Starting phenix.real_space_refine on Wed Jun 25 22:20:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x43_38041/06_2025/8x43_38041_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x43_38041/06_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_38041/06_2025/8x43_38041.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x43_38041/06_2025/8x43_38041.map" model { file = "/net/cci-nas-00/data/ceres_data/8x43_38041/06_2025/8x43_38041_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x43_38041/06_2025/8x43_38041_neut_trim.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 14.62, per 1000 atoms: 0.48 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: 8.25 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 1.94 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: 10.85 Time building geometry restraints manager: 9.95 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: 0.010 Normalize map: mean=0, sd=1: 1.270 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: 0.500 Extract box with map and model: 1.160 Check model and map are aligned: 0.220 Set scattering table: 0.280 Process input model: 62.830 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.780 ------------------------------------------------------------------------------- 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 : 12.43 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.008 0.001 TRP G 91 HIS 0.003 0.001 HIS C 228 PHE 0.017 0.001 PHE C 329 TYR 0.010 0.001 TYR G 74 ARG 0.003 0.000 ARG A 581 Details of bonding type rmsd hydrogen bonds : bond 0.09558 ( 1170) hydrogen bonds : angle 5.22496 ( 3498) covalent geometry : bond 0.00494 (15504) covalent geometry : angle 0.56355 (20912) *********************** 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 : 2.194 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: 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: 0.6218 (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: 0.7818 (m110) REVERT: A 342 SER cc_start: 0.6464 (OUTLIER) cc_final: 0.6033 (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: 0.3269 (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: 0.7080 (mt-10) REVERT: C 334 ASN cc_start: 0.8006 (m-40) cc_final: 0.7791 (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: -0.3313 (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: 0.6226 (t80) REVERT: D 146 MET cc_start: 0.6280 (mmm) cc_final: 0.5630 (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: 0.7055 (mt-10) REVERT: E 334 ASN cc_start: 0.8013 (m-40) cc_final: 0.7755 (m110) REVERT: E 342 SER cc_start: 0.6372 (OUTLIER) cc_final: 0.5950 (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: 0.4004 (m-30) REVERT: F 142 PHE cc_start: 0.6706 (t80) cc_final: 0.6361 (t80) REVERT: F 146 MET cc_start: 0.6143 (mmm) cc_final: 0.5492 (mmm) REVERT: G 89 ARG cc_start: 0.6246 (ptp90) cc_final: 0.5681 (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: 0.7226 (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: 0.5947 (m) REVERT: G 553 ARG cc_start: 0.7587 (mpt180) cc_final: 0.7037 (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: 0.4957 (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: 2.7317 time to fit residues: 948.4449 Evaluate side-chains 255 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 247 time to evaluate : 2.722 ------------------------------------------------------------------------------- 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 155 optimal weight: 1.9990 chunk 139 optimal weight: 7.9990 chunk 77 optimal weight: 9.9990 chunk 47 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 74 optimal weight: 9.9990 chunk 144 optimal weight: 0.6980 chunk 55 optimal weight: 9.9990 chunk 87 optimal weight: 7.9990 chunk 107 optimal weight: 0.5980 chunk 167 optimal weight: 9.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- 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 = 0.4773 r_free = 0.4773 target = 0.226211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.132514 restraints weight = 55515.623| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 3.78 r_work: 0.3328 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.1945 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= 0.214 Angle : 0.537 5.360 20912 Z= 0.293 Chirality : 0.035 0.136 2288 Planarity : 0.004 0.034 2636 Dihedral : 4.478 51.228 2084 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.53 % Allowed : 22.54 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.19), residues: 1848 helix: 1.99 (0.13), residues: 1476 sheet: None (None), residues: 0 loop : -0.94 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 91 HIS 0.005 0.001 HIS E 228 PHE 0.015 0.001 PHE E 329 TYR 0.013 0.001 TYR A 74 ARG 0.003 0.000 ARG G 144 Details of bonding type rmsd hydrogen bonds : bond 0.04232 ( 1170) hydrogen bonds : angle 4.52937 ( 3498) covalent geometry : bond 0.00473 (15504) covalent geometry : angle 0.53715 (20912) *********************** 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 286 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 246 time to evaluate : 2.191 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: A 89 ARG cc_start: 0.6569 (ptp90) cc_final: 0.6051 (ptm-80) REVERT: A 123 GLU cc_start: 0.7246 (tp30) cc_final: 0.6651 (tt0) REVERT: A 322 GLU cc_start: 0.7991 (tp30) cc_final: 0.7715 (mt-10) REVERT: A 334 ASN cc_start: 0.7917 (m-40) cc_final: 0.7663 (m110) REVERT: A 342 SER cc_start: 0.6191 (OUTLIER) cc_final: 0.5633 (m) REVERT: A 544 CYS cc_start: 0.5466 (OUTLIER) cc_final: 0.4034 (m) REVERT: A 553 ARG cc_start: 0.7632 (mpt180) cc_final: 0.7050 (tpt-90) REVERT: A 578 MET cc_start: 0.7492 (ptt) cc_final: 0.6923 (mmm) REVERT: B 72 MET cc_start: 0.1612 (tmm) cc_final: 0.1209 (tmm) REVERT: B 77 MET cc_start: 0.1381 (OUTLIER) cc_final: -0.0223 (mtt) REVERT: B 107 ARG cc_start: 0.3414 (mtt90) cc_final: 0.3136 (tpp-160) REVERT: B 134 ASP cc_start: 0.5311 (p0) cc_final: 0.4057 (t0) REVERT: C 89 ARG cc_start: 0.6591 (ptp90) cc_final: 0.6063 (ptm-80) REVERT: C 123 GLU cc_start: 0.7255 (tp30) cc_final: 0.6658 (tt0) REVERT: C 322 GLU cc_start: 0.7982 (tp30) cc_final: 0.7761 (mt-10) REVERT: C 334 ASN cc_start: 0.7920 (m-40) cc_final: 0.7692 (m110) REVERT: C 342 SER cc_start: 0.6255 (OUTLIER) cc_final: 0.5724 (m) REVERT: C 544 