_final: -0.2428 (ttm) REVERT: F 90 PHE cc_start: 0.7645 (OUTLIER) cc_final: 0.7251 (t80) REVERT: F 91 ARG cc_start: 0.8464 (ptm160) cc_final: 0.8048 (ptm160) REVERT: F 134 ASP cc_start: 0.4635 (p0) cc_final: 0.3278 (t0) REVERT: F 142 PHE cc_start: 0.7027 (t80) cc_final: 0.6599 (t80) REVERT: F 146 MET cc_start: 0.6558 (mmm) cc_final: 0.6298 (mmm) REVERT: G 83 ASN cc_start: 0.7794 (t0) cc_final: 0.7547 (m-40) REVERT: G 89 ARG cc_start: 0.6521 (ptp90) cc_final: 0.6043 (ptm-80) REVERT: G 123 GLU cc_start: 0.7045 (tp30) cc_final: 0.6044 (tm-30) REVERT: G 322 GLU cc_start: 0.7954 (tp30) cc_final: 0.7641 (mt-10) REVERT: G 334 ASN cc_start: 0.7895 (m-40) cc_final: 0.7627 (m110) REVERT: G 342 SER cc_start: 0.6191 (OUTLIER) cc_final: 0.5594 (m) REVERT: G 544 CYS cc_start: 0.5047 (OUTLIER) cc_final: 0.3906 (m) REVERT: G 546 MET cc_start: 0.5441 (OUTLIER) cc_final: 0.5194 (mmp) REVERT: G 553 ARG cc_start: 0.7529 (mpt180) cc_final: 0.7021 (tpt-90) REVERT: H 72 MET cc_start: -0.0537 (OUTLIER) cc_final: -0.0862 (tmm) REVERT: H 73 MET cc_start: -0.1862 (tpt) cc_final: -0.2856 (ttm) REVERT: H 90 PHE cc_start: 0.7700 (OUTLIER) cc_final: 0.7289 (t80) REVERT: H 134 ASP cc_start: 0.4638 (p0) cc_final: 0.3233 (t0) outliers start: 31 outliers final: 8 residues processed: 251 average time/residue: 1.0419 time to fit residues: 293.2210 Evaluate side-chains 243 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 221 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain B residue 77 MET Chi-restraints excluded: chain B residue 112 ASN Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain C residue 544 CYS Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain D residue 112 ASN Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain E residue 544 CYS Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain G residue 342 SER Chi-restraints excluded: chain G residue 544 CYS Chi-restraints excluded: chain G residue 546 MET Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain H residue 90 PHE Chi-restraints excluded: chain H residue 121 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 158 optimal weight: 2.9990 chunk 44 optimal weight: 0.0370 chunk 151 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 73 optimal weight: 20.0000 chunk 146 optimal weight: 5.9990 chunk 1 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 119 optimal weight: 20.0000 chunk 101 optimal weight: 0.3980 chunk 89 optimal weight: 30.0000 overall best weight: 1.4062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4790 r_free = 0.4790 target = 0.228379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.129314 restraints weight = 56001.067| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.31 r_work: 0.3421 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15504 Z= 0.141 Angle : 0.512 8.401 20912 Z= 0.267 Chirality : 0.033 0.119 2288 Planarity : 0.003 0.032 2636 Dihedral : 4.156 50.840 2078 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.02 % Allowed : 25.32 % Favored : 72.66 % 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 aren not related in a simple way. whole: 2.95 (0.19), residues: 1848 helix: 2.62 (0.13), residues: 1480 sheet: None (None), residues: 0 loop : -0.99 (0.34), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 588 TYR 0.009 0.001 TYR A 74 PHE 0.012 0.001 PHE A 329 TRP 0.020 0.001 TRP G 344 HIS 0.003 0.001 HIS G 96 Details of bonding type rmsd covalent geometry : bond 0.00309 (15504) covalent geometry : angle 0.51151 (20912) hydrogen bonds : bond 0.03597 ( 1170) hydrogen bonds : angle 4.08240 ( 3498) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 263 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 231 time to evaluate : 1.000 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: 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 123 GLU cc_start: 0.7103 (tp30) cc_final: 0.6087 (tm-30) REVERT: A 322 GLU cc_start: 0.7782 (tp30) cc_final: 0.7540 (mt-10) REVERT: A 334 ASN cc_start: 0.7928 (m-40) cc_final: 0.7722 (m110) REVERT: A 342 SER cc_start: 0.6037 (OUTLIER) cc_final: 0.5448 (m) REVERT: A 544 CYS cc_start: 0.5242 (OUTLIER) cc_final: 0.3715 (m) REVERT: A 553 ARG cc_start: 0.7589 (mpt180) cc_final: 0.6782 (tpp80) REVERT: A 570 GLN cc_start: 0.7874 (tm-30) cc_final: 0.7393 (tm-30) REVERT: A 578 MET cc_start: 0.6894 (ptt) cc_final: 0.6528 (mmm) REVERT: B 32 GLU cc_start: 0.5485 (mt-10) cc_final: 0.5059 (mm-30) REVERT: B 90 PHE cc_start: 0.7733 (OUTLIER) cc_final: 0.7324 (t80) REVERT: B 134 ASP cc_start: 0.4551 (p0) cc_final: 0.3182 (t0) REVERT: C 89 ARG cc_start: 0.6515 (ptp90) cc_final: 0.6028 (ptm-80) REVERT: C 123 GLU cc_start: 0.7083 (tp30) cc_final: 0.6101 (tm-30) REVERT: C 322 GLU cc_start: 0.7924 (tp30) cc_final: 0.7629 (mt-10) REVERT: C 334 ASN cc_start: 0.7898 (m-40) cc_final: 0.7682 (m110) REVERT: C 342 SER cc_start: 0.6172 (OUTLIER) cc_final: 0.5644 (m) REVERT: C 544 CYS cc_start: 0.4725 (OUTLIER) cc_final: 0.3415 (m) REVERT: C 553 ARG cc_start: 0.7542 (mpt180) cc_final: 0.7326 (tpp80) REVERT: D 55 GLU cc_start: 0.3027 (mt-10) cc_final: 0.2122 (tp30) REVERT: D 73 MET cc_start: -0.2266 (ttt) cc_final: -0.2509 (ttm) REVERT: D 90 PHE cc_start: 0.7697 (OUTLIER) cc_final: 0.7237 (t80) REVERT: D 134 ASP cc_start: 0.4834 (p0) cc_final: 0.3440 (t0) REVERT: E 123 GLU cc_start: 0.7109 (tp30) cc_final: 0.6106 (tm-30) REVERT: E 176 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.7179 (mp) REVERT: E 322 GLU cc_start: 0.7892 (tp30) cc_final: 0.7523 (mt-10) REVERT: E 334 ASN cc_start: 0.7937 (m-40) cc_final: 0.7653 (m110) REVERT: E 342 SER cc_start: 0.6224 (OUTLIER) cc_final: 0.5630 (m) REVERT: E 544 CYS cc_start: 0.5090 (OUTLIER) cc_final: 0.3894 (m) REVERT: E 553 ARG cc_start: 0.7551 (mpt180) cc_final: 0.6987 (tpt-90) REVERT: F 72 MET cc_start: 0.0044 (ptt) cc_final: -0.0258 (tmm) REVERT: F 73 MET cc_start: -0.2174 (mmm) cc_final: -0.2585 (ttm) REVERT: F 90 PHE cc_start: 0.7641 (OUTLIER) cc_final: 0.7223 (t80) REVERT: F 91 ARG cc_start: 0.8411 (ptm160) cc_final: 0.8042 (ptm160) REVERT: F 134 ASP cc_start: 0.4640 (p0) cc_final: 0.3329 (t0) REVERT: F 142 PHE cc_start: 0.6955 (t80) cc_final: 0.6489 (t80) REVERT: F 146 MET cc_start: 0.6586 (mmm) cc_final: 0.6340 (mmm) REVERT: G 83 ASN cc_start: 0.7792 (t0) cc_final: 0.7543 (m-40) REVERT: G 89 ARG cc_start: 0.6583 (ptp90) cc_final: 0.6086 (ptm-80) REVERT: G 123 GLU cc_start: 0.7107 (tp30) cc_final: 0.6105 (tm-30) REVERT: G 322 GLU cc_start: 0.7957 (tp30) cc_final: 0.7644 (mt-10) REVERT: G 334 ASN cc_start: 0.7908 (m-40) cc_final: 0.7644 (m110) REVERT: G 342 SER cc_start: 0.6266 (OUTLIER) cc_final: 0.5637 (m) REVERT: G 544 CYS cc_start: 0.5073 (OUTLIER) cc_final: 0.3924 (m) REVERT: G 546 MET cc_start: 0.5441 (OUTLIER) cc_final: 0.5192 (mmp) REVERT: G 553 ARG cc_start: 0.7516 (mpt180) cc_final: 0.6817 (tpp80) REVERT: H 72 MET cc_start: -0.0558 (OUTLIER) cc_final: -0.0875 (tmm) REVERT: H 73 MET cc_start: -0.1890 (tpt) cc_final: -0.2903 (ttm) REVERT: H 90 PHE cc_start: 0.7650 (OUTLIER) cc_final: 0.7239 (t80) REVERT: H 134 ASP cc_start: 0.4663 (p0) cc_final: 0.3273 (t0) outliers start: 32 outliers final: 10 residues processed: 251 average time/residue: 1.0105 time to fit residues: 284.8391 Evaluate side-chains 250 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 225 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain A residue 563 ASP Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain B residue 77 MET Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 112 ASN Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain C residue 544 CYS Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain D residue 112 ASN Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain E residue 544 CYS Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain G residue 342 SER Chi-restraints excluded: chain G residue 544 CYS Chi-restraints excluded: chain G residue 546 MET Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain H residue 90 PHE Chi-restraints excluded: chain H residue 121 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 3 optimal weight: 2.9990 chunk 100 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 60 optimal weight: 0.8980 chunk 37 optimal weight: 20.0000 chunk 152 optimal weight: 0.8980 chunk 27 optimal weight: 6.9990 chunk 113 optimal weight: 0.8980 chunk 121 optimal weight: 4.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4787 r_free = 0.4787 target = 0.228059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.128824 restraints weight = 55586.798| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.30 r_work: 0.3421 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15504 Z= 0.144 Angle : 0.522 8.794 20912 Z= 0.272 Chirality : 0.034 0.120 2288 Planarity : 0.003 0.032 2636 Dihedral : 4.166 50.921 2078 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.96 % Allowed : 25.76 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.00 (0.19), residues: 1848 helix: 2.66 (0.13), residues: 1480 sheet: None (None), residues: 0 loop : -0.96 (0.34), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 588 TYR 0.009 0.001 TYR A 74 PHE 0.013 0.001 PHE H 142 TRP 0.015 0.001 TRP G 344 HIS 0.003 0.001 HIS E 575 Details of bonding type rmsd covalent geometry : bond 0.00318 (15504) covalent geometry : angle 0.52219 (20912) hydrogen bonds : bond 0.03596 ( 1170) hydrogen bonds : angle 4.05795 ( 3498) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 256 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 225 time to evaluate : 0.841 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: 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 123 GLU cc_start: 0.7107 (tp30) cc_final: 0.6094 (tm-30) REVERT: A 322 GLU cc_start: 0.7794 (tp30) cc_final: 0.7553 (mt-10) REVERT: A 334 ASN cc_start: 0.7923 (m-40) cc_final: 0.7716 (m110) REVERT: A 342 SER cc_start: 0.6156 (OUTLIER) cc_final: 0.5569 (m) REVERT: A 544 CYS cc_start: 0.5167 (OUTLIER) cc_final: 0.3567 (m) REVERT: A 553 ARG cc_start: 0.7632 (mpt180) cc_final: 0.6817 (tpp80) REVERT: A 570 GLN cc_start: 0.7863 (tm-30) cc_final: 0.7391 (tm-30) REVERT: A 578 MET cc_start: 0.6851 (ptt) cc_final: 0.6547 (mmm) REVERT: B 90 PHE cc_start: 0.7730 (OUTLIER) cc_final: 0.7208 (t80) REVERT: B 134 ASP cc_start: 0.4460 (p0) cc_final: 0.3062 (t0) REVERT: C 89 