Starting phenix.real_space_refine on Sat Sep 12 10:28:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u0j_26261/09_2026/7u0j_26261.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u0j_26261/09_2026/7u0j_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_26261/09_2026/7u0j_26261.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u0j_26261/09_2026/7u0j_26261.map" model { file = "/net/cci-nas-00/data/ceres_data/7u0j_26261/09_2026/7u0j_26261.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u0j_26261/09_2026/7u0j_26261.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 3.65, per 1000 atoms: 0.23 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: 1.28 Conformation dependent library (CDL) restraints added in 535.4 milliseconds 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: 2.23 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: 3.10 Time building geometry restraints manager: 1.73 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: 2619 0.137 - 0.275: 34 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: 1.450 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.100 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 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 : 0.009 0.192 16533 Z= 0.673 Angle : 1.039 29.745 23626 Z= 0.774 Chirality : 0.057 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (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 ARG 0.013 0.000 ARG D 100 TYR 0.045 0.002 TYR H 41 PHE 0.029 0.003 PHE A 78 TRP 0.010 0.002 TRP N 58 HIS 0.006 0.002 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00906 / 0.67 (16529) covalent geometry : angle 1.03910 / 0.77 (23618) SS BOND : bond 0.00303 / 0.20 ( 4) SS BOND : angle 1.23296 / 0.67 ( 8) hydrogen bonds : bond 0.11540 / 8.05 ( 856) hydrogen bonds : angle 5.36986 / 3.90 ( 2178) *********************** 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 : 0.394 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: 0.7906 time to fit residues: 150.3970 Evaluate side-chains 136 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 135 time to evaluate : 0.469 ------------------------------------------------------------------------------- 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 98 optimal weight: 20.0000 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 9.9990 chunk 55 optimal weight: 2.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 57 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.134146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.092477 restraints weight = 22432.388| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.75 r_work: 0.3214 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 16533 Z= 0.243 Angle : 0.707 8.285 23626 Z= 0.396 Chirality : 0.050 0.319 2663 Planarity : 0.005 0.082 1949 Dihedral : 29.837 155.623 4680 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.52 % Allowed : 22.11 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.24), residues: 1186 helix: 1.25 (0.22), residues: 541 sheet: -0.06 (0.34), residues: 234 loop : -1.12 (0.28), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 131 TYR 0.019 0.002 TYR C 50 PHE 0.013 0.002 PHE N 229 TRP 0.015 0.002 TRP N 58 HIS 0.008 0.002 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.24 (16529) covalent geometry : angle 0.70692 / 0.40 (23618) SS BOND : bond 0.00595 / 0.35 ( 4) SS BOND : angle 1.20579 / 0.71 ( 8) hydrogen bonds : bond 0.05187 / 3.46 ( 856) hydrogen bonds : angle 3.96166 / 2.96 ( 2178) *********************** 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 183 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 147 time to evaluate : 0.470 Fit side-chains REVERT: B 79 LYS cc_start: 0.8088 (OUTLIER) cc_final: 0.7733 (mttp) REVERT: C 51 MET cc_start: 0.8621 (tpp) cc_final: 0.8356 (ttm) REVERT: D 40 ILE cc_start: 0.7966 (OUTLIER) cc_final: 0.7529 (pt) REVERT: D 77 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.7139 (tm-30) REVERT: E 50 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7467 (mt-10) REVERT: E 59 GLU cc_start: 0.8157 (pm20) cc_final: 0.7849 (pm20) REVERT: E 120 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.7494 (mtt) REVERT: G 116 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8112 (mm) REVERT: H 69 ASP cc_start: 0.8431 (t70) cc_final: 0.8088 (t0) REVERT: H 87 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.7254 (mtt90) REVERT: K 111 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7832 (pp20) REVERT: K 161 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.7939 (ptpp) REVERT: N 95 ASP cc_start: 0.7970 (t70) cc_final: 0.7665 (t70) REVERT: N 247 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7473 (tp) outliers start: 36 outliers final: 16 residues processed: 165 average time/residue: 0.7681 time to fit residues: 136.9940 Evaluate side-chains 153 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 0.457 ------------------------------------------------------------------------------- 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 114 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 89 THR 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 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 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 68 GLU 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 9 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 73 optimal weight: 20.0000 chunk 133 optimal weight: 8.9990 chunk 97 optimal weight: 10.9990 chunk 118 optimal weight: 7.9990 chunk 85 optimal weight: 30.0000 chunk 105 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.142305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.102269 restraints weight = 23769.271| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 1.70 r_work: 0.3452 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 16533 Z= 0.268 Angle : 0.719 9.333 23626 Z= 0.395 Chirality : 0.050 0.331 2663 Planarity : 0.005 0.067 1949 Dihedral : 30.170 156.216 4680 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 4.11 % Allowed : 23.09 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.24), residues: 1186 helix: 1.51 (0.22), residues: 546 sheet: -0.01 (0.34), residues: 234 loop : -1.14 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 20 TYR 0.018 0.002 TYR N 72 PHE 0.013 0.002 PHE E 104 TRP 0.017 0.002 TRP N 58 HIS 0.009 0.002 HIS H 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00590 / 0.27 (16529) covalent geometry : angle 0.71884 / 0.40 (23618) SS BOND : bond 0.00684 / 0.39 ( 4) SS BOND : angle 1.23953 / 0.74 ( 8) hydrogen bonds : bond 0.05510 / 3.69 ( 856) hydrogen bonds : angle 3.84461 / 2.86 ( 2178) *********************** 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 184 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 142 time to evaluate : 0.464 Fit side-chains REVERT: A 59 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.6868 (pp20) REVERT: B 79 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7644 (mttt) REVERT: C 51 MET cc_start: 0.8690 (tpp) cc_final: 0.8439 (ttm) REVERT: C 73 ASN cc_start: 0.8278 (OUTLIER) cc_final: 0.8026 (t0) REVERT: C 91 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8140 (tt0) REVERT: D 77 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.6896 (tm-30) REVERT: E 50 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7614 (mt-10) REVERT: E 59 GLU cc_start: 0.8156 (pm20) cc_final: 0.7855 (pm20) REVERT: E 120 MET cc_start: 0.8594 (OUTLIER) cc_final: 0.7802 (mtt) REVERT: G 73 ASN cc_start: 0.7489 (t0) cc_final: 0.7267 (t0) REVERT: G 91 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.7340 (tt0) REVERT: G 116 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8268 (mm) REVERT: H 69 ASP cc_start: 0.8425 (t70) cc_final: 0.8014 (t0) REVERT: H 87 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7368 (mtt90) REVERT: K 103 MET cc_start: 0.8271 (OUTLIER) cc_final: 0.5872 (tpt) REVERT: K 111 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8005 (pp20) REVERT: K 161 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.8031 (ptpp) REVERT: K 235 ASN cc_start: 0.7390 (p0) cc_final: 0.7158 (p0) REVERT: N 95 ASP cc_start: 0.8160 (t70) cc_final: 0.7733 (t70) outliers start: 42 outliers final: 19 residues processed: 166 average time/residue: 0.7157 time to fit residues: 128.9287 Evaluate side-chains 160 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 129 time to evaluate : 0.410 ------------------------------------------------------------------------------- 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 41 GLU 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 77 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 52 ASP 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 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 191 LEU 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 80 THR Chi-restraints excluded: chain N residue 101 VAL Chi-restraints excluded: chain N residue 137 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 92 optimal weight: 9.9990 chunk 122 optimal weight: 20.0000 chunk 64 optimal weight: 1.9990 chunk 100 optimal weight: 7.9990 chunk 25 optimal weight: 0.2980 chunk 14 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 127 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 73 optimal weight: 20.0000 chunk 52 optimal weight: 6.