Starting phenix.real_space_refine on Fri Jun 13 18:05:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u0j_26261/06_2025/7u0j_26261.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u0j_26261/06_2025/7u0j_26261.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7u0j_26261/06_2025/7u0j_26261.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u0j_26261/06_2025/7u0j_26261.map" model { file = "/net/cci-nas-00/data/ceres_data/7u0j_26261/06_2025/7u0j_26261.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u0j_26261/06_2025/7u0j_26261.cif" } resolution = 2.7 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= 0.005 sd= 0.103 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 298 5.49 5 S 32 5.16 5 C 8914 2.51 5 N 2817 2.21 5 O 3561 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15622 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 633 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 820 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 736 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "G" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 816 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 736 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 3084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 3084 Classifications: {'DNA': 149} Link IDs: {'rna3p': 148} Chain: "J" Number of atoms: 3025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 3025 Classifications: {'DNA': 149} Link IDs: {'rna3p': 148} Chain: "K" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1759 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1769 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Time building chain proxies: 8.72, per 1000 atoms: 0.56 Number of scatterers: 15622 At special positions: 0 Unit cell: (139.392, 125.664, 128.832, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 P 298 15.00 O 3561 8.00 N 2817 7.00 C 8914 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS K 44 " - pdb=" SG CYS K 118 " distance=2.03 Simple disulfide: pdb=" SG CYS K 181 " - pdb=" SG CYS K 246 " distance=2.03 Simple disulfide: pdb=" SG CYS N 44 " - pdb=" SG CYS N 118 " distance=2.03 Simple disulfide: pdb=" SG CYS N 181 " - pdb=" SG CYS N 246 " distance=2.03 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: 4.02 Conformation dependent library (CDL) restraints added in 1.5 seconds 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2250 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 21 sheets defined 46.9% alpha, 19.8% beta 134 base pairs and 273 stacking pairs defined. Time for finding SS restraints: 7.39 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.592A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.804A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 72 removed outlier: 3.645A pdb=" N LEU C 55 " --> pdb=" O MET C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 removed outlier: 3.547A pdb=" N LEU C 116 " --> pdb=" O ALA C 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 50 removed outlier: 3.609A pdb=" N TYR D 43 " --> pdb=" O SER D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 85 Processing helix chain 'D' and resid 91 through 103 Processing helix chain 'D' and resid 104 through 123 Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.530A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.746A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 89 removed outlier: 3.511A pdb=" N ASN G 89 " --> pdb=" O LEU G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 removed outlier: 3.621A pdb=" N LEU G 116 " --> pdb=" O ALA G 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 50 Processing helix chain 'H' and resid 56 through 85 removed outlier: 3.548A pdb=" N ASN H 85 " --> pdb=" O LEU H 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 103 Processing helix chain 'H' and resid 104 through 125 Processing helix chain 'K' and resid 50 through 52 No H-bonds generated for 'chain 'K' and resid 50 through 52' Processing helix chain 'K' and resid 109 through 113 removed outlier: 4.114A pdb=" N SER K 113 " --> pdb=" O SER K 110 " (cutoff:3.500A) Processing helix chain 'N' and resid 50 through 52 No H-bonds generated for 'chain 'N' and resid 50 through 52' Processing helix chain 'N' and resid 84 through 87 removed outlier: 3.828A pdb=" N LYS N 87 " --> pdb=" O GLU N 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 84 through 87' Processing helix chain 'N' and resid 109 through 113 removed outlier: 3.674A pdb=" N ASP N 112 " --> pdb=" O THR N 109 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N SER N 113 " --> pdb=" O SER N 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 109 through 113' Processing helix chain 'N' and resid 237 through 241 removed outlier: 3.708A pdb=" N ASP N 240 " --> pdb=" O GLU N 237 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N THR N 241 " --> pdb=" O SER N 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 237 through 241' Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.970A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.572A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.154A pdb=" N ARG C 42 " --> pdb=" O ILE D 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.501A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.140A pdb=" N ARG G 42 " --> pdb=" O ILE H 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 25 through 28 removed outlier: 3.564A pdb=" N VAL K 101 " --> pdb=" O CYS K 44 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 32 through 34 removed outlier: 7.998A pdb=" N TYR K 54 " --> pdb=" O TYR K 74 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N TYR K 74 " --> pdb=" O TYR K 54 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ILE K 56 " --> pdb=" O TYR K 72 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N TYR K 72 " --> pdb=" O ILE K 56 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TRP K 58 " --> pdb=" O ILE K 70 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 168 through 171 removed outlier: 3.501A pdb=" N MET K 169 " --> pdb=" O LYS