CYS cc_start: 0.4793 (OUTLIER) cc_final: 0.3651 (m) REVERT: D 72 MET cc_start: 0.1544 (tmm) cc_final: 0.1279 (tmm) REVERT: D 73 MET cc_start: -0.2770 (mmt) cc_final: -0.3160 (ttm) REVERT: D 134 ASP cc_start: 0.5292 (p0) cc_final: 0.3939 (t0) REVERT: D 142 PHE cc_start: 0.6930 (t80) cc_final: 0.6643 (t80) REVERT: D 146 MET cc_start: 0.6364 (mmm) cc_final: 0.6071 (mmm) REVERT: E 89 ARG cc_start: 0.6615 (ptp90) cc_final: 0.6064 (ptm-80) REVERT: E 123 GLU cc_start: 0.7283 (tp30) cc_final: 0.6692 (tt0) REVERT: E 176 LEU cc_start: 0.7465 (OUTLIER) cc_final: 0.7192 (mp) REVERT: E 322 GLU cc_start: 0.7978 (tp30) cc_final: 0.7661 (mt-10) REVERT: E 334 ASN cc_start: 0.7999 (m-40) cc_final: 0.7723 (m110) REVERT: E 342 SER cc_start: 0.6076 (OUTLIER) cc_final: 0.5606 (m) REVERT: E 544 CYS cc_start: 0.5139 (OUTLIER) cc_final: 0.3723 (m) REVERT: E 570 GLN cc_start: 0.8002 (tm-30) cc_final: 0.7593 (tm-30) REVERT: F 72 MET cc_start: 0.0047 (ptt) cc_final: -0.0293 (tmm) REVERT: F 73 MET cc_start: -0.2053 (mmm) cc_final: -0.2468 (ttm) REVERT: F 77 MET cc_start: 0.0772 (OUTLIER) cc_final: 0.0378 (mtt) REVERT: F 134 ASP cc_start: 0.5155 (p0) cc_final: 0.3875 (t0) REVERT: F 142 PHE cc_start: 0.6968 (t80) cc_final: 0.6583 (t80) REVERT: F 146 MET cc_start: 0.6451 (mmm) cc_final: 0.5941 (mmm) REVERT: G 89 ARG cc_start: 0.6673 (ptp90) cc_final: 0.6071 (ptm-80) REVERT: G 123 GLU cc_start: 0.7274 (tp30) cc_final: 0.6689 (tt0) REVERT: G 322 GLU cc_start: 0.8179 (tp30) cc_final: 0.7811 (mt-10) REVERT: G 334 ASN cc_start: 0.7960 (m-40) cc_final: 0.7681 (m110) REVERT: G 342 SER cc_start: 0.6269 (OUTLIER) cc_final: 0.5756 (m) REVERT: G 544 CYS cc_start: 0.5195 (OUTLIER) cc_final: 0.3924 (m) REVERT: G 553 ARG cc_start: 0.7680 (mpt180) cc_final: 0.7194 (tpt-90) REVERT: H 72 MET cc_start: -0.0488 (OUTLIER) cc_final: -0.0827 (tmm) REVERT: H 73 MET cc_start: -0.1736 (tpt) cc_final: -0.2797 (ttm) REVERT: H 134 ASP cc_start: 0.5243 (p0) cc_final: 0.3983 (t0) outliers start: 40 outliers final: 8 residues processed: 271 average time/residue: 2.4978 time to fit residues: 753.7224 Evaluate side-chains 246 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 226 time to evaluate : 2.124 ------------------------------------------------------------------------------- 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 577 ASP Chi-restraints excluded: chain B residue 77 MET 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 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 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 150 optimal weight: 0.2980 chunk 42 optimal weight: 20.0000 chunk 110 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 76 optimal weight: 20.0000 chunk 105 optimal weight: 2.9990 chunk 169 optimal weight: 20.0000 chunk 104 optimal weight: 6.9990 chunk 94 optimal weight: 0.9990 chunk 93 optimal weight: 6.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- 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 = 0.4782 r_free = 0.4782 target = 0.227293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.128106 restraints weight = 55826.623| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.23 r_work: 0.3413 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15504 Z= 0.148 Angle : 0.491 4.994 20912 Z= 0.263 Chirality : 0.034 0.122 2288 Planarity : 0.003 0.034 2636 Dihedral : 4.242 50.513 2078 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.89 % Allowed : 24.31 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (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 TRP 0.006 0.001 TRP G 91 HIS 0.003 0.001 HIS C 575 PHE 0.012 0.001 PHE B 142 TYR 0.010 0.001 TYR A 74 ARG 0.006 0.000 ARG B 91 Details of bonding type rmsd hydrogen bonds : bond 0.03902 ( 1170) hydrogen bonds : angle 4.32448 ( 3498) covalent geometry : bond 0.00319 (15504) covalent geometry : angle 0.49097 (20912) *********************** 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 263 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 233 time to evaluate : 2.340 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: A 89 ARG cc_start: 0.6466 (ptp90) cc_final: 0.5987 (ptm-80) REVERT: A 123 GLU cc_start: 0.7091 (tp30) cc_final: 0.6469 (tt0) REVERT: A 322 GLU cc_start: 0.7840 (tp30) cc_final: 0.7567 (mt-10) REVERT: A 334 ASN cc_start: 0.7931 (m-40) cc_final: 0.7677 (m110) REVERT: A 342 SER cc_start: 0.6205 (OUTLIER) cc_final: 0.5610 (m) REVERT: A 544 CYS cc_start: 0.5285 (OUTLIER) cc_final: 0.3824 (m) REVERT: A 553 ARG cc_start: 0.7597 (mpt180) cc_final: 0.6994 (tpt-90) REVERT: A 578 MET cc_start: 0.7060 (ptt) cc_final: 0.6814 (mmm) REVERT: B 91 ARG cc_start: 0.8415 (ptm160) cc_final: 0.8183 (ptm160) REVERT: B 106 LEU cc_start: 0.7128 (OUTLIER) cc_final: 0.6854 (tm) REVERT: B 107 ARG cc_start: 0.3448 (mtt90) cc_final: 0.3148 (tpp-160) REVERT: B 125 MET cc_start: 0.6209 (tmm) cc_final: 0.6003 (tpt) REVERT: B 134 ASP cc_start: 0.4973 (p0) cc_final: 0.3620 (t0) REVERT: C 89 ARG cc_start: 0.6438 (ptp90) cc_final: 0.5966 (ptm-80) REVERT: C 123 GLU cc_start: 0.7082 (tp30) cc_final: 0.6454 (tt0) REVERT: C 322 GLU cc_start: 0.7916 (tp30) cc_final: 0.7573 (mt-10) REVERT: C 334 ASN cc_start: 0.7898 (m-40) cc_final: 0.7655 (m110) REVERT: C 342 SER cc_start: 0.6283 (OUTLIER) cc_final: 0.5726 (m) REVERT: C 544 CYS cc_start: 0.4667 (OUTLIER) cc_final: 0.3392 (m) REVERT: C 553 ARG cc_start: 0.7708 (mpt180) cc_final: 0.7118 (tpt-90) REVERT: D 72 MET cc_start: 0.1387 (tmm) cc_final: 0.1059 (tmm) REVERT: D 73 MET cc_start: -0.2813 (mmt) cc_final: -0.3062 (ttm) REVERT: D 134 ASP cc_start: 0.5046 (p0) cc_final: 0.3672 (t0) REVERT: D 142 PHE cc_start: 0.6947 (t80) cc_final: 0.6600 (t80) REVERT: D 146 MET cc_start: 0.6372 (mmm) cc_final: 0.6073 (mmm) REVERT: E 123 GLU cc_start: 0.7073 (tp30) cc_final: 0.6440 (tt0) REVERT: E 176 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.7235 (mp) REVERT: E 322 GLU cc_start: 0.7848 (tp30) cc_final: 0.7511 (mt-10) REVERT: E 334 ASN cc_start: 0.7995 (m-40) cc_final: 0.7713 (m110) REVERT: E 342 SER cc_start: 0.6049 (OUTLIER) cc_final: 0.5531 (m) REVERT: E 544 CYS cc_start: 0.5167 (OUTLIER) cc_final: 0.3768 (m) REVERT: E 553 ARG cc_start: 0.7714 (mpt180) cc_final: 0.7140 (tpt-90) REVERT: E 570 GLN cc_start: 0.7843 (tm-30) cc_final: 0.7610 (tm-30) REVERT: F 72 MET cc_start: -0.0092 (ptt) cc_final: -0.0464 (tmm) REVERT: F 73 MET cc_start: -0.2232 (mmm) cc_final: -0.2478 (ttm) REVERT: F 134 ASP cc_start: 0.4799 (p0) cc_final: 0.3548 (t0) REVERT: F 142 PHE cc_start: 0.6962 (t80) cc_final: 0.6652 (t80) REVERT: F 145 MET cc_start: 0.5338 (ttp) cc_final: 0.5127 (ttp) REVERT: F 146 MET cc_start: 0.6305 (mmm) cc_final: 0.5900 (mmm) REVERT: G 89 ARG cc_start: 0.6572 (ptp90) cc_final: 0.6120 (ptm-80) REVERT: G 123 GLU cc_start: 0.7091 (tp30) cc_final: 0.6473 (tt0) REVERT: G 322 GLU cc_start: 0.8009 (tp30) cc_final: 0.7676 (mt-10) REVERT: G 334 ASN cc_start: 0.7962 (m-40) cc_final: 0.7671 (m110) REVERT: G 342 SER cc_start: 0.6249 (OUTLIER) cc_final: 0.5695 (m) REVERT: G 544 CYS cc_start: 0.5106 (OUTLIER) cc_final: 0.3945 (m) REVERT: G 553 ARG cc_start: 0.7657 (mpt180) cc_final: 0.7118 (tpt-90) REVERT: H 72 MET cc_start: -0.0457 (OUTLIER) cc_final: -0.0809 (tmm) REVERT: H 73 MET cc_start: -0.1857 (tpt) cc_final: -0.2881 (ttm) REVERT: H 134 ASP cc_start: 0.4912 (p0) cc_final: 0.3568 (t0) outliers start: 30 outliers final: 11 residues processed: 256 average time/residue: 2.3040 time to fit residues: 661.6577 Evaluate side-chains 245 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 223 time to evaluate : 2.326 ------------------------------------------------------------------------------- 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 577 ASP Chi-restraints excluded: chain B residue 106 LEU 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 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 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 H residue 72 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 51 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 chunk 26 optimal weight: 8.9990 chunk 78 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 111 optimal weight: 0.1980 chunk 125 optimal weight: 50.0000 chunk 160 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 151 optimal weight: 3.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- 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 = 0.4773 r_free = 0.4773 target = 0.226280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.127621 restraints weight = 55899.870| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.61 r_work: 0.3369 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.2706 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= 0.200 Angle : 0.512 5.514 20912 Z= 0.276 Chirality : 0.034 0.130 2288 Planarity : 0.003 0.034 2636 Dihedral : 4.330 51.106 2078 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.46 % Allowed : 23.61 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.19), residues: 1848 helix: 2.16 (0.13), residues: 1480 sheet: None (None), residues: 0 loop : -0.94 (0.34), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 91 HIS 0.004 0.001 HIS G 96 PHE 0.016 0.001 PHE C 329 TYR 0.013 0.001 TYR A 74 ARG 0.004 0.000 ARG C 588 Details of bonding type rmsd hydrogen bonds : bond 0.04032 ( 1170) hydrogen bonds : angle 4.31750 ( 3498) covalent geometry : bond 0.00443 (15504) covalent geometry : angle 0.51180 (20912) *********************** 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 266 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 227 time to evaluate : 2.770 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 89 ARG cc_start: 0.6521 (ptp90) cc_final: 0.6076 (ptm-80) REVERT: A 123 GLU cc_start: 0.7087 (tp30) cc_final: 0.6073 (tm-30) REVERT: A 322 GLU cc_start: 0.7855 (tp30) cc_final: 0.7535 (mt-10) REVERT: A 334 ASN cc_start: 0.7939 (m-40) cc_final: 0.7707 (m110) REVERT: A 342 SER cc_start: 0.6223 (OUTLIER) cc_final: 0.5686 (m) REVERT: A 544 CYS cc_start: 0.5246 (OUTLIER) cc_final: 0.3883 (m) REVERT: A 553 ARG cc_start: 0.7597 (mpt180) cc_final: 0.7011 (tpt-90) REVERT: A 578 MET cc_start: 0.6978 (ptt) cc_final: 0.6700 (mmm) REVERT: B 91 ARG cc_start: 0.8362 (ptm160) cc_final: 0.8128 (ptm-80) REVERT: B 107 ARG cc_start: 0.3363 (mtt90) cc_final: 0.3112 (tpp-160) REVERT: B 134 ASP cc_start: 0.5135 (p0) cc_final: 0.3790 (t0) REVERT: C 89 ARG cc_start: 0.6595 (ptp90) cc_final: 0.6043 (ptm-80) REVERT: C 123 GLU cc_start: 0.7085 (tp30) cc_final: 0.6091 (tm-30) REVERT: C 322 GLU cc_start: 0.7909 (tp30) cc_final: 0.7569 (mt-10) REVERT: C 334 ASN cc_start: 0.7931 (m-40) cc_final: 0.7679 (m110) REVERT: C 342 SER cc_start: 0.6284 (OUTLIER) cc_final: 0.5807 (m) REVERT: C 544 CYS cc_start: 0.4686 (OUTLIER) cc_final: 0.3463 (m) REVERT: C 553 ARG cc_start: 0.7674 (mpt180) cc_final: 0.7122 (tpt-90) REVERT: D 72 MET cc_start: 0.1461 (tmm) cc_final: 0.1247 (tmm) REVERT: D 73 MET cc_start: -0.2722 (mmt) cc_final: -0.2987 (ttt) REVERT: D 77 MET cc_start: 0.2169 (mmt) cc_final: 0.1763 (mmt) REVERT: D 134 ASP cc_start: 0.5279 (p0) cc_final: 0.3911 (t0) REVERT: D 142 PHE cc_start: 0.7078 (t80) cc_final: 0.6798 (t80) REVERT: E 89 ARG cc_start: 0.6607 (ptp90) cc_final: 0.6023 (ptm-80) REVERT: E 123 GLU cc_start: 0.7095 (tp30) cc_final: 0.6079 (tm-30) REVERT: E 176 LEU cc_start: 0.7392 (OUTLIER) cc_final: 0.7147 (mp) REVERT: E 322 GLU cc_start: 0.7842 (tp30) cc_final: 0.7522 (mt-10) REVERT: E 334 ASN cc_start: 0.7988 (m-40) cc_final: 0.7721 (m110) REVERT: E 342 SER cc_start: 0.6032 (OUTLIER) cc_final: 0.5519 (m) REVERT: E 544 CYS cc_start: 0.4986 (OUTLIER) cc_final: 0.3777 (m) REVERT: E 553 ARG cc_start: 0.7671 (mpt180) cc_final: 0.7079 (tpt-90) REVERT: E 570 GLN cc_start: 0.7860 (tm-30) cc_final: 0.7659 (tm-30) REVERT: F 72 MET cc_start: -0.0040 (ptt) cc_final: -0.0409 (tmm) REVERT: F 73 MET cc_start: -0.2107 (mmm) cc_final: -0.2427 (ttm) REVERT: F 90 PHE cc_start: 0.7771 (OUTLIER) cc_final: 0.7399 (t80) REVERT: F 134 ASP cc_start: 0.5037 (p0) cc_final: 0.3751 (t0) REVERT: F 142 PHE cc_start: 0.6945 (t80) cc_final: 0.6577 (t80) REVERT: F 146 MET cc_start: 0.6390 (mmm) cc_final: 0.6002 (mmm) REVERT: G 89 ARG cc_start: 0.6642 (ptp90) cc_final: 0.6089 (ptm-80) REVERT: G 123 GLU cc_start: 0.7084 (tp30) cc_final: 0.6076 (tm-30) REVERT: G 322 GLU cc_start: 0.7989 (tp30) cc_final: 0.7611 (mt-10) REVERT: G 334 ASN cc_start: 0.7996 (m-40) cc_final: 0.7718 (m110) REVERT: G 342 SER cc_start: 0.6210 (OUTLIER) cc_final: 0.5685 (m) REVERT: G 544 CYS cc_start: 0.5042 (OUTLIER) cc_final: 0.3890 (m) REVERT: G 553 ARG cc_start: 0.7635 (mpt180) cc_final: 0.7144 (tpt-90) REVERT: H 72 MET cc_start: -0.0504 (OUTLIER) cc_final: -0.0855 (tmm) REVERT: H 73 MET cc_start: -0.1785 (tpt) cc_final: -0.2823 (ttm) REVERT: H 134 ASP cc_start: 0.5218 (p0) cc_final: 0.3911 (t0) outliers start: 39 outliers final: 14 residues processed: 257 average time/residue: 2.7273 time to fit residues: 791.6395 Evaluate side-chains 234 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 209 time to evaluate : 2.120 ------------------------------------------------------------------------------- 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 577 ASP Chi-restraints excluded: chain B residue 112 ASN Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 179 SER 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 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 577 ASP Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 112 ASN 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 79 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 30 optimal weight: 20.0000 chunk 5 optimal weight: 3.9990 chunk 71 optimal weight: 9.9990 chunk 121 optimal weight: 8.9990 chunk 106 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 8 optimal weight: 8.9990 chunk 165 optimal weight: 30.0000 chunk 81 optimal weight: 6.9990 chunk 100 optimal weight: 10.0000 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4765 r_free = 0.4765 target = 0.225753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.126769 restraints weight = 55983.930| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.60 r_work: 0.3355 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 15504 Z= 0.208 Angle : 0.525 6.456 20912 Z= 0.282 Chirality : 0.035 0.130 2288 Planarity : 0.004 0.035 2636 Dihedral : 4.385 51.198 2078 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.71 % Allowed : 23.93 % Favored : 73.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.19), residues: 1848 helix: 2.18 (0.13), residues: 1484 sheet: None (None), residues: 0 loop : -1.01 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 91 HIS 0.004 0.001 HIS G 96 PHE 0.017 0.001 PHE C 329 TYR 0.013 0.001 TYR A 74 ARG 0.006 0.000 ARG C 588 Details of bonding type rmsd hydrogen bonds : bond 0.04044 ( 1170) hydrogen bonds : angle 4.30100 ( 3498) covalent geometry : bond 0.00463 (15504) covalent geometry : angle 0.52486 (20912) *********************** 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 256 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 213 time to evaluate : 2.550 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: A 89 ARG cc_start: 0.6605 (ptp90) cc_final: 0.5993 (ptm-80) REVERT: A 123 GLU cc_start: 0.7048 (tp30) cc_final: 0.6101 (tm-30) REVERT: A 322 GLU cc_start: 0.7884 (tp30) cc_final: 0.7583 (mt-10) REVERT: A 334 ASN cc_start: 0.7944 (m-40) cc_final: 0.7706 (m110) REVERT: A 544 CYS cc_start: 0.5250 (OUTLIER) cc_final: 0.3843 (m) REVERT: A 553 ARG cc_start: 0.7611 (mpt180) cc_final: 0.6995 (tpt-90) REVERT: A 578 MET cc_start: 0.6929 (ptt) cc_final: 0.6675 (mmm) REVERT: B 91 ARG cc_start: 0.8353 (ptm160) cc_final: 0.8143 (ptm-80) REVERT: B 107 ARG cc_start: 0.3450 (mtt90) cc_final: 0.3209 (tpp-160) REVERT: B 134 ASP cc_start: 0.5304 (p0) cc_final: 0.3853 (t0) REVERT: C 89 ARG cc_start: 0.6588 (ptp90) cc_final: 0.5960 (ptm-80) REVERT: C 123 GLU cc_start: 0.7068 (tp30) cc_final: 0.6122 (tm-30) REVERT: C 322 GLU cc_start: 0.7943 (tp30) cc_final: 0.7590 (mt-10) REVERT: C 334 ASN cc_start: 0.7942 (m-40) cc_final: 0.7687 (m110) REVERT: C 342 SER cc_start: 0.6261 (OUTLIER) cc_final: 0.5775 (m) REVERT: C 544 CYS cc_start: 0.4780 (OUTLIER) cc_final: 0.3528 (m) REVERT: C 553 ARG cc_start: 0.7690 (mpt180) cc_final: 0.7103 (tpt-90) REVERT: D 72 MET cc_start: 0.1545 (tmm) cc_final: 0.1331 (tmm) REVERT: D 73 MET cc_start: -0.2747 (mmt) cc_final: -0.2985 (ttt) REVERT: D 134 ASP cc_start: 0.5346 (p0) cc_final: 0.3889 (t0) REVERT: E 89 ARG cc_start: 0.6640 (ptp90) cc_final: 0.5993 (ptm-80) REVERT: E 123 GLU cc_start: 0.7027 (tp30) cc_final: 0.6079 (tm-30) REVERT: E 176 LEU cc_start: 0.7471 (OUTLIER) cc_final: 0.7239 (mp) REVERT: E 322 GLU cc_start: 0.7895 (tp30) cc_final: 0.7576 (mt-10) REVERT: E 334 ASN cc_start: 0.7982 (m-40) cc_final: 0.7713 (m110) REVERT: E 342 SER cc_start: 0.6348 (OUTLIER) cc_final: 0.5875 (m) REVERT: E 544 CYS cc_start: 0.4982 (OUTLIER) cc_final: 0.3854 (m) REVERT: E 546 MET cc_start: 0.5850 (OUTLIER) cc_final: 0.5625 (mmp) REVERT: E 553 ARG cc_start: 0.7571 (mpt180) cc_final: 0.7273 (tmt170) REVERT: F 72 MET cc_start: -0.0189 (ptt) cc_final: -0.0525 (tmm) REVERT: F 73 MET cc_start: -0.2200 (mmm) cc_final: -0.2536 (ttm) REVERT: F 90 PHE cc_start: 0.7714 (OUTLIER) cc_final: 0.7295 (t80) REVERT: F 91 ARG cc_start: 0.8564 (ptm160) cc_final: 0.8085 (ptm160) REVERT: F 134 ASP cc_start: 0.5293 (p0) cc_final: 0.3929 (t0) REVERT: F 142 PHE cc_start: 0.6904 (t80) cc_final: 0.6554 (t80) REVERT: F 146 MET cc_start: 0.6412 (mmm) cc_final: 0.6104 (mmm) REVERT: G 89 ARG cc_start: 0.6709 (ptp90) cc_final: 0.6179 (ptm-80) REVERT: G 123 GLU cc_start: 0.7027 (tp30) cc_final: 0.6083 (tm-30) REVERT: G 322 GLU cc_start: 0.8007 (tp30) cc_final: 0.7654 (mt-10) REVERT: G 334 ASN cc_start: 0.8000 (m-40) cc_final: 0.7749 (m110) REVERT: G 342 SER cc_start: 0.6261 (OUTLIER) cc_final: 0.5750 (m) REVERT: G 544 CYS cc_start: 0.5031 (OUTLIER) cc_final: 0.3948 (m) REVERT: G 553 ARG cc_start: 0.7549 (mpt180) cc_final: 0.7059 (tpt-90) REVERT: H 72 MET cc_start: -0.0556 (OUTLIER) cc_final: -0.0908 (tmm) REVERT: H 73 MET cc_start: -0.1811 (tpt) cc_final: -0.2857 (ttm) REVERT: H 134 ASP cc_start: 0.5348 (p0) cc_final: 0.3921 (t0) outliers start: 43 outliers final: 15 residues processed: 243 average time/residue: 2.9763 time to fit residues: 826.3997 Evaluate side-chains 235 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 209 time to evaluate : 3.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain A residue 563 ASP 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 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 546 MET Chi-restraints excluded: chain E residue 563 ASP Chi-restraints excluded: chain E residue 577 ASP Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 112 ASN 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 79 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 173 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 85 optimal weight: 40.0000 chunk 149 optimal weight: 9.9990 chunk 37 optimal weight: 30.0000 chunk 125 optimal weight: 40.0000 chunk 177 optimal weight: 30.0000 chunk 131 optimal weight: 40.0000 chunk 176 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 90 optimal weight: 0.7980 overall best weight: 6.