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.144291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.104099 restraints weight = 23886.854| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 1.71 r_work: 0.3476 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3366 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16533 Z= 0.154 Angle : 0.663 9.785 23626 Z= 0.368 Chirality : 0.047 0.339 2663 Planarity : 0.004 0.057 1949 Dihedral : 30.156 155.917 4680 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 4.40 % Allowed : 23.68 % Favored : 71.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.24), residues: 1186 helix: 1.94 (0.22), residues: 546 sheet: 0.12 (0.35), residues: 234 loop : -1.04 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 45 TYR 0.014 0.001 TYR N 72 PHE 0.009 0.001 PHE N 229 TRP 0.011 0.001 TRP N 58 HIS 0.004 0.001 HIS H 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.15 (16529) covalent geometry : angle 0.66305 / 0.37 (23618) SS BOND : bond 0.00541 / 0.31 ( 4) SS BOND : angle 1.00186 / 0.55 ( 8) hydrogen bonds : bond 0.04387 / 2.93 ( 856) hydrogen bonds : angle 3.68662 / 2.75 ( 2178) *********************** 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 179 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 134 time to evaluate : 0.413 Fit side-chains REVERT: B 79 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7573 (mttt) REVERT: C 73 ASN cc_start: 0.8237 (OUTLIER) cc_final: 0.7979 (t0) REVERT: C 91 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8068 (tt0) REVERT: D 40 ILE cc_start: 0.8023 (OUTLIER) cc_final: 0.7645 (pt) REVERT: D 77 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.6849 (tm-30) REVERT: E 49 ARG cc_start: 0.7817 (OUTLIER) cc_final: 0.6420 (ptp90) REVERT: E 50 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7621 (mt-10) REVERT: E 59 GLU cc_start: 0.8190 (pm20) cc_final: 0.7811 (pm20) REVERT: E 120 MET cc_start: 0.8466 (OUTLIER) cc_final: 0.7711 (mtt) REVERT: G 73 ASN cc_start: 0.7306 (t0) cc_final: 0.7066 (t0) REVERT: G 116 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8195 (mm) REVERT: H 69 ASP cc_start: 0.8277 (t70) cc_final: 0.7919 (t0) REVERT: K 103 MET cc_start: 0.8182 (OUTLIER) cc_final: 0.5865 (tpt) REVERT: K 111 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7970 (pp20) REVERT: K 235 ASN cc_start: 0.7359 (p0) cc_final: 0.7111 (p0) REVERT: N 95 ASP cc_start: 0.8107 (t70) cc_final: 0.7670 (t70) outliers start: 45 outliers final: 20 residues processed: 159 average time/residue: 0.7282 time to fit residues: 125.5255 Evaluate side-chains 160 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 130 time to evaluate : 0.433 ------------------------------------------------------------------------------- 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 C residue 114 VAL 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 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 163 THR Chi-restraints excluded: chain K residue 173 LEU 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 101 VAL 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 137 optimal weight: 4.9990 chunk 135 optimal weight: 9.9990 chunk 3 optimal weight: 1.9990 chunk 93 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.145373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.105480 restraints weight = 23792.846| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 1.75 r_work: 0.3493 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16533 Z= 0.146 Angle : 0.624 7.749 23626 Z= 0.351 Chirality : 0.044 0.339 2663 Planarity : 0.004 0.050 1949 Dihedral : 30.031 155.007 4680 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.72 % Allowed : 24.56 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.25), residues: 1186 helix: 2.22 (0.22), residues: 546 sheet: 0.25 (0.35), residues: 234 loop : -0.93 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 20 TYR 0.013 0.001 TYR N 72 PHE 0.008 0.001 PHE F 61 TRP 0.008 0.001 TRP N 58 HIS 0.004 0.001 HIS H 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.15 (16529) covalent geometry : angle 0.62402 / 0.35 (23618) SS BOND : bond 0.00479 / 0.27 ( 4) SS BOND : angle 0.89690 / 0.50 ( 8) hydrogen bonds : bond 0.04090 / 2.75 ( 856) hydrogen bonds : angle 3.52466 / 2.63 ( 2178) *********************** 