K 261 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLU K 263 " --> pdb=" O MET K 169 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA K 171 " --> pdb=" O GLU K 263 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LEU K 191 " --> pdb=" O TYR K 207 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N TYR K 207 " --> pdb=" O LEU K 191 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N TRP K 193 " --> pdb=" O LEU K 205 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 168 through 171 removed outlier: 3.501A pdb=" N MET K 169 " --> pdb=" O LYS K 261 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLU K 263 " --> pdb=" O MET K 169 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA K 171 " --> pdb=" O GLU K 263 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR K 255 " --> pdb=" O GLN K 248 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 177 through 180 Processing sheet with id=AB7, first strand: chain 'N' and resid 25 through 27 Processing sheet with id=AB8, first strand: chain 'N' and resid 32 through 34 removed outlier: 6.274A pdb=" N LYS N 60 " --> pdb=" O TRP N 69 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N TRP N 69 " --> pdb=" O LYS N 60 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N THR N 62 " --> pdb=" O LEU N 67 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N LEU N 67 " --> pdb=" O THR N 62 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 32 through 34 removed outlier: 4.029A pdb=" N TYR N 131 " --> pdb=" O ARG N 120 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 39 through 43 Processing sheet with id=AC2, first strand: chain 'N' and resid 162 through 164 removed outlier: 3.956A pdb=" N PHE N 229 " --> pdb=" O CYS N 181 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP N 228 " --> pdb=" O SER N 225 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'N' and resid 168 through 171 removed outlier: 6.816A pdb=" N LEU N 191 " --> pdb=" O TYR N 207 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N TYR N 207 " --> pdb=" O LEU N 191 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N TRP N 193 " --> pdb=" O LEU N 205 " (cutoff:3.500A) 543 hydrogen bonds defined for protein. 1530 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 324 hydrogen bonds 648 hydrogen bond angles 0 basepair planarities 134 basepair parallelities 273 stacking parallelities Total time for adding SS restraints: 6.43 Time building geometry restraints manager: 4.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.04 - 1.20: 15 1.20 - 1.36: 4542 1.36 - 1.51: 7106 1.51 - 1.67: 4815 1.67 - 1.83: 51 Bond restraints: 16529 Sorted by residual: bond pdb=" C LEU B 90 " pdb=" O LEU B 90 " ideal model delta sigma weight residual 1.237 1.052 0.184 1.19e-02 7.06e+03 2.40e+02 bond pdb=" C MET C 51 " pdb=" O MET C 51 " ideal model delta sigma weight residual 1.236 1.045 0.192 1.29e-02 6.01e+03 2.20e+02 bond pdb=" C LEU C 93 " pdb=" O LEU C 93 " ideal model delta sigma weight residual 1.237 1.069 0.168 1.17e-02 7.31e+03 2.05e+02 bond pdb=" C ASN C 94 " pdb=" O ASN C 94 " ideal model delta sigma weight residual 1.237 1.087 0.150 1.17e-02 7.31e+03 1.65e+02 bond pdb=" CA MET C 51 " pdb=" C MET C 51 " ideal model delta sigma weight residual 1.523 1.361 0.161 1.37e-02 5.33e+03 1.39e+02 ... (remaining 16524 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.95: 23552 5.95 - 11.90: 55 11.90 - 17.85: 9 17.85 - 23.80: 1 23.80 - 29.74: 1 Bond angle restraints: 23618 Sorted by residual: angle pdb=" N SER H 33 " pdb=" CA SER H 33 " pdb=" C SER H 33 " ideal model delta sigma weight residual 110.61 126.95 -16.34 1.25e+00 6.40e-01 1.71e+02 angle pdb=" CB MET C 51 " pdb=" CG MET C 51 " pdb=" SD MET C 51 " ideal model delta sigma weight residual 112.70 82.96 29.74 3.00e+00 1.11e-01 9.83e+01 angle pdb=" N LYS C 13 " pdb=" CA LYS C 13 " pdb=" C LYS C 13 " ideal model delta sigma weight residual 110.80 128.74 -17.94 2.13e+00 2.20e-01 7.10e+01 angle pdb=" C LYS C 13 " pdb=" N ALA C 14 " pdb=" CA ALA C 14 " ideal model delta sigma weight residual 121.54 134.09 -12.55 1.91e+00 2.74e-01 4.32e+01 angle pdb=" CA GLN B 93 " pdb=" CB GLN B 93 " pdb=" CG GLN B 93 " ideal model delta sigma weight residual 114.10 101.78 12.32 2.00e+00 2.50e-01 3.79e+01 ... (remaining 23613 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.74: 7400 32.74 - 65.48: 1800 65.48 - 98.22: 38 98.22 - 130.95: 1 130.95 - 163.69: 3 Dihedral angle restraints: 9242 sinusoidal: 5730 harmonic: 3512 Sorted by residual: dihedral pdb=" C LEU E 82 " pdb=" N LEU E 82 " pdb=" CA LEU E 82 " pdb=" CB LEU E 82 " ideal model delta harmonic sigma weight residual -122.60 -108.48 -14.12 0 2.50e+00 1.60e-01 3.19e+01 dihedral pdb=" C SER H 33 " pdb=" N SER H 33 " pdb=" CA SER H 33 " pdb=" CB SER H 33 " ideal model delta harmonic sigma weight residual -122.60 -134.48 11.88 0 2.50e+00 1.60e-01 2.26e+01 dihedral pdb=" CA PRO D 104 " pdb=" C PRO D 104 " pdb=" N GLY D 105 " pdb=" CA GLY D 105 " ideal model delta harmonic sigma weight residual -180.00 -156.77 -23.23 0 5.00e+00 4.00e-02 2.16e+01 ... (remaining 9239 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.137: 2621 0.137 - 0.275: 32 0.275 - 0.412: 6 0.412 - 0.549: 2 0.549 - 0.687: 2 Chirality restraints: 2663 Sorted by residual: chirality pdb=" CA SER H 33 " pdb=" N SER H 33 " pdb=" C SER H 33 " pdb=" CB SER H 33 " both_signs ideal model delta sigma weight residual False 2.51 1.82 0.69 2.00e-01 2.50e+01 1.18e+01 chirality pdb=" CG LEU C 93 " pdb=" CB LEU C 93 " pdb=" CD1 LEU C 93 " pdb=" CD2 LEU C 93 " both_signs ideal model delta sigma weight residual False -2.59 -1.94 -0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" CA LYS C 13 " pdb=" N LYS C 13 " pdb=" C LYS C 13 " pdb=" CB LYS C 13 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.44 2.00e-01 2.50e+01 4.73e+00 ... (remaining 2660 not shown) Planarity restraints: 1949 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU C 92 " 0.035 2.00e-02 2.50e+03 7.33e-02 5.37e+01 pdb=" C GLU C 92 " -0.127 2.00e-02 2.50e+03 pdb=" O GLU