ARG cc_start: 0.6535 (ptp90) cc_final: 0.6053 (ptm-80) REVERT: C 123 GLU cc_start: 0.7089 (tp30) cc_final: 0.6115 (tm-30) REVERT: C 322 GLU cc_start: 0.7917 (tp30) cc_final: 0.7629 (mt-10) REVERT: C 334 ASN cc_start: 0.7886 (m-40) cc_final: 0.7665 (m110) REVERT: C 342 SER cc_start: 0.6194 (OUTLIER) cc_final: 0.5664 (m) REVERT: C 544 CYS cc_start: 0.4841 (OUTLIER) cc_final: 0.3338 (m) REVERT: C 553 ARG cc_start: 0.7557 (mpt180) cc_final: 0.7332 (tpp80) REVERT: D 55 GLU cc_start: 0.3018 (mt-10) cc_final: 0.2168 (tp30) REVERT: D 73 MET cc_start: -0.2270 (ttt) cc_final: -0.2493 (ttm) REVERT: D 90 PHE cc_start: 0.7667 (OUTLIER) cc_final: 0.7263 (t80) REVERT: D 134 ASP cc_start: 0.4773 (p0) cc_final: 0.3338 (t0) REVERT: E 123 GLU cc_start: 0.7113 (tp30) cc_final: 0.6112 (tm-30) REVERT: E 176 LEU cc_start: 0.7390 (OUTLIER) cc_final: 0.7171 (mp) REVERT: E 342 SER cc_start: 0.6202 (OUTLIER) cc_final: 0.5612 (m) REVERT: E 544 CYS cc_start: 0.5084 (OUTLIER) cc_final: 0.3865 (m) REVERT: E 553 ARG cc_start: 0.7589 (mpt180) cc_final: 0.6874 (tpp80) REVERT: F 72 MET cc_start: -0.0017 (ptt) cc_final: -0.0292 (tmm) REVERT: F 73 MET cc_start: -0.2242 (mmm) cc_final: -0.2634 (ttm) REVERT: F 90 PHE cc_start: 0.7631 (OUTLIER) cc_final: 0.7192 (t80) REVERT: F 113 LEU cc_start: 0.5815 (mp) cc_final: 0.5058 (tt) REVERT: F 134 ASP cc_start: 0.4528 (p0) cc_final: 0.3176 (t0) REVERT: F 142 PHE cc_start: 0.6959 (t80) cc_final: 0.6535 (t80) REVERT: G 83 ASN cc_start: 0.7835 (t0) cc_final: 0.7571 (m-40) REVERT: G 89 ARG cc_start: 0.6593 (ptp90) cc_final: 0.6099 (ptm-80) REVERT: G 123 GLU cc_start: 0.7101 (tp30) cc_final: 0.6113 (tm-30) REVERT: G 342 SER cc_start: 0.6292 (OUTLIER) cc_final: 0.5676 (m) REVERT: G 544 CYS cc_start: 0.5036 (OUTLIER) cc_final: 0.3807 (m) REVERT: G 546 MET cc_start: 0.5455 (OUTLIER) cc_final: 0.5216 (mmp) REVERT: G 553 ARG cc_start: 0.7529 (mpt180) cc_final: 0.6821 (tpp80) REVERT: H 72 MET cc_start: -0.0555 (OUTLIER) cc_final: -0.0878 (tmm) REVERT: H 73 MET cc_start: -0.2052 (tpt) cc_final: -0.3113 (ttm) REVERT: H 90 PHE cc_start: 0.7674 (OUTLIER) cc_final: 0.7250 (t80) REVERT: H 113 LEU cc_start: 0.6113 (mp) cc_final: 0.5147 (tp) REVERT: H 134 ASP cc_start: 0.4549 (p0) cc_final: 0.3146 (t0) outliers start: 31 outliers final: 10 residues processed: 246 average time/residue: 1.1352 time to fit residues: 312.4854 Evaluate side-chains 247 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 222 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain A residue 563 ASP Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain B residue 77 MET Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 112 ASN Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain C residue 544 CYS Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain D residue 112 ASN Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain E residue 544 CYS Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain G residue 342 SER Chi-restraints excluded: chain G residue 544 CYS Chi-restraints excluded: chain G residue 546 MET Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain H residue 90 PHE Chi-restraints excluded: chain H residue 121 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 2 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 135 optimal weight: 20.0000 chunk 177 optimal weight: 40.0000 chunk 39 optimal weight: 8.9990 chunk 176 optimal weight: 30.0000 chunk 17 