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: 38 poor density : 139 time to evaluate : 0.331 Fit side-chains REVERT: A 59 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.6796 (pp20) REVERT: C 73 ASN cc_start: 0.8167 (OUTLIER) cc_final: 0.7924 (t0) REVERT: C 91 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8120 (tt0) REVERT: D 40 ILE cc_start: 0.7906 (OUTLIER) cc_final: 0.7606 (pt) REVERT: D 48 GLN cc_start: 0.7944 (OUTLIER) cc_final: 0.7726 (mt0) REVERT: D 77 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.6817 (tm-30) REVERT: E 49 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.6400 (ptp90) REVERT: E 59 GLU cc_start: 0.8212 (pm20) cc_final: 0.7937 (pm20) REVERT: E 120 MET cc_start: 0.8377 (OUTLIER) cc_final: 0.7548 (mtt) REVERT: F 93 GLN cc_start: 0.7812 (mt0) cc_final: 0.7469 (mp10) REVERT: G 116 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8196 (mm) REVERT: H 69 ASP cc_start: 0.8272 (t70) cc_final: 0.7902 (t0) REVERT: K 103 MET cc_start: 0.8122 (OUTLIER) cc_final: 0.5756 (tpt) REVERT: K 111 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.7945 (pp20) REVERT: K 161 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.8047 (ptpp) REVERT: N 95 ASP cc_start: 0.8124 (t70) cc_final: 0.7729 (t70) REVERT: N 163 THR cc_start: 0.8696 (m) cc_final: 0.8240 (p) REVERT: N 176 ARG cc_start: 0.7142 (ttm110) cc_final: 0.6494 (mtp180) outliers start: 38 outliers final: 16 residues processed: 161 average time/residue: 0.7044 time to fit residues: 122.7760 Evaluate side-chains 162 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 134 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU 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 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 49 ARG 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 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 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 173 LEU 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 125 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 107 optimal weight: 9.9990 chunk 113 optimal weight: 8.9990 chunk 56 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 133 optimal weight: 6.9990 chunk 59 optimal weight: 0.6980 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.144248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.104486 restraints weight = 23538.999| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 1.69 r_work: 0.3483 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16533 Z= 0.184 Angle : 0.646 8.770 23626 Z= 0.360 Chirality : 0.046 0.338 2663 Planarity : 0.004 0.047 1949 Dihedral : 30.048 156.104 4680 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 4.40 % Allowed : 24.07 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.25), residues: 1186 helix: 2.21 (0.22), residues: 546 sheet: 0.39 (0.34), residues: 256 loop : -0.90 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 176 TYR 0.016 0.001 TYR N 72 PHE 0.008 0.001 PHE N 229 TRP 0.012 0.001 TRP N 58 HIS 0.006 0.001 HIS H 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.18 (16529) covalent geometry : angle 0.64607 / 0.36 (23618) SS BOND : bond 0.00524 / 0.30 ( 4) SS BOND : angle 0.90728 / 0.53 ( 8) hydrogen bonds : bond 0.04417 / 2.96 ( 856) hydrogen bonds : angle 3.55382 / 2.66 ( 2178) *********************** 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: 45 poor density : 134 time to evaluate : 0.488 Fit side-chains REVERT: A 59 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.6893 (pp20) REVERT: B 79 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7614 (mttt) REVERT: C 73 ASN cc_start: 0.8221 (OUTLIER) cc_final: 0.7958 (t0) REVERT: C 91 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8101 (tt0) REVERT: D 40 ILE cc_start: 0.8038 (OUTLIER) cc_final: 0.7720 (pt) REVERT: D 48 GLN cc_start: 0.8269 (mt0) cc_final: 0.8058 (mt0) REVERT: D 77 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.6789 (tm-30) REVERT: E 49 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.6388 (ptp90) REVERT: E 59 GLU cc_start: 0.8211 (pm20) cc_final: 0.7928 (pm20) REVERT: E 120 MET cc_start: 0.8466 (OUTLIER) cc_final: 0.7663 (mtt) REVERT: G 64 GLU cc_start: 0.8113 (tt0) cc_final: 0.7771 (tp30) REVERT: G 91 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.7438 (tt0) REVERT: G 116 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8227 (mm) REVERT: H 69 ASP cc_start: 0.8314 (t70) cc_final: 0.7924 (t0) REVERT: K 103 MET cc_start: 0.8204 (OUTLIER) cc_final: 0.5790 (tpt) REVERT: K 111 