C 92 " 0.049 2.00e-02 2.50e+03 pdb=" N LEU C 93 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET C 51 " 0.027 2.00e-02 2.50e+03 5.37e-02 2.89e+01 pdb=" C MET C 51 " -0.093 2.00e-02 2.50e+03 pdb=" O MET C 51 " 0.035 2.00e-02 2.50e+03 pdb=" N ALA C 52 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR N 62 " 0.084 5.00e-02 4.00e+02 1.26e-01 2.55e+01 pdb=" N PRO N 63 " -0.218 5.00e-02 4.00e+02 pdb=" CA PRO N 63 " 0.068 5.00e-02 4.00e+02 pdb=" CD PRO N 63 " 0.066 5.00e-02 4.00e+02 ... (remaining 1946 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 262 2.65 - 3.21: 11930 3.21 - 3.78: 28256 3.78 - 4.34: 38800 4.34 - 4.90: 56217 Nonbonded interactions: 135465 Sorted by model distance: nonbonded pdb=" O SER H 33 " pdb=" OG SER H 33 " model vdw 2.088 3.040 nonbonded pdb=" CG LYS C 13 " pdb=" N ALA C 14 " model vdw 2.181 3.520 nonbonded pdb=" CA MET C 51 " pdb=" SD MET C 51 " model vdw 2.308 3.064 nonbonded pdb=" O MET C 51 " pdb=" CG MET C 51 " model vdw 2.318 3.440 nonbonded pdb=" OG SER C 18 " pdb=" O PHE C 25 " model vdw 2.325 3.040 ... (remaining 135460 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 38 through 133) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 23 through 101) } ncs_group { reference = (chain 'C' and (resid 12 through 117 or (resid 118 and (name N or name CA or nam \ e C or name O or name CB )))) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 32 through 125) selection = (chain 'H' and resid 32 through 125) } ncs_group { reference = chain 'K' selection = (chain 'N' and (resid 23 through 187 or (resid 188 and (name N or name CA or nam \ e C or name O or name CB )) or resid 189 through 264 or (resid 265 and (name N o \ r name CA or name C or name O or name CB )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 41.730 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:34.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 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 : 0.008 0.192 16533 Z= 0.491 Angle : 0.933 29.745 23626 Z= 0.528 Chirality : 0.053 0.687 2663 Planarity : 0.007 0.126 1949 Dihedral : 27.006 163.693 6980 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.64 % Favored : 95.28 % Rotamer: Outliers : 0.39 % Allowed : 21.92 % Favored : 77.69 % Cbeta Deviations : 0.27 % 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: -0.97 (0.22), residues: 1186 helix: -0.21 (0.19), residues: 537 sheet: -0.23 (0.34), residues: 234 loop : -1.27 (0.27), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP N 58 HIS 0.006 0.002 HIS C 31 PHE 0.029 0.003 PHE A 78 TYR 0.045 0.002 TYR H 41 ARG 0.013 0.000 ARG D 100 Details of bonding type rmsd hydrogen bonds : bond 0.11540 ( 856) hydrogen bonds : angle 5.36986 ( 2178) SS BOND : bond 0.00303 ( 4) SS BOND : angle 1.23296 ( 8) covalent geometry : bond 0.00814 (16529) covalent geometry : angle 0.93257 (23618) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 172 time to evaluate : 1.319 Fit side-chains revert: symmetry clash REVERT: H 69 ASP cc_start: 0.8354 (t70) cc_final: 0.8114 (t0) outliers start: 4 outliers final: 1 residues processed: 176 average time/residue: 1.6244 time to fit residues: 309.2602 Evaluate side-chains 135 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 134 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 59 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 0.9990 chunk 108 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 73 optimal weight: 8.9990 chunk 57 optimal weight: 4.9990 chunk 112 optimal weight: 10.0000 chunk 43 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 129 optimal weight: 9.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 57 GLN K 196 GLN N 196 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.136325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.095031 restraints weight = 22505.493| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.76 r_work: 0.3259 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16533 Z= 0.173 Angle : 0.573 7.604 23626 Z= 0.336 Chirality : 0.035 0.183 2663 Planarity : 0.005 0.080 1949 Dihedral : 29.573 152.521 4680 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.94 % Allowed : 22.80 % Favored : 74.27 % 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: 0.49 (0.24), residues: 1186 helix: 1.50 (0.22), residues: 546 sheet: -0.03 (0.34), residues: 234 loop : -1.03 (0.28), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 58 HIS 0.005 0.001 HIS H 50 PHE 0.010 0.001 PHE N 229 TYR 0.027 0.001 TYR H 41 ARG 0.004 0.000 ARG H 34 Details of bonding type rmsd hydrogen bonds : bond 0.03963 ( 856) hydrogen bonds : angle 3.62338 ( 2178) SS BOND : bond 0.00522 ( 4) SS BOND : angle 0.87981 ( 8) covalent geometry : bond 0.00386 (16529) covalent geometry : angle 0.57246 (23618) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 148 time to evaluate : 1.167 Fit side-chains REVERT: D 40 ILE cc_start: 0.7800 (OUTLIER) cc_final: 0.7525 (pt) REVERT: D 48 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7927 (mt0) REVERT: D 77 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.6895 (tm-30) REVERT: E 50 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7516 (mt-10) REVERT: E 59 GLU cc_start: 0.8163 (pm20) cc_final: 0.7844 (pm20) REVERT: H 69 ASP cc_start: 0.8309 (t70) cc_final: 0.7948 (t0) REVERT: K 103 MET cc_start: 0.7937 (OUTLIER) cc_final: 0.5570 (tpt) REVERT: K 111 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7926 (pp20) REVERT: N 95 ASP cc_start: 0.8008 (t70) cc_final: 0.7542 (t70) outliers start: 30 outliers final: 13 residues processed: 164 average time/residue: 1.8244 time to fit residues: 323.7042 Evaluate side-chains 145 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 1.