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4724 r_free = 0.4724 target = 0.220847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.118944 restraints weight = 56267.041| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.35 r_work: 0.3312 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.074 15504 Z= 0.444 Angle : 0.684 6.674 20912 Z= 0.378 Chirality : 0.044 0.187 2288 Planarity : 0.005 0.053 2636 Dihedral : 5.123 53.284 2077 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.85 % Allowed : 24.05 % Favored : 72.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.19), residues: 1848 helix: 1.56 (0.12), residues: 1472 sheet: None (None), residues: 0 loop : -1.43 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 91 HIS 0.007 0.002 HIS C 96 PHE 0.036 0.002 PHE C 329 TYR 0.024 0.002 TYR A 74 ARG 0.006 0.001 ARG G 588 Details of bonding type rmsd hydrogen bonds : bond 0.05121 ( 1170) hydrogen bonds : angle 4.74843 ( 3498) covalent geometry : bond 0.01005 (15504) covalent geometry : angle 0.68396 (20912) *********************** 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 272 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 211 time to evaluate : 2.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.6910 (ptp90) cc_final: 0.6378 (ptm-80) REVERT: A 322 GLU cc_start: 0.7876 (tp30) cc_final: 0.7612 (mt-10) REVERT: A 544 CYS cc_start: 0.5238 (OUTLIER) cc_final: 0.3835 (m) REVERT: A 553 ARG cc_start: 0.7648 (mpt180) cc_final: 0.7078 (tpt-90) REVERT: A 578 MET cc_start: 0.6927 (ptt) cc_final: 0.6519 (mmm) REVERT: B 77 MET cc_start: 0.1699 (OUTLIER) cc_final: 0.1357 (mmt) REVERT: B 107 ARG cc_start: 0.3568 (mtt90) cc_final: 0.3181 (tpp-160) REVERT: C 89 ARG cc_start: 0.6866 (ptp90) cc_final: 0.6327 (ptm-80) REVERT: C 214 ARG cc_start: 0.6833 (ptt180) cc_final: 0.6598 (ptt180) REVERT: C 322 GLU cc_start: 0.7913 (tp30) cc_final: 0.7683 (mt-10) REVERT: C 544 CYS cc_start: 0.4816 (OUTLIER) cc_final: 0.3587 (m) REVERT: C 553 ARG cc_start: 0.7650 (mpt180) cc_final: 0.7086 (tpt-90) REVERT: C 565 MET cc_start: 0.7513 (tpt) cc_final: 0.7108 (ptm) REVERT: E 89 ARG cc_start: 0.6899 (ptp90) cc_final: 0.6344 (ptm-80) REVERT: E 176 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7358 (mp) REVERT: E 322 GLU cc_start: 0.7927 (tp30) cc_final: 0.7713 (mt-10) REVERT: E 544 CYS cc_start: 0.5047 (OUTLIER) cc_final: 0.4021 (m) REVERT: E 546 MET cc_start: 0.5742 (OUTLIER) cc_final: 0.5516 (mmp) REVERT: E 553 ARG cc_start: 0.7651 (mpt180) cc_final: 0.7341 (tmt170) REVERT: F 72 MET cc_start: -0.0408 (ptt) cc_final: -0.0640 (tmm) REVERT: F 73 MET cc_start: -0.2340 (mmm) cc_final: -0.2733 (ttm) REVERT: F 90 PHE cc_start: 0.7756 (OUTLIER) cc_final: 0.7295 (t80) REVERT: F 113 LEU cc_start: 0.5878 (mp) cc_final: 0.5080 (tt) REVERT: F 142 PHE cc_start: 0.6898 (t80) cc_final: 0.6523 (t80) REVERT: G 89 ARG cc_start: 0.6990 (ptp90) cc_final: 0.6351 (ptm-80) REVERT: G 322 GLU cc_start: 0.8039 (tp30) cc_final: 0.7743 (mt-10) REVERT: G 544 CYS cc_start: 0.4973 (OUTLIER) cc_final: 0.3945 (m) REVERT: G 553 ARG cc_start: 0.7575 (mpt180) cc_final: 0.7098 (tpt-90) REVERT: H 72 MET cc_start: -0.0708 (ptt) cc_final: -0.1050 (tmm) REVERT: H 73 MET cc_start: -0.2086 (tpt) cc_final: -0.3099 (ttm) outliers start: 61 outliers final: 33 residues processed: 256 average time/residue: 2.4889 time to fit residues: 713.5530 Evaluate side-chains 242 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 201 time to evaluate : 2.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 323 GLN 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 112 ASN Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 323 GLN Chi-restraints excluded: chain C residue 544 CYS Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain D residue 112 ASN Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 323 GLN Chi-restraints excluded: chain E residue 544 CYS Chi-restraints excluded: chain E residue 546 MET Chi-restraints excluded: chain E residue 563 ASP Chi-restraints excluded: chain E residue 577 ASP Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 112 ASN Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 139 VAL 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 323 GLN Chi-restraints excluded: chain G residue 544 CYS Chi-restraints excluded: chain H residue 79 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 7 optimal weight: 6.9990 chunk 165 optimal weight: 20.0000 chunk 19 optimal weight: 0.5980 chunk 83 optimal weight: 30.0000 chunk 119 optimal weight: 20.0000 chunk 152 optimal weight: 0.4980 chunk 138 optimal weight: 10.0000 chunk 123 optimal weight: 10.0000 chunk 147 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 chunk 94 optimal weight: 0.0670 overall best weight: 2.2322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 350 ASN ** 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 = 0.4765 r_free = 0.4765 target = 0.225588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.130035 restraints weight = 56437.019| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 3.54 r_work: 0.3331 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.3605 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= 0.182 Angle : 0.545 8.038 20912 Z= 0.289 Chirality : 0.034 0.120 2288 Planarity : 0.004 0.039 2636 Dihedral : 4.749 52.111 2074 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.65 % Allowed : 26.64 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.19), residues: 1848 helix: 1.96 (0.13), residues: 1484 sheet: None (None), residues: 0 loop : -1.25 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 269 HIS 0.003 0.001 HIS G 96 PHE 0.017 0.001 PHE C 329 TYR 0.012 0.001 TYR A 74 ARG 0.003 0.000 ARG D 107 Details of bonding type rmsd hydrogen bonds : bond 0.04139 ( 1170) hydrogen bonds : angle 4.37648 ( 3498) covalent geometry : bond 0.00400 (15504) covalent geometry : angle 0.54527 (20912) *********************** 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 