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7924 (pp20) REVERT: K 161 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.8035 (ptpp) REVERT: N 95 ASP cc_start: 0.8148 (t70) cc_final: 0.7725 (t70) REVERT: N 163 THR cc_start: 0.8729 (m) cc_final: 0.8262 (p) outliers start: 45 outliers final: 22 residues processed: 160 average time/residue: 0.6892 time to fit residues: 119.5440 Evaluate side-chains 167 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 132 time to evaluate : 0.439 ------------------------------------------------------------------------------- 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 50 ILE Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 41 GLU 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 77 GLU Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 71 VAL 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 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 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 80 THR Chi-restraints excluded: chain N residue 137 SER Chi-restraints excluded: chain N residue 139 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 39 optimal weight: 1.9990 chunk 75 optimal weight: 20.0000 chunk 33 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 134 optimal weight: 9.9990 chunk 57 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 115 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.144621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.104883 restraints weight = 23573.197| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 1.70 r_work: 0.3486 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3375 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1603 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= 0.159 Angle : 0.639 7.962 23626 Z= 0.357 Chirality : 0.045 0.338 2663 Planarity : 0.004 0.045 1949 Dihedral : 30.049 156.220 4680 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.01 % Allowed : 24.66 % Favored : 71.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.25), residues: 1186 helix: 2.26 (0.22), residues: 546 sheet: 0.42 (0.34), residues: 256 loop : -0.88 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG N 176 TYR 0.017 0.001 TYR H 41 PHE 0.008 0.001 PHE N 229 TRP 0.011 0.001 TRP N 58 HIS 0.005 0.001 HIS H 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.16 (16529) covalent geometry : angle 0.63874 / 0.36 (23618) SS BOND : bond 0.00490 / 0.28 ( 4) SS BOND : angle 0.86976 / 0.50 ( 8) hydrogen bonds : bond 0.04248 / 2.85 ( 856) hydrogen bonds : angle 3.54102 / 2.65 ( 2178) *********************** 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 175 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 134 time to evaluate : 0.446 Fit side-chains REVERT: A 59 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.6884 (pp20) REVERT: B 79 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7600 (mttt) REVERT: C 73 ASN cc_start: 0.8207 (OUTLIER) cc_final: 0.7944 (t0) REVERT: C 91 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8087 (tt0) REVERT: D 40 ILE cc_start: 0.7938 (OUTLIER) cc_final: 0.7623 (pt) REVERT: D 77 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.6837 (tm-30) REVERT: E 49 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.6393 (ptp90) REVERT: E 59 GLU cc_start: 0.8201 (pm20) cc_final: 0.7905 (pm20) REVERT: E 120 MET cc_start: 0.8418 (OUTLIER) cc_final: 0.7599 (mtt) REVERT: G 51 MET cc_start: 0.8574 (OUTLIER) cc_final: 0.8254 (ttp) REVERT: G 64 GLU cc_start: 0.8108 (tt0) cc_final: 0.7768 (tp30) REVERT: G 91 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7464 (tt0) REVERT: G 116 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8213 (mm) REVERT: H 69 ASP cc_start: 0.8299 (t70) cc_final: 0.7901 (t0) REVERT: K 103 MET cc_start: 0.8183 (OUTLIER) cc_final: 0.5772 (tpt) REVERT: K 111 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7914 (pp20) REVERT: K 161 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.8027 (ptpp) REVERT: N 95 ASP cc_start: 0.8147 (t70) cc_final: 0.7714 (t70) REVERT: N 163 THR cc_start: 0.8731 (m) cc_final: 0.8259 (p) REVERT: N 176 ARG cc_start: 0.6964 (ttm110) cc_final: 0.6278 (mtp180) REVERT: N 261 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7956 (tmmt) outliers start: 41 outliers final: 20 residues processed: 160 average time/residue: 0.7348 time to fit residues: 127.5251 Evaluate side-chains 165 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 130 time to evaluate : 0.529 ------------------------------------------------------------------------------- 