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 48 GLN Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain K residue 103 MET Chi-restraints excluded: chain K residue 111 GLU Chi-restraints excluded: chain K residue 191 LEU Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 80 THR Chi-restraints excluded: chain N residue 137 SER Chi-restraints excluded: chain N residue 139 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 119 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 95 optimal weight: 6.9990 chunk 114 optimal weight: 0.9990 chunk 4 optimal weight: 0.0370 chunk 27 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 overall best weight: 0.7662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 196 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.137337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.096056 restraints weight = 22541.818| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.75 r_work: 0.3275 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16533 Z= 0.143 Angle : 0.560 9.055 23626 Z= 0.329 Chirality : 0.035 0.292 2663 Planarity : 0.004 0.063 1949 Dihedral : 29.561 153.313 4680 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.03 % Allowed : 23.97 % Favored : 72.99 % 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: 1.01 (0.24), residues: 1186 helix: 2.08 (0.22), residues: 546 sheet: 0.04 (0.34), residues: 234 loop : -0.89 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 58 HIS 0.004 0.001 HIS H 50 PHE 0.009 0.001 PHE N 229 TYR 0.019 0.001 TYR H 41 ARG 0.001 0.000 ARG F 45 Details of bonding type rmsd hydrogen bonds : bond 0.03625 ( 856) hydrogen bonds : angle 3.51445 ( 2178) SS BOND : bond 0.00396 ( 4) SS BOND : angle 0.75194 ( 8) covalent geometry : bond 0.00313 (16529) covalent geometry : angle 0.55977 (23618) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 148 time to evaluate : 1.230 Fit side-chains REVERT: C 73 ASN cc_start: 0.7962 (OUTLIER) cc_final: 0.7673 (t0) REVERT: C 91 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.8013 (tt0) REVERT: D 40 ILE cc_start: 0.7809 (OUTLIER) cc_final: 0.7560 (pt) REVERT: D 48 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7903 (mt0) REVERT: D 77 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.6904 (tm-30) REVERT: E 50 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7519 (mt-10) REVERT: E 59 GLU cc_start: 0.8109 (pm20) cc_final: 0.7774 (pm20) REVERT: E 120 MET cc_start: 0.8164 (OUTLIER) cc_final: 0.7345 (mtt) REVERT: F 93 GLN cc_start: 0.7802 (mt0) cc_final: 0.7445 (mp10) REVERT: G 116 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8059 (mm) REVERT: K 111 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7830 (pp20) REVERT: K 161 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.7987 (ptpp) REVERT: N 95 ASP cc_start: 0.8027 (t70) cc_final: 0.7634 (t70) REVERT: N 247 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7519 (tp) outliers start: 31 outliers final: 13 residues processed: 162 average time/residue: 1.5453 time to fit residues: 271.7882 Evaluate side-chains 157 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 1.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 48 GLN Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain K residue 111 GLU Chi-restraints excluded: chain K residue 161 LYS Chi-restraints excluded: chain K residue 191 LEU Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 80 THR Chi-restraints excluded: chain N residue 137 SER Chi-restraints excluded: chain N residue 247 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 72 optimal weight: 10.0000 chunk 101 optimal weight: 3.9990 chunk 85 optimal weight: 10.0000 chunk 139 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 112 optimal weight: 0.0060 chunk 64 optimal weight: 2.9990 chunk 133 optimal weight: 7.9990 overall best weight: 3.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 164 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 = 0.3847 r_free = 0.3847 target = 0.131837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.090141 restraints weight = 22540.567| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.79 r_work: 0.3177 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 16533 Z= 0.306 Angle : 0.649 8.254 23626 Z= 0.374 Chirality : 0.041 0.140 2663 Planarity : 0.005 0.059 1949 Dihedral : 29.963 156.788 4680 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 4.79 % Allowed : 22.80 % Favored : 72.41 % 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: 0.92 (0.24), residues: 1186 helix: 1.86 (0.22), residues: 546 sheet: 0.25 (0.33), residues: 256 loop : -0.94 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP N 58 HIS 0.008 0.002 HIS H 50 PHE 0.011 0.002 PHE N 229 TYR 0.019 0.002 TYR N 72 ARG 0.005 0.001 ARG F 45 Details of bonding type rmsd hydrogen bonds : bond 0.04900 ( 856) hydrogen bonds : angle 3.71793 ( 2178) SS BOND : bond 0.00779 ( 4) SS BOND : angle 1.04195 ( 8) covalent geometry : bond 0.00707 (16529) covalent geometry : angle 0.64910 (23618) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 145 time to evaluate : 1.239 Fit side-chains REVERT: A 59 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7044 (pp20) REVERT: B 79 LYS cc_start: 0.8091 (OUTLIER) cc_final: 0.7738 (mttp) REVERT: C 24 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.7317 (mp10) REVERT: C 73 ASN cc_start: 0.8178 (OUTLIER) cc_final: 0.7903 (t0) REVERT: C 91 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.8020 (tt0) REVERT: D 48 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.7872 (mt0) REVERT: D 77 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.6781 (tm-30) REVERT: E 49 ARG cc_start: 0.7788 (OUTLIER) cc_final: 0.6383 (ptp90) REVERT: E 59 GLU cc_start: 0.7988 (pm20) cc_final: 0.7723 (pm20) REVERT: E 120 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.7647 (mtt) REVERT: G 64 GLU cc_start: 0.8107 (tt0) cc_final: 0.7764 (tp30) REVERT: G 73 ASN cc_start: 0.7569 (t0) cc_final: 0.7311 (t0) REVERT: G 91 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7135 (tt0) REVERT: G 116 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8207 (mm) REVERT: H 69 ASP cc_start: 0.8419 (t0) cc_final: 0.8056 (t0) REVERT: H 87 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7166 (mtt90) REVERT: K 103 MET cc_start: 0.8176 (OUTLIER) cc_final: 0.5668 (tpt) REVERT: K 111 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7863 (pp20) REVERT: K 161 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.8123 (ptpp) REVERT: N 73 ILE cc_start: 0.8380 (OUTLIER) cc_final: 0.8154 (tp) REVERT: N 95 ASP cc_start: 0.8032 (t70) cc_final: 0.7597 (t70) REVERT: N 163 THR cc_start: 0.8713 (m) cc_final: 0.8266 (p) REVERT: N 176 ARG cc_start: 0.7348 (ttm110) cc_final: 0.6611 (mtp180) outliers start: 49 outliers final: 22 residues processed: 172 average time/residue: 1.8221 time to fit residues: 339.4129 Evaluate side-chains 169 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 131 time to evaluate : 1.