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 169 optimal weight: 10.0000 chunk 147 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 570 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4763 r_free = 0.4763 target = 0.225540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.124866 restraints weight = 55610.821| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.31 r_work: 0.3366 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 15504 Z= 0.242 Angle : 0.575 9.160 20912 Z= 0.305 Chirality : 0.036 0.143 2288 Planarity : 0.004 0.038 2636 Dihedral : 4.378 51.788 2078 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.02 % Allowed : 25.76 % Favored : 72.22 % 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 aren not related in a simple way. whole: 2.72 (0.19), residues: 1848 helix: 2.45 (0.13), residues: 1484 sheet: None (None), residues: 0 loop : -1.06 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 588 TYR 0.014 0.001 TYR A 74 PHE 0.019 0.002 PHE A 329 TRP 0.014 0.001 TRP C 91 HIS 0.004 0.001 HIS A 96 Details of bonding type rmsd covalent geometry : bond 0.00540 (15504) covalent geometry : angle 0.57545 (20912) hydrogen bonds : bond 0.04085 ( 1170) hydrogen bonds : angle 4.24159 ( 3498) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Residue TYR 347 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue TYR 100 is missing expected H atoms. Skipping. Residue TYR 139 is missing expected H atoms. Skipping. Evaluate side-chains 249 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 217 time to evaluate : 0.645 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: 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: symmetry clash revert: symmetry clash REVERT: A 89 ARG cc_start: 0.6607 (ptp90) cc_final: 0.6110 (ptm-80) REVERT: A 123 GLU cc_start: 0.7104 (tp30) cc_final: 0.6144 (tm-30) REVERT: A 176 LEU cc_start: 0.7727 (OUTLIER) cc_final: 0.7480 (tt) REVERT: A 322 GLU cc_start: 0.7805 (tp30) cc_final: 0.7551 (mt-10) REVERT: A 342 SER cc_start: 0.6102 (OUTLIER) cc_final: 0.5585 (m) REVERT: A 544 CYS cc_start: 0.5279 (OUTLIER) cc_final: 0.3695 (m) REVERT: A 553 ARG cc_start: 0.7602 (mpt180) cc_final: 0.6785 (tpp80) REVERT: A 578 MET cc_start: 0.6924 (ptt) cc_final: 0.6508 (mmm) REVERT: B 32 GLU cc_start: 0.5631 (mt-10) cc_final: 0.5168 (mm-30) REVERT: B 90 PHE cc_start: 0.7829 (OUTLIER) cc_final: 0.7298 (t80) REVERT: B 134 ASP cc_start: 0.4758 (p0) cc_final: 0.3408 (t0) REVERT: C 89 ARG cc_start: 0.6575 (ptp90) cc_final: 0.6093 (ptm-80) REVERT: C 123 GLU cc_start: 0.7112 (tp30) cc_final: 0.6157 (tm-30) REVERT: C 322 GLU cc_start: 0.7902 (tp30) cc_final: 0.7590 (mt-10) REVERT: C 342 SER cc_start: 0.6114 (OUTLIER) cc_final: 0.5606 (m) REVERT: C 544 CYS cc_start: 0.4951 (OUTLIER) cc_final: 0.3532 (m) REVERT: D 90 PHE cc_start: 0.7709 (OUTLIER) cc_final: 0.7308 (t80) REVERT: D 134 ASP cc_start: 0.5010 (p0) cc_final: 0.3507 (t0) REVERT: E 89 ARG cc_start: 0.6585 (ptp90) cc_final: 0.6105 (ptm-80) REVERT: E 123 GLU cc_start: 0.7116 (tp30) cc_final: 0.6170 (tm-30) REVERT: E 176 LEU cc_start: 0.7421 (OUTLIER) cc_final: 0.7168 (mp) REVERT: E 342 SER cc_start: 0.6236 (OUTLIER) cc_final: 0.5705 (m) REVERT: E 544 CYS cc_start: 0.5006 (OUTLIER) cc_final: 0.3972 (m) REVERT: E 553 ARG cc_start: 0.7583 (mpt180) cc_final: 0.7222 (tmt170) REVERT: F 72 MET cc_start: -0.0244 (ptt) cc_final: -0.0511 (tmm) REVERT: F 73 MET cc_start: -0.2179 (mmm) cc_final: -0.2656 (ttm) REVERT: F 90 PHE cc_start: 0.7666 (OUTLIER) cc_final: 0.7274 (t80) REVERT: F 134 ASP cc_start: 0.4747 (p0) cc_final: 0.3416 (t0) REVERT: G 83 ASN cc_start: 0.7796 (t0) cc_final: 0.7570 (m-40) REVERT: G 89 ARG cc_start: 0.6612 (ptp90) cc_final: 0.6082 (ptm-80) REVERT: G 123 GLU cc_start: 0.7121 (tp30) cc_final: 0.6185 (tm-30) REVERT: G 322 GLU cc_start: 0.7923 (tp30) cc_final: 0.7597 (mt-10) REVERT: G 342 SER cc_start: 0.6333 (OUTLIER) cc_final: 0.5743 (m) REVERT: G 553 ARG cc_start: 0.7566 (mpt180) cc_final: 0.6857 (tpp80) REVERT: H 32 GLU cc_start: 0.5682 (mt-10) cc_final: 0.5280 (mm-30) REVERT: H 72 MET cc_start: -0.0557 (OUTLIER) cc_final: -0.0884 (tmm) REVERT: H 73 MET cc_start: -0.1891 (tpt) cc_final: -0.2925 (ttm) REVERT: H 90 PHE cc_start: 0.7760 (OUTLIER) cc_final: 0.7338 (t80) REVERT: H 134 ASP cc_start: 0.4870 (p0) cc_final: 0.3510 (t0) outliers start: 32 outliers final: 14 residues processed: 238 average time/residue: 1.1897 time to fit residues: 314.8813 Evaluate side-chains 242 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 214 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain A residue 563 ASP Chi-restraints excluded: chain B residue 77 MET Chi-restraints excluded: chain B residue 90 PHE Chi-restraints excluded: chain B residue 112 ASN Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain C residue 544 CYS Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain D residue 112 ASN Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain E residue 544 CYS Chi-restraints excluded: chain E residue 570 GLN Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 202 PHE Chi-restraints excluded: chain G residue 342 SER Chi-restraints excluded: chain G residue 544 CYS Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain H residue 90 PHE Chi-restraints excluded: chain H residue 121 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 69 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 32 optimal weight: 0.0030 chunk 72 optimal weight: 20.0000 chunk 157 optimal weight: 0.6980 chunk 182 optimal weight: 9.9990 chunk 89 optimal weight: 0.0870 chunk 88 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 128 optimal weight: 30.0000 chunk 85 optimal weight: 30.0000 overall best weight: 0.7170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4769 r_free = 0.4769 target = 0.226015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.125524 restraints weight = 55868.490| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.38 r_work: 0.3376 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.179 15504 Z= 0.189 Angle : 0.783 59.194 20912 Z= 0.441 Chirality : 0.035 0.471 2288 Planarity : 0.004 0.032 2636 Dihedral : 4.371 51.741 2078 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.08 % Allowed : 25.63 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.73 (0.19), residues: 1848 helix: 2.46 (0.13), residues: 1484 sheet: None (None), residues: 0 loop : -1.06 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 588 TYR 0.013 0.001 TYR A 74 PHE 0.018 0.001 PHE A 329 TRP 0.011 0.001 TRP C 91 HIS 0.004 0.001 HIS A 96 Details of bonding type rmsd covalent geometry : bond 0.00429 (15504) covalent geometry : angle 0.78283 (20912) hydrogen bonds : bond 0.04060 ( 1170) hydrogen bonds : angle 4.23398 ( 3498) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14916.84 seconds wall clock time: 252 minutes 44.20 seconds (15164.20 seconds total)