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 40 ILE Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 71 VAL 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 G residue 51 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 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 163 THR 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 Chi-restraints excluded: chain N residue 261 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 136 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 134 optimal weight: 9.9990 chunk 36 optimal weight: 4.9990 chunk 72 optimal weight: 50.0000 chunk 98 optimal weight: 30.0000 chunk 35 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.143566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.103610 restraints weight = 23712.967| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 1.73 r_work: 0.3471 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3360 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16533 Z= 0.200 Angle : 0.659 7.849 23626 Z= 0.365 Chirality : 0.046 0.336 2663 Planarity : 0.004 0.045 1949 Dihedral : 30.084 156.897 4680 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.50 % Allowed : 24.27 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.25), residues: 1186 helix: 2.16 (0.22), residues: 546 sheet: 0.41 (0.34), residues: 256 loop : -0.89 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 176 TYR 0.020 0.002 TYR H 41 PHE 0.009 0.001 PHE N 229 TRP 0.014 0.002 TRP N 58 HIS 0.006 0.001 HIS H 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.20 (16529) covalent geometry : angle 0.65891 / 0.37 (23618) SS BOND : bond 0.00570 / 0.33 ( 4) SS BOND : angle 0.93999 / 0.56 ( 8) hydrogen bonds : bond 0.04591 / 3.08 ( 856) hydrogen bonds : angle 3.58496 / 2.68 ( 2178) *********************** 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 182 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 136 time to evaluate : 0.417 Fit side-chains REVERT: A 59 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.6892 (pp20) REVERT: B 79 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7801 (mttp) REVERT: C 73 ASN cc_start: 0.8247 (OUTLIER) cc_final: 0.7994 (t0) REVERT: C 91 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8098 (tt0) REVERT: D 40 ILE cc_start: 0.8048 (OUTLIER) cc_final: 0.7700 (pt) REVERT: D 77 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.6785 (tm-30) REVERT: E 49 ARG cc_start: 0.7817 (OUTLIER) cc_final: 0.6379 (ptp90) REVERT: E 59 GLU cc_start: 0.8073 (pm20) cc_final: 0.7695 (pm20) REVERT: E 120 MET cc_start: 0.8484 (OUTLIER) cc_final: 0.7708 (mtt) REVERT: G 51 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.8287 (ttp) REVERT: G 64 GLU cc_start: 0.8077 (tt0) cc_final: 0.7716 (tp30) REVERT: G 91 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.7465 (tt0) REVERT: G 116 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8206 (mm) REVERT: H 69 ASP cc_start: 0.8337 (t70) cc_final: 0.7934 (t0) REVERT: K 103 MET cc_start: 0.8293 (OUTLIER) cc_final: 0.5896 (tpt) REVERT: K 111 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7854 (pp20) REVERT: K 161 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.8085 (ptpp) REVERT: K 185 GLN cc_start: 0.7532 (OUTLIER) cc_final: 0.7178 (mt0) REVERT: N 95 ASP cc_start: 0.8179 (t70) cc_final: 0.7741 (t70) REVERT: N 163 THR cc_start: 0.8728 (m) cc_final: 0.8255 (p) REVERT: N 261 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7964 (tmmt) outliers start: 46 outliers final: 23 residues processed: 166 average time/residue: 0.7490 time to fit residues: 134.4007 Evaluate side-chains 172 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 133 time to evaluate : 0.372 ------------------------------------------------------------------------------- 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 50 ILE Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 41 GLU 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 40 ILE Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 71 VAL 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 G residue 51 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 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 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 185 GLN 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 Chi-restraints excluded: chain N residue 261 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 86 optimal weight: 30.0000 chunk 118 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 chunk 90 optimal weight: 20.0000 