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 48 GLN Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain K residue 35 GLU Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 103 MET Chi-restraints excluded: chain K residue 111 GLU Chi-restraints excluded: chain K residue 161 LYS Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain K residue 191 LEU Chi-restraints excluded: chain K residue 219 ARG Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 68 GLU Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain N residue 80 THR Chi-restraints excluded: chain N residue 137 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 124 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 132 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 133 optimal weight: 4.9990 chunk 86 optimal weight: 7.9990 chunk 60 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 58 optimal weight: 0.2980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 164 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 = 0.3950 r_free = 0.3950 target = 0.139154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.099581 restraints weight = 22641.182| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.68 r_work: 0.3355 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16533 Z= 0.151 Angle : 0.574 7.740 23626 Z= 0.336 Chirality : 0.036 0.220 2663 Planarity : 0.004 0.050 1949 Dihedral : 29.804 154.921 4680 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.82 % Allowed : 24.07 % Favored : 72.11 % 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: 1.30 (0.25), residues: 1186 helix: 2.27 (0.22), residues: 545 sheet: 0.33 (0.33), residues: 256 loop : -0.82 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 58 HIS 0.003 0.001 HIS H 50 PHE 0.006 0.001 PHE F 61 TYR 0.014 0.001 TYR N 72 ARG 0.003 0.000 ARG C 71 Details of bonding type rmsd hydrogen bonds : bond 0.03770 ( 856) hydrogen bonds : angle 3.47010 ( 2178) SS BOND : bond 0.00429 ( 4) SS BOND : angle 0.88533 ( 8) covalent geometry : bond 0.00335 (16529) covalent geometry : angle 0.57352 (23618) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 138 time to evaluate : 1.183 Fit side-chains REVERT: B 79 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7734 (mttp) REVERT: C 73 ASN cc_start: 0.8118 (OUTLIER) cc_final: 0.7850 (t0) REVERT: C 91 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.8067 (tt0) REVERT: D 40 ILE cc_start: 0.7894 (OUTLIER) cc_final: 0.7563 (pt) REVERT: D 48 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7969 (mt0) REVERT: D 77 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.6756 (tm-30) REVERT: E 59 GLU cc_start: 0.8131 (pm20) cc_final: 0.7910 (pm20) REVERT: E 120 MET cc_start: 0.8350 (OUTLIER) cc_final: 0.7513 (mtt) REVERT: F 93 GLN cc_start: 0.7872 (mt0) cc_final: 0.7567 (mp10) REVERT: G 64 GLU cc_start: 0.8136 (tt0) cc_final: 0.7797 (tp30) REVERT: G 73 ASN cc_start: 0.7488 (t0) cc_final: 0.7206 (t0) REVERT: G 116 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8292 (mm) REVERT: K 103 MET cc_start: 0.8086 (OUTLIER) cc_final: 0.5746 (tpt) REVERT: K 111 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7867 (pp20) REVERT: K 161 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.8089 (ptpp) REVERT: N 73 ILE cc_start: 0.8432 (OUTLIER) cc_final: 0.8214 (tp) REVERT: N 95 ASP cc_start: 0.8074 (t70) cc_final: 0.7677 (t70) REVERT: N 163 THR cc_start: 0.8763 (m) cc_final: 0.8352 (p) outliers start: 39 outliers final: 16 residues processed: 160 average time/residue: 1.7054 time to fit residues: 296.5524 Evaluate side-chains 159 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 48 GLN Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 52 ASP Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain K residue 35 GLU Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain K residue 103 MET Chi-restraints excluded: chain K residue 111 GLU Chi-restraints excluded: chain K residue 161 LYS Chi-restraints excluded: chain K residue 191 LEU Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain N residue 80 THR Chi-restraints excluded: chain N residue 137 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 40 optimal weight: 0.9990 chunk 130 optimal weight: 7.9990 chunk 91 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 115 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 chunk 112 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 164 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 = 0.3909 r_free = 0.3909 target = 0.135855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.097099 restraints weight = 22504.477| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.65 r_work: 0.3314 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 16533 Z= 0.291 Angle : 0.635 7.970 23626 Z= 0.366 Chirality : 0.040 0.139 2663 Planarity : 0.004 0.049 1949 Dihedral : 29.824 156.184 4680 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 4.50 % Allowed : 23.78 % Favored : 71.72 % 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: 1.07 (0.25), residues: 1186 helix: 2.02 (0.22), residues: 546 sheet: 0.32 (0.33), residues: 256 loop : -0.93 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP N 58 HIS 0.007 0.002 HIS H 50 PHE 0.012 0.002 PHE N 229 TYR 0.019 0.002 TYR N 72 ARG 0.005 0.000 ARG F 45 Details of bonding type rmsd hydrogen bonds : bond 0.04921 ( 856) hydrogen bonds : angle 3.63746 ( 2178) SS BOND : bond 0.00684 ( 4) SS