242 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 200 time to evaluate : 2.159 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: A 89 ARG cc_start: 0.6747 (ptp90) cc_final: 0.6201 (ptm-80) REVERT: A 322 GLU cc_start: 0.7876 (tp30) cc_final: 0.7575 (mt-10) REVERT: A 342 SER cc_start: 0.6063 (OUTLIER) cc_final: 0.5488 (m) REVERT: A 544 CYS cc_start: 0.5197 (OUTLIER) cc_final: 0.3777 (m) REVERT: A 553 ARG cc_start: 0.7706 (mpt180) cc_final: 0.7094 (tpt-90) REVERT: A 570 GLN cc_start: 0.7989 (tm-30) cc_final: 0.7529 (tm-30) REVERT: A 578 MET cc_start: 0.6953 (ptt) cc_final: 0.6599 (mmm) REVERT: B 107 ARG cc_start: 0.3474 (mtt90) cc_final: 0.3205 (tpt-90) REVERT: C 89 ARG cc_start: 0.6720 (ptp90) cc_final: 0.6182 (ptm-80) REVERT: C 214 ARG cc_start: 0.6713 (ptt180) cc_final: 0.6505 (ptt180) REVERT: C 322 GLU cc_start: 0.7951 (tp30) cc_final: 0.7630 (mt-10) REVERT: C 544 CYS cc_start: 0.4893 (OUTLIER) cc_final: 0.3562 (m) REVERT: C 553 ARG cc_start: 0.7666 (mpt180) cc_final: 0.7087 (tpt-90) REVERT: C 565 MET cc_start: 0.7588 (tpt) cc_final: 0.7077 (ptm) REVERT: D 90 PHE cc_start: 0.7660 (OUTLIER) cc_final: 0.7230 (t80) REVERT: E 89 ARG cc_start: 0.6734 (ptp90) cc_final: 0.6180 (ptm-80) REVERT: E 176 LEU cc_start: 0.7459 (OUTLIER) cc_final: 0.7201 (mp) REVERT: E 322 GLU cc_start: 0.7948 (tp30) cc_final: 0.7614 (mt-10) REVERT: E 544 CYS cc_start: 0.4895 (OUTLIER) cc_final: 0.3915 (m) REVERT: E 546 MET cc_start: 0.5612 (OUTLIER) cc_final: 0.5386 (mmp) REVERT: F 72 MET cc_start: -0.0366 (ptt) cc_final: -0.0575 (tmm) REVERT: F 73 MET cc_start: -0.2168 (mmm) cc_final: -0.2691 (ttm) REVERT: F 90 PHE cc_start: 0.7676 (OUTLIER) cc_final: 0.7301 (t80) REVERT: F 91 ARG cc_start: 0.8435 (ptm160) cc_final: 0.7990 (ptm160) REVERT: F 113 LEU cc_start: 0.6023 (mp) cc_final: 0.5272 (tt) REVERT: G 89 ARG cc_start: 0.6805 (ptp90) cc_final: 0.6194 (ptm-80) REVERT: G 322 GLU cc_start: 0.8070 (tp30) cc_final: 0.7721 (mt-10) REVERT: G 544 CYS cc_start: 0.5021 (OUTLIER) cc_final: 0.3957 (m) REVERT: G 553 ARG cc_start: 0.7609 (mpt180) cc_final: 0.7094 (tpt-90) REVERT: H 72 MET cc_start: -0.0833 (OUTLIER) cc_final: -0.1131 (tmm) REVERT: H 73 MET cc_start: -0.1979 (tpt) cc_final: -0.2983 (ttt) REVERT: H 90 PHE cc_start: 0.7825 (OUTLIER) cc_final: 0.7429 (t80) outliers start: 42 outliers final: 19 residues processed: 229 average time/residue: 2.7855 time to fit residues: 713.9445 Evaluate side-chains 226 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 196 time to evaluate : 2.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 139 VAL 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 112 ASN Chi-restraints excluded: chain C residue 145 ILE 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 135 VAL Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 544 CYS Chi-restraints excluded: chain E residue 546 MET Chi-restraints excluded: chain E residue 563 ASP Chi-restraints excluded: chain E residue 577 ASP Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 112 ASN Chi-restraints excluded: chain G residue 135 VAL 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 544 CYS Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain H residue 77 MET Chi-restraints excluded: chain H residue 90 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 88 optimal weight: 7.9990 chunk 29 optimal weight: 9.9990 chunk 130 optimal weight: 50.0000 chunk 9 optimal weight: 7.9990 chunk 171 optimal weight: 50.0000 chunk 72 optimal weight: 10.0000 chunk 121 optimal weight: 8.9990 chunk 181 optimal weight: 7.9990 chunk 31 optimal weight: 7.9990 chunk 176 optimal weight: 30.0000 chunk 177 optimal weight: 40.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 350 ASN ** 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 = 0.4617 r_free = 0.4617 target = 0.215551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.143162 restraints weight = 57680.978| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 3.55 r_work: 0.3198 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.093 15504 Z= 0.516 Angle : 0.726 7.805 20912 Z= 0.401 Chirality : 0.048 0.203 2288 Planarity : 0.006 0.061 2636 Dihedral : 5.086 53.936 2074 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 4.36 % Allowed : 25.51 % Favored : 70.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.19), residues: 1848 helix: 1.38 (0.13), residues: 1480 sheet: None (None), residues: 0 loop : -1.61 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP G 91 HIS 0.007 0.002 HIS A 228 PHE 0.043 0.002 PHE G 329 TYR 0.024 0.003 TYR A 74 ARG 0.004 0.001 ARG B 75 Details of bonding type rmsd hydrogen bonds : bond 0.05257 ( 1170) hydrogen bonds : angle 4.85238 ( 3498) covalent geometry : bond 0.01167 (15504) covalent geometry : angle 0.72628 (20912) *********************** 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 277 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 208 time to evaluate : 2.542 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 89 ARG cc_start: 0.6790 (ptp90) cc_final: 0.6370 (ptm-80) REVERT: A 176 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7542 (tp) REVERT: A 544 CYS cc_start: 0.5141 (OUTLIER) cc_final: 0.3769 (m) REVERT: A 553 ARG cc_start: 0.7712 (mpt180) cc_final: 0.7107 (tpt-90) REVERT: A 565 MET cc_start: 0.7563 (tpt) cc_final: 0.7075 (ptm) REVERT: A 569 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7332 (tm-30) REVERT: A 578 MET cc_start: 0.6923 (ptt) cc_final: 0.6381 (mmm) REVERT: B 107 ARG cc_start: 0.3825 (mtt90) cc_final: 0.3487 (tpp-160) REVERT: C 89 ARG cc_start: 0.6795 (ptp90) cc_final: 0.6356 (ptm-80) REVERT: C 544 CYS cc_start: 0.4910 (OUTLIER) cc_final: 0.3507 (m) REVERT: C 553 ARG cc_start: 0.7724 (mpt180) cc_final: 0.7104 (tpt-90) REVERT: C 562 TYR cc_start: 0.5382 (OUTLIER) cc_final: 0.5177 (t80) REVERT: D 90 PHE cc_start: 0.7857 (OUTLIER) cc_final: 0.7390 (t80) REVERT: E 89 ARG cc_start: 0.6828 (ptp90) cc_final: 0.6386 (ptm-80) REVERT: E 176 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.7336 (mp) REVERT: E 544 CYS cc_start: 0.4996 (OUTLIER) cc_final: 0.4030 (m) REVERT: E 546 MET cc_start: 0.5761 (OUTLIER) cc_final: 0.5531 (mmp) REVERT: E 553 ARG cc_start: 0.7657 (mpt180) cc_final: 0.7390 (tmt170) REVERT: F 73 MET cc_start: -0.2675 (mmm) cc_final: -0.3247 (ttm) REVERT: F 90 PHE cc_start: 0.7848 (OUTLIER) cc_final: 0.7394 (t80) REVERT: F 91 ARG cc_start: 0.8425 (ptm160) cc_final: 0.8031 (ptm160) REVERT: F 113 LEU cc_start: 0.6247 (mp) cc_final: 0.5544 (tp) REVERT: G 89 ARG cc_start: 0.6954 (ptp90) cc_final: 0.6371 (ptm-80) REVERT: G 322 GLU cc_start: 0.7994 (tp30) cc_final: 0.7794 (mt-10) REVERT: G 544 CYS cc_start: 0.5037 (OUTLIER) cc_final: 0.3962 (m) REVERT: G 553 ARG cc_start: 0.7671 (mpt180) cc_final: 0.7155 (tpt-90) REVERT: H 72 MET cc_start: -0.1030 (ptt) cc_final: -0.1313 (tmm) REVERT: H 73 MET cc_start: -0.2455 (tpt) cc_final: -0.3382 (ttt) REVERT: H 77 MET cc_start: 0.1469 (OUTLIER) cc_final: 0.1047 (mmt) REVERT: H 90 PHE cc_start: 0.7934 (OUTLIER) cc_final: 0.7553 (t80) REVERT: H 91 ARG cc_start: 0.8386 (tmm-80) cc_final: 0.8080 (ptm160) outliers start: 69 outliers final: 32 residues processed: 256 average time/residue: 2.3263 time to fit residues: 683.2672 Evaluate side-chains 243 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 198 time to evaluate : 2.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 323 GLN Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain A residue 563 ASP Chi-restraints excluded: chain A residue 569 GLU Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 112 ASN Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 544 CYS Chi-restraints excluded: chain C residue 562 TYR 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 99 VAL Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 544 CYS Chi-restraints excluded: chain E residue 546 MET Chi-restraints excluded: chain E residue 563 ASP Chi-restraints excluded: chain E residue 577 ASP Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 112 ASN Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 139 VAL 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 544 CYS Chi-restraints excluded: chain H residue 77 MET Chi-restraints excluded: chain H residue 79 ASP Chi-restraints excluded: chain H residue 90 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 11 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 183 optimal weight: 0.8980 chunk 101 optimal weight: 8.9990 chunk 43 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 35 optimal weight: 40.0000 chunk 144 optimal weight: 1.9990 chunk 161 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 350 ASN ** 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 = 0.4695 r_free = 0.4695 target = 0.223135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.126091 restraints weight = 56841.041| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.00 r_work: 0.3300 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15504 Z= 0.189 Angle : 0.571 10.416 20912 Z= 0.299 Chirality : 0.034 0.121 2288 Planarity : 0.004 0.041 2636 Dihedral : 4.836 52.917 2074 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.40 % Allowed : 27.40 % Favored : 70.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.19), residues: 1848 helix: 1.86 (0.13), residues: 1484 sheet: None (None), residues: 0 loop : -1.35 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 269 HIS 0.003 0.001 HIS E 575 PHE 0.017 0.001 PHE C 329 TYR 0.012 0.001 TYR A 74 ARG 0.003 0.000 ARG F 75 Details of bonding type rmsd hydrogen bonds : bond 0.04198 ( 1170) hydrogen bonds : angle 4.43676 ( 3498) covalent geometry : bond 0.00416 (15504) covalent geometry : angle 0.57123 (20912) *********************** 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 235 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 197 time to evaluate : 2.944 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 89 ARG cc_start: 0.6570 (ptp90) cc_final: 0.6075 (ptm-80) REVERT: A 123 GLU cc_start: 0.6981 (tp30) cc_final: 0.6095 (tm-30) REVERT: A 544 CYS cc_start: 0.5178 (OUTLIER) cc_final: 0.3730 (m) REVERT: A 553 ARG cc_start: 0.7713 (mpt180) cc_final: 0.7081 (tpt-90) REVERT: A 570 GLN cc_start: 0.7915 (tm-30) cc_final: 0.7521 (tm-30) REVERT: A 578 MET cc_start: 0.6917 (ptt) cc_final: 0.6410 (mmm) REVERT: B 107 ARG cc_start: 0.3830 (mtt90) cc_final: 0.3563 (tpp-160) REVERT: C 89 ARG cc_start: 0.6560 (ptp90) cc_final: 0.6066 (ptm-80) REVERT: C 544 CYS cc_start: 0.4953 (OUTLIER) cc_final: 0.3618 (m) REVERT: C 553 ARG cc_start: 0.7721 (mpt180) cc_final: 0.7083 (tpt-90) REVERT: D 90 PHE cc_start: 0.7691 (OUTLIER) cc_final: 0.7291 (t80) REVERT: E 89 ARG cc_start: 0.6604 (ptp90) cc_final: 0.6091 (ptm-80) REVERT: E 176 LEU cc_start: 0.7449 (OUTLIER) cc_final: 0.7177 (mp) REVERT: E 544 CYS cc_start: 0.4976 (OUTLIER) cc_final: 0.3805 (m) REVERT: E 546 MET cc_start: 0.5675 (OUTLIER) cc_final: 0.5463 (mmp) REVERT: E 553 ARG cc_start: 0.7698 (mpt180) cc_final: 0.7362 (tmt170) REVERT: F 72 MET cc_start: 0.1336 (tmm) cc_final: 0.1099 (tmm) REVERT: F 73 MET cc_start: -0.2472 (mmm) cc_final: -0.2760 (ttm) REVERT: F 90 PHE cc_start: 0.7763 (OUTLIER) cc_final: 0.7365 (t80) REVERT: F 91 ARG cc_start: 0.8404 (ptm160) cc_final: 0.7945 (ptm160) REVERT: F 113 LEU cc_start: 0.6170 (mp) cc_final: 0.5483 (tp) REVERT: G 89 ARG cc_start: 0.6698 (ptp90) cc_final: 0.6153 (ptm-80) REVERT: G 322 GLU cc_start: 0.7956 (tp30) cc_final: 0.7703 (mt-10) REVERT: G 544 CYS cc_start: 0.4966 (OUTLIER) cc_final: 0.3799 (m) REVERT: G 553 ARG cc_start: 0.7658 (mpt180) cc_final: 0.7118 (tpt-90) REVERT: H 72 MET cc_start: -0.1062 (OUTLIER) cc_final: -0.1343 (tmm) REVERT: H 73 MET cc_start: -0.2452 (tpt) cc_final: -0.3427 (ttt) REVERT: H 90 PHE cc_start: 0.7851 (OUTLIER) cc_final: 0.7489 (t80) REVERT: H 91 ARG cc_start: 0.8321 (tmm-80) cc_final: 0.8008 (ptm160) outliers start: 38 outliers final: 24 residues processed: 221 average time/residue: 3.0289 time to fit residues: 753.1177 Evaluate side-chains 226 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 192 time to evaluate : 3.