chunk 109 optimal weight: 5.9990 chunk 110 optimal weight: 6.9990 chunk 84 optimal weight: 20.0000 chunk 46 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 0 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN D 48 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 61 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.142034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.102083 restraints weight = 23800.237| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 1.72 r_work: 0.3474 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.070 16533 Z= 0.377 Angle : 0.799 8.768 23626 Z= 0.427 Chirality : 0.054 0.329 2663 Planarity : 0.006 0.048 1949 Dihedral : 30.327 159.097 4680 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 5.58 % Allowed : 23.39 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.25), residues: 1186 helix: 1.59 (0.22), residues: 546 sheet: 0.16 (0.33), residues: 258 loop : -1.07 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG N 176 TYR 0.028 0.003 TYR H 41 PHE 0.014 0.003 PHE E 104 TRP 0.024 0.003 TRP N 58 HIS 0.009 0.002 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00857 / 0.38 (16529) covalent geometry : angle 0.79880 / 0.43 (23618) SS BOND : bond 0.00914 / 0.53 ( 4) SS BOND : angle 1.32810 / 0.92 ( 8) hydrogen bonds : bond 0.06579 / 4.42 ( 856) hydrogen bonds : angle 3.94560 / 2.94 ( 2178) *********************** 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 189 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 132 time to evaluate : 0.464 Fit side-chains REVERT: A 59 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.6902 (pp20) REVERT: B 79 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.7915 (mttp) REVERT: C 24 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.7558 (mp10) REVERT: C 73 ASN cc_start: 0.8401 (OUTLIER) cc_final: 0.8192 (t0) REVERT: C 91 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8080 (tt0) REVERT: D 77 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.6854 (tm-30) REVERT: E 49 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.6465 (ptp90) REVERT: E 59 GLU cc_start: 0.8122 (pm20) cc_final: 0.7729 (pm20) REVERT: E 120 MET cc_start: 0.8745 (OUTLIER) cc_final: 0.7993 (mtt) REVERT: G 51 MET cc_start: 0.8672 (OUTLIER) cc_final: 0.8361 (ttp) REVERT: G 64 GLU cc_start: 0.8150 (tt0) cc_final: 0.7786 (tp30) REVERT: G 91 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.7379 (tt0) REVERT: G 116 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8333 (mm) REVERT: H 69 ASP cc_start: 0.8531 (t70) cc_final: 0.8008 (t0) REVERT: H 87 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7395 (mtt90) REVERT: K 103 MET cc_start: 0.8483 (OUTLIER) cc_final: 0.5890 (tpt) REVERT: K 111 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7918 (pp20) REVERT: K 161 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.8104 (ptpp) REVERT: K 185 GLN cc_start: 0.7598 (OUTLIER) cc_final: 0.7183 (mt0) REVERT: N 95 ASP cc_start: 0.8258 (t70) cc_final: 0.7842 (t70) REVERT: N 163 THR cc_start: 0.8824 (m) cc_final: 0.8333 (p) outliers start: 57 outliers final: 27 residues processed: 166 average time/residue: 0.7386 time to fit residues: 133.0558 Evaluate side-chains 174 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 131 time to evaluate : 0.449 ------------------------------------------------------------------------------- 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 50 ILE 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 73 ASN Chi-restraints excluded: chain C residue 76 THR 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 77 GLU Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain E residue 71 VAL 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 G residue 51 MET Chi-restraints excluded: chain G residue 91 GLU 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 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 138 VAL Chi-restraints excluded: chain K residue 161 LYS Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain K residue 185 GLN 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 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 138 optimal weight: 3.9990 chunk 85 optimal weight: 30.0000 chunk 107 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 89 optimal weight: 10.9990 chunk 5 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 81 optimal weight: 20.0000 chunk 142 optimal weight: 0.0470 chunk 13 optimal weight: 1.9990 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.146520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.107361 restraints weight = 23522.442| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 1.71 r_work: 0.3532 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3425 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 16533 Z= 0.132 Angle : 0.684 8.927 23626 Z= 0.377 Chirality : 0.048 0.342 2663 Planarity : 0.004 0.045 1949 Dihedral : 30.309 158.470 4680 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.94 % Allowed : 25.73 % Favored : 71.