BOND : angle 0.98820 ( 8) covalent geometry : bond 0.00676 (16529) covalent geometry : angle 0.63452 (23618) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 133 time to evaluate : 1.279 Fit side-chains REVERT: A 59 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7088 (pp20) REVERT: B 79 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7833 (mttp) REVERT: C 24 GLN cc_start: 0.8706 (OUTLIER) cc_final: 0.7389 (mp10) REVERT: C 73 ASN cc_start: 0.8281 (OUTLIER) cc_final: 0.7982 (t0) REVERT: C 91 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.8099 (tt0) REVERT: D 48 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7840 (mt0) REVERT: D 77 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.6806 (tm-30) REVERT: D 87 ARG cc_start: 0.7617 (OUTLIER) cc_final: 0.6981 (ttm-80) REVERT: E 49 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.6485 (ptp90) REVERT: E 59 GLU cc_start: 0.8097 (pm20) cc_final: 0.7755 (pm20) REVERT: E 120 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.7751 (mtt) REVERT: G 64 GLU cc_start: 0.8179 (tt0) cc_final: 0.7844 (tp30) REVERT: G 73 ASN cc_start: 0.7660 (t0) cc_final: 0.7384 (t0) REVERT: G 91 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7378 (tt0) REVERT: G 116 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8341 (mm) REVERT: H 69 ASP cc_start: 0.8511 (t0) cc_final: 0.7989 (t0) REVERT: K 103 MET cc_start: 0.8257 (OUTLIER) cc_final: 0.5748 (tpt) REVERT: K 111 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7860 (pp20) REVERT: K 161 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.8141 (ptpp) REVERT: N 73 ILE cc_start: 0.8492 (OUTLIER) cc_final: 0.8281 (tp) REVERT: N 95 ASP cc_start: 0.8099 (t70) cc_final: 0.7670 (t70) REVERT: N 163 THR cc_start: 0.8784 (m) cc_final: 0.8366 (p) outliers start: 46 outliers final: 20 residues processed: 159 average time/residue: 1.7813 time to fit residues: 307.0647 Evaluate side-chains 166 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 130 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 48 GLN Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 87 ARG Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain K residue 35 GLU Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain K residue 103 MET Chi-restraints excluded: chain K residue 111 GLU Chi-restraints excluded: chain K residue 161 LYS Chi-restraints excluded: chain K residue 191 LEU Chi-restraints excluded: chain K residue 219 ARG Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain N residue 80 THR Chi-restraints excluded: chain N residue 137 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 61 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 126 optimal weight: 0.0570 chunk 106 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 119 optimal weight: 3.9990 chunk 138 optimal weight: 0.3980 chunk 142 optimal weight: 4.9990 chunk 105 optimal weight: 8.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 164 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 = 0.3948 r_free = 0.3948 target = 0.138986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.100464 restraints weight = 22446.840| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 1.57 r_work: 0.3367 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16533 Z= 0.138 Angle : 0.582 8.362 23626 Z= 0.341 Chirality : 0.036 0.141 2663 Planarity : 0.004 0.045 1949 Dihedral : 29.833 156.462 4680 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.42 % Allowed : 24.95 % Favored : 71.62 % 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: 1.36 (0.25), residues: 1186 helix: 2.31 (0.22), residues: 549 sheet: 0.36 (0.33), residues: 256 loop : -0.81 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 58 HIS 0.003 0.001 HIS K 249 PHE 0.007 0.001 PHE N 229 TYR 0.011 0.001 TYR N 72 ARG 0.005 0.000 ARG N 176 Details of bonding type rmsd hydrogen bonds : bond 0.03649 ( 856) hydrogen bonds : angle 3.46616 ( 2178) SS BOND : bond 0.00357 ( 4) SS BOND : angle 0.87100 ( 8) covalent geometry : bond 0.00294 (16529) covalent geometry : angle 0.58163 (23618) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 139 time to evaluate : 1.415 Fit side-chains REVERT: B 79 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7554 (mttt) REVERT: C 73 ASN cc_start: 0.8149 (OUTLIER) cc_final: 0.7861 (t0) REVERT: C 91 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.8006 (tt0) REVERT: D 40 ILE cc_start: 0.7899 (OUTLIER) cc_final: 0.7544 (pt) REVERT: D 48 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.7849 (mt0) REVERT: D 77 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.6803 (tm-30) REVERT: E 49 ARG cc_start: 0.7850 (OUTLIER) cc_final: 0.6631 (ptp90) REVERT: E 59 GLU cc_start: 0.8162 (pm20) cc_final: 0.7881 (pm20) REVERT: F 93 GLN cc_start: 0.7817 (mt0) cc_final: 0.7546 (mp10) REVERT: G 73 ASN cc_start: 0.7475 (t0) cc_final: 0.7183 (t0) REVERT: H 69 ASP cc_start: 0.8324 (t0) cc_final: 0.7736 (t0) REVERT: H 102 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8370 (mm) REVERT: K 103 MET cc_start: 0.8115 (OUTLIER) cc_final: 0.5774 (tpt) REVERT: K 111 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7867 (pp20) REVERT: N 73 ILE cc_start: 0.8427 (OUTLIER) cc_final: 0.8190 (tp) REVERT: N 95 ASP cc_start: 0.7994 (t70) cc_final: 0.7575 (t70) REVERT: N 163 THR cc_start: 0.8699 (m) cc_final: 0.8298 (p) REVERT: N 176 ARG cc_start: 0.7043 (OUTLIER) cc_final: 0.6617 (mmm160) outliers start: 35 outliers final: 13 residues processed: 158 average time/residue: 1.6896 time to fit residues: 289.1753 Evaluate side-chains 158 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 48 GLN Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain K residue 103 MET Chi-restraints excluded: chain K residue 111 GLU Chi-restraints excluded: chain K residue 191 LEU Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain N residue 80 THR Chi-restraints excluded: chain N residue 137 SER Chi-restraints excluded: chain N residue 176 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 32 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 