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 145 ILE 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 112 ASN Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 323 GLN 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 99 VAL Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 323 GLN Chi-restraints excluded: chain E residue 544 CYS Chi-restraints excluded: chain E residue 546 MET Chi-restraints excluded: chain E residue 563 ASP Chi-restraints excluded: chain E residue 577 ASP Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 112 ASN Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 135 VAL 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 544 CYS Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain H residue 90 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 61 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 31 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 91 optimal weight: 10.0000 chunk 167 optimal weight: 10.0000 chunk 5 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4707 r_free = 0.4707 target = 0.224359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.129334 restraints weight = 57154.263| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.81 r_work: 0.3276 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.4069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15504 Z= 0.152 Angle : 0.560 9.671 20912 Z= 0.290 Chirality : 0.034 0.122 2288 Planarity : 0.004 0.041 2636 Dihedral : 4.548 52.663 2074 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.21 % Allowed : 27.65 % Favored : 70.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.19), residues: 1848 helix: 2.13 (0.13), residues: 1484 sheet: None (None), residues: 0 loop : -1.26 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 344 HIS 0.003 0.001 HIS C 96 PHE 0.013 0.001 PHE A 329 TYR 0.011 0.001 TYR C 571 ARG 0.005 0.000 ARG C 588 Details of bonding type rmsd hydrogen bonds : bond 0.03932 ( 1170) hydrogen bonds : angle 4.27892 ( 3498) covalent geometry : bond 0.00336 (15504) covalent geometry : angle 0.55965 (20912) ********************** 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 245 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 210 time to evaluate : 2.054 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: 0.6625 (ptp90) cc_final: 0.6018 (ptm-80) REVERT: A 123 GLU cc_start: 0.7020 (tp30) cc_final: 0.6091 (tm-30) REVERT: A 544 CYS cc_start: 0.5047 (OUTLIER) cc_final: 0.3672 (m) REVERT: A 553 ARG cc_start: 0.7675 (mpt180) cc_final: 0.6887 (tpp80) REVERT: A 570 GLN cc_start: 0.7843 (tm-30) cc_final: 0.7506 (tm-30) REVERT: A 578 MET cc_start: 0.6862 (ptt) cc_final: 0.6445 (mmm) REVERT: B 107 ARG cc_start: 0.3665 (mtt90) cc_final: 0.3450 (tpp-160) REVERT: C 89 ARG cc_start: 0.6560 (ptp90) cc_final: 0.5998 (ptm-80) REVERT: C 123 GLU cc_start: 0.7037 (tp30) cc_final: 0.6101 (tm-30) REVERT: C 544 CYS cc_start: 0.4982 (OUTLIER) cc_final: 0.3532 (m) REVERT: C 553 ARG cc_start: 0.7700 (mpt180) cc_final: 0.7073 (tpt-90) REVERT: D 90 PHE cc_start: 0.7653 (OUTLIER) cc_final: 0.7301 (t80) REVERT: D 113 LEU cc_start: 0.5792 (mp) cc_final: 0.5082 (tt) REVERT: E 89 ARG cc_start: 0.6622 (ptp90) cc_final: 0.6039 (ptm-80) REVERT: E 123 GLU cc_start: 0.7025 (tp30) cc_final: 0.6099 (tm-30) REVERT: E 176 LEU cc_start: 0.7340 (OUTLIER) cc_final: 0.7074 (mp) REVERT: E 544 CYS cc_start: 0.4946 (OUTLIER) cc_final: 0.3828 (m) REVERT: E 546 MET cc_start: 0.5530 (OUTLIER) cc_final: 0.5316 (mmp) REVERT: E 553 ARG cc_start: 0.7681 (mpt180) cc_final: 0.7326 (tmt170) REVERT: F 72 MET cc_start: 0.1286 (tmm) cc_final: 0.1062 (tmm) REVERT: F 73 MET cc_start: -0.2425 (mmm) cc_final: -0.2649 (ttt) REVERT: F 90 PHE cc_start: 0.7648 (OUTLIER) cc_final: 0.7278 (t80) REVERT: F 91 ARG cc_start: 0.8459 (ptm160) cc_final: 0.8001 (ptm160) REVERT: F 113 LEU cc_start: 0.6181 (mp) cc_final: 0.5586 (tp) REVERT: G 89 ARG cc_start: 0.6643 (ptp90) cc_final: 0.5972 (ptm-80) REVERT: G 322 GLU cc_start: 0.7987 (tp30) cc_final: 0.7670 (mt-10) REVERT: G 544 CYS cc_start: 0.4963 (OUTLIER) cc_final: 0.3768 (m) REVERT: G 553 ARG cc_start: 0.7658 (mpt180) cc_final: 0.7110 (tpt-90) REVERT: H 72 MET cc_start: -0.0812 (OUTLIER) cc_final: -0.1127 (tmm) REVERT: H 73 MET cc_start: -0.2353 (tpt) cc_final: -0.3277 (ttt) REVERT: H 90 PHE cc_start: 0.7781 (OUTLIER) cc_final: 0.7441 (t80) outliers start: 35 outliers final: 22 residues processed: 233 average time/residue: 2.7953 time to fit residues: 743.3066 Evaluate side-chains 233 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 201 time to evaluate : 5.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain A residue 563 ASP Chi-restraints excluded: chain B residue 112 ASN Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 323 GLN 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 99 VAL Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 323 GLN Chi-restraints excluded: chain E residue 544 CYS Chi-restraints excluded: chain E residue 546 MET Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 112 ASN Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 135 VAL 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 544 CYS Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain H residue 90 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 10.0000 chunk 27 optimal weight: 20.0000 chunk 150 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 179 optimal weight: 0.9980 chunk 72 optimal weight: 20.0000 chunk 79 optimal weight: 40.0000 chunk 157 optimal weight: 1.9990 chunk 89 optimal weight: 20.0000 chunk 106 optimal weight: 0.5980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4668 r_free = 0.4668 target = 0.221124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.143495 restraints weight = 57009.534| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 2.71 r_work: 0.3338 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.4092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15504 Z= 0.177 Angle : 0.568 9.443 20912 Z= 0.296 Chirality : 0.034 0.122 2288 Planarity : 0.004 0.041 2636 Dihedral : 4.446 52.782 2074 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.15 % Allowed : 28.54 % Favored : 69.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.19), residues: 1848 helix: 2.23 (0.13), residues: 1484 sheet: None (None), residues: 0 loop : -1.23 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 344 HIS 0.003 0.001 HIS G 96 PHE 0.016 0.001 PHE C 329 TYR 0.010 0.001 TYR A 74 ARG 0.005 0.000 ARG E 588 Details of bonding type rmsd hydrogen bonds : bond 0.03980 ( 1170) hydrogen bonds : angle 4.26500 ( 3498) covalent geometry : bond 0.00392 (15504) covalent geometry : angle 0.56835 (20912) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 29225.14 seconds wall clock time: 511 minutes 41.25 seconds (30701.25 seconds total)