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.25), residues: 1186 helix: 2.04 (0.22), residues: 549 sheet: 0.27 (0.33), residues: 256 loop : -0.95 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 176 TYR 0.021 0.002 TYR H 41 PHE 0.008 0.001 PHE D 71 TRP 0.008 0.001 TRP N 58 HIS 0.005 0.001 HIS K 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.13 (16529) covalent geometry : angle 0.68373 / 0.38 (23618) SS BOND : bond 0.00439 / 0.27 ( 4) SS BOND : angle 0.97216 / 0.52 ( 8) hydrogen bonds : bond 0.04247 / 2.85 ( 856) hydrogen bonds : angle 3.66829 / 2.74 ( 2178) ********************** 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 170 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 140 time to evaluate : 0.465 Fit side-chains REVERT: A 59 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.6902 (pp20) REVERT: B 79 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7777 (mttp) REVERT: C 73 ASN cc_start: 0.8325 (OUTLIER) cc_final: 0.8071 (t0) REVERT: C 91 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8094 (tt0) REVERT: C 99 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.7922 (mtpt) REVERT: D 77 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.6789 (tm-30) REVERT: E 49 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.6484 (ptp90) REVERT: E 59 GLU cc_start: 0.8124 (pm20) cc_final: 0.7730 (pm20) REVERT: G 64 GLU cc_start: 0.8092 (tt0) cc_final: 0.7764 (tp30) REVERT: G 116 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8308 (mm) REVERT: K 103 MET cc_start: 0.8334 (OUTLIER) cc_final: 0.5895 (tpt) REVERT: K 111 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7856 (pp20) REVERT: N 95 ASP cc_start: 0.8103 (t70) cc_final: 0.7737 (t70) REVERT: N 163 THR cc_start: 0.8756 (m) cc_final: 0.8283 (p) outliers start: 30 outliers final: 14 residues processed: 157 average time/residue: 0.7506 time to fit residues: 127.6023 Evaluate side-chains 160 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 136 time to evaluate : 0.443 ------------------------------------------------------------------------------- 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 99 LYS Chi-restraints excluded: chain C residue 114 VAL 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 G residue 116 LEU Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 124 SER 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 138 VAL Chi-restraints excluded: chain K residue 163 THR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 30 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 134 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 95 optimal weight: 20.0000 chunk 139 optimal weight: 10.0000 chunk 102 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 98 optimal weight: 30.0000 chunk 103 optimal weight: 4.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.144237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.104571 restraints weight = 23607.199| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 1.69 r_work: 0.3506 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3398 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 16533 Z= 0.232 Angle : 0.704 11.114 23626 Z= 0.383 Chirality : 0.048 0.334 2663 Planarity : 0.004 0.045 1949 Dihedral : 30.253 157.835 4680 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.64 % Allowed : 26.22 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.25), residues: 1186 helix: 1.99 (0.22), residues: 549 sheet: 0.28 (0.34), residues: 256 loop : -0.97 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 176 TYR 0.018 0.002 TYR N 72 PHE 0.009 0.002 PHE N 229 TRP 0.014 0.002 TRP N 58 HIS 0.006 0.001 HIS H 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.23 (16529) covalent geometry : angle 0.70405 / 0.38 (23618) SS BOND : bond 0.00627 / 0.37 ( 4) SS BOND : angle 0.98308 / 0.62 ( 8) hydrogen bonds : bond 0.04844 / 3.26 ( 856) hydrogen bonds : angle 3.71945 / 2.78 ( 2178) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6019.55 seconds wall clock time: 102 minutes 57.55 seconds (6177.55 seconds total)