113 optimal weight: 8.9990 chunk 118 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 110 optimal weight: 9.9990 chunk 58 optimal weight: 0.8980 chunk 139 optimal weight: 9.9990 chunk 132 optimal weight: 10.0000 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 164 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 = 0.3928 r_free = 0.3928 target = 0.137297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.097719 restraints weight = 22385.779| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.69 r_work: 0.3331 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 16533 Z= 0.216 Angle : 0.597 7.902 23626 Z= 0.347 Chirality : 0.037 0.137 2663 Planarity : 0.004 0.045 1949 Dihedral : 29.727 156.156 4680 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.82 % Allowed : 25.05 % Favored : 71.14 % 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: 1.29 (0.25), residues: 1186 helix: 2.25 (0.22), residues: 549 sheet: 0.36 (0.33), residues: 256 loop : -0.86 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 58 HIS 0.006 0.001 HIS H 50 PHE 0.009 0.001 PHE N 229 TYR 0.025 0.002 TYR H 41 ARG 0.003 0.000 ARG N 176 Details of bonding type rmsd hydrogen bonds : bond 0.04126 ( 856) hydrogen bonds : angle 3.48824 ( 2178) SS BOND : bond 0.00507 ( 4) SS BOND : angle 0.93378 ( 8) covalent geometry : bond 0.00497 (16529) covalent geometry : angle 0.59729 (23618) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 135 time to evaluate : 1.163 Fit side-chains REVERT: A 59 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7058 (pp20) REVERT: B 79 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7804 (mttp) REVERT: C 73 ASN cc_start: 0.8214 (OUTLIER) cc_final: 0.7940 (t0) REVERT: C 91 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.8061 (tt0) REVERT: D 77 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.6816 (tm-30) REVERT: E 49 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.6497 (ptp90) REVERT: E 59 GLU cc_start: 0.8120 (pm20) cc_final: 0.7736 (pm20) REVERT: E 120 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.7720 (mtt) REVERT: F 93 GLN cc_start: 0.7945 (mt0) cc_final: 0.7597 (mp10) REVERT: G 64 GLU cc_start: 0.8133 (tt0) cc_final: 0.7801 (tp30) REVERT: G 73 ASN cc_start: 0.7613 (t0) cc_final: 0.7317 (t0) REVERT: H 69 ASP cc_start: 0.8354 (t0) cc_final: 0.7964 (t0) REVERT: H 102 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8443 (mm) REVERT: K 103 MET cc_start: 0.8194 (OUTLIER) cc_final: 0.5709 (tpt) REVERT: K 111 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7907 (pp20) REVERT: N 73 ILE cc_start: 0.8462 (OUTLIER) cc_final: 0.8246 (tp) REVERT: N 95 ASP cc_start: 0.8104 (t70) cc_final: 0.7685 (t70) REVERT: N 163 THR cc_start: 0.8712 (m) cc_final: 0.8264 (p) outliers start: 39 outliers final: 16 residues processed: 156 average time/residue: 1.5145 time to fit residues: 256.7129 Evaluate side-chains 160 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 133 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain H residue 35 LYS Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain K residue 103 MET Chi-restraints excluded: chain K residue 111 GLU Chi-restraints excluded: chain K residue 191 LEU Chi-restraints excluded: chain K residue 219 ARG Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain N residue 80 THR Chi-restraints excluded: chain N residue 137 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 138 optimal weight: 0.9990 chunk 118 optimal weight: 0.8980 chunk 88 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 116 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 132 optimal weight: 6.9990 chunk 34 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 164 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 = 0.3938 r_free = 0.3938 target = 0.138203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.099449 restraints weight = 22406.129| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 1.57 r_work: 0.3349 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16533 Z= 0.155 Angle : 0.590 10.968 23626 Z= 0.343 Chirality : 0.036 0.141 2663 Planarity : 0.004 0.043 1949 Dihedral : 29.732 156.231 4680 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.13 % Allowed : 25.64 % Favored : 71.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.39 (0.25), residues: 1186 helix: 2.36 (0.22), residues: 549 sheet: 0.37 (0.33), residues: 256 loop : -0.84 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 58 HIS 0.005 0.001 HIS H 50 PHE 0.008 0.001 PHE N 229 TYR 0.032 0.001 TYR H 41 ARG 0.006 0.000 ARG N 176 Details of bonding type rmsd hydrogen bonds : bond 0.03887 ( 856) hydrogen bonds : angle 3.45378 ( 2178) SS BOND : bond 0.00475 ( 4) SS BOND : angle 0.85727 ( 8) covalent geometry : bond 0.00343 (16529) covalent geometry : angle 0.58983 (23618) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 134 time to evaluate : 1.171 Fit side-chains REVERT: A 59 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7065 (pp20) REVERT: B 79 LYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7571 (mttt) REVERT: C 73 ASN cc_start: 0.8168 (OUTLIER) cc_final: 0.7878 (t0) REVERT: C 91 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.8046 (tt0) REVERT: D 40 ILE cc_start: 0.7935 (OUTLIER) cc_final: 0.7543 (pt) REVERT: D 77 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.6830 (tm-30) REVERT: E 49 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.6484 (ptp90) REVERT: E 59 GLU cc_start: 0.8111 (pm20) cc_final: 0.7720 (pm20) REVERT: E 120 MET cc_start: 0.8423 (OUTLIER) cc_final: 0.7665 (mtt) REVERT: F 93 GLN cc_start: 0.7901 (mt0) cc_final: 0.7600 (mp10) REVERT: G 64 GLU cc_start: 0.8122 (tt0) cc_final: 0.7791 (tp30) REVERT: G 73 ASN cc_start: 0.7489 (t0) cc_final: 0.7190 (t0) REVERT: H 69 ASP cc_start: 0.8324 (t0) cc_final: 0.7765 (t0) REVERT: H 102 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8384 (mm) REVERT: K 103 MET cc_start: 0.8155 (OUTLIER) cc_final: 0.5748 (tpt) REVERT: K 111 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7901 (pp20) REVERT: N 73 ILE cc_start: 0.8431 (OUTLIER) cc_final: 0.8195 (tp) REVERT: N 95 ASP cc_start: 0.8071 (t70) cc_final: 0.7652 (t70) REVERT: N 163 THR cc_start: 0.8686 (m) cc_final: 0.8243 (p) outliers start: 32 outliers final: 17 residues processed: 150 average time/residue: 1.5699 time to fit residues: 255.2084 Evaluate side-chains 162 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 133 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain H residue 52 ASP Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain K residue 23 GLU Chi-restraints excluded: chain K residue 35 GLU Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain K residue 103 MET Chi-restraints excluded: chain K residue 111 GLU Chi-restraints excluded: chain K residue 191 LEU Chi-restraints excluded: chain K residue 219 ARG Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain N residue 80 THR Chi-restraints excluded: chain N residue 137 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 142 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 47 optimal weight: 4.9990 chunk 7 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 chunk 28 optimal weight: 0.1980 chunk 115 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 164 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 = 0.3944 r_free = 0.3944 target = 0.138690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.099983 restraints weight = 22624.281| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 1.58 r_work: 0.3358 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16533 Z= 0.146 Angle : 0.583 8.687 23626 Z= 0.340 Chirality : 0.035 0.141 2663 Planarity : 0.004 0.043 1949 Dihedral : 29.719 156.182 4680 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.84 % Allowed : 26.03 % Favored : 71.14 % 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: 1.43 (0.25), residues: 1186 helix: 2.40 (0.22), residues: 549 sheet: 0.37 (0.33), residues: 256 loop : -0.82 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 58 HIS 0.004 0.001 HIS H 50 PHE 0.007 0.001 PHE N 229 TYR 0.013 0.001 TYR N 72 ARG 0.005 0.000 ARG N 176 Details of bonding type rmsd hydrogen bonds : bond 0.03718 ( 856) hydrogen bonds : angle 3.42905 ( 2178) SS BOND : bond 0.00386 ( 4) SS BOND : angle 0.81657 ( 8) covalent geometry : bond 0.00320 (16529) covalent geometry : angle 0.58263 (23618) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 134 time to evaluate : 1.408 Fit side-chains REVERT: B 79 LYS cc_start: 0.8087 (OUTLIER) cc_final: 0.7513 (mttt) REVERT: C 73 ASN cc_start: 0.8104 (OUTLIER) cc_final: 0.7793 (t0) REVERT: C 91 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.8010 (tt0) REVERT: D 40 ILE cc_start: 0.7853 (OUTLIER) cc_final: 0.7476 (pt) REVERT: D 77 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.6741 (tm-30) REVERT: D 87 ARG cc_start: 0.7461 (OUTLIER) cc_final: 0.6783 (ttm-80) REVERT: E 49 ARG cc_start: 0.7788 (OUTLIER) cc_final: 0.6407 (ptp90) REVERT: E 59 GLU cc_start: 0.8059 (pm20) cc_final: 0.7648 (pm20) REVERT: E 120 MET cc_start: 0.8341 (OUTLIER) cc_final: 0.7591 (mtt) REVERT: F 93 GLN cc_start: 0.7855 (mt0) cc_final: 0.7545 (mp10) REVERT: G 64 GLU cc_start: 0.8066 (tt0) cc_final: 0.7727 (tp30) REVERT: G 73 ASN cc_start: 0.7450 (t0) cc_final: 0.7129 (t0) REVERT: H 69 ASP cc_start: 0.8254 (t0) cc_final: 0.7673 (t0) REVERT: H 102 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8303 (mm) REVERT: K 103 MET cc_start: 0.8111 (OUTLIER) cc_final: 0.5742 (tpt) REVERT: K 111 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7901 (pp20) REVERT: N 73 ILE cc_start: 0.8387 (OUTLIER) cc_final: 0.8160 (tp) REVERT: N 95 ASP cc_start: 0.8025 (t70) cc_final: 0.7589 (t70) REVERT: N 163 THR cc_start: 0.8670 (m) cc_final: 0.8235 (p) REVERT: N 176 ARG cc_start: 0.6969 (ttm110) cc_final: 0.6339 (mtp180) outliers start: 29 outliers final: 16 residues processed: 149 average time/residue: 1.6533 time to fit residues: 266.6150 Evaluate side-chains 160 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 132 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 87 ARG Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain K residue 23 GLU Chi-restraints excluded: chain K residue 35 GLU Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain K residue 103 MET Chi-restraints excluded: chain K residue 111 GLU Chi-restraints excluded: chain K residue 191 LEU Chi-restraints excluded: chain K residue 219 ARG Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain N residue 80 THR Chi-restraints excluded: chain N residue 137 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 42 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 89 optimal weight: 5.9990 chunk 141 optimal weight: 8.9990 chunk 54 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 164 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 = 0.3935 r_free = 0.3935 target = 0.137928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.099206 restraints weight = 22504.254| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.60 r_work: 0.3347 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16533 Z= 0.195 Angle : 0.588 9.115 23626 Z= 0.341 Chirality : 0.036 0.138 2663 Planarity : 0.004 0.043 1949 Dihedral : 29.651 156.479 4680 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.03 % Allowed : 26.03 % Favored : 70.94 % 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: 1.41 (0.25), residues: 1186 helix: 2.39 (0.22), residues: 545 sheet: 0.41 (0.34), residues: 256 loop : -0.83 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 58 HIS 0.005 0.001 HIS H 50 PHE 0.009 0.001 PHE N 229 TYR 0.016 0.001 TYR N 72 ARG 0.008 0.000 ARG N 176 Details of bonding type rmsd hydrogen bonds : bond 0.03941 ( 856) hydrogen bonds : angle 3.43278 ( 2178) SS BOND : bond 0.00472 ( 4) SS BOND : angle 0.85153 ( 8) covalent geometry : bond 0.00445 (16529) covalent geometry : angle 0.58741 (23618) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13665.09 seconds wall clock time: 239 minutes 48.47 seconds (14388.47 seconds total)