Starting phenix.real_space_refine on Sat Jun 14 13:55:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sps_40683/06_2025/8sps_40683.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sps_40683/06_2025/8sps_40683.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sps_40683/06_2025/8sps_40683.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sps_40683/06_2025/8sps_40683.map" model { file = "/net/cci-nas-00/data/ceres_data/8sps_40683/06_2025/8sps_40683.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sps_40683/06_2025/8sps_40683.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.051 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 294 5.49 5 S 37 5.16 5 C 9478 2.51 5 N 2996 2.21 5 O 3710 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16515 Number of models: 1 Model: "" Number of chains: 14 Chain: "I" Number of atoms: 3055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3055 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 2972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2972 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "L" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 602 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 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: "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 Chain: "M" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 373 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 46} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 19 Time building chain proxies: 9.96, per 1000 atoms: 0.60 Number of scatterers: 16515 At special positions: 0 Unit cell: (139.392, 145.728, 157.344, 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 37 16.00 P 294 15.00 O 3710 8.00 N 2996 7.00 C 9478 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: 3.94 Conformation dependent library (CDL) restraints added in 1.5 seconds 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2484 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 21 sheets defined 50.6% alpha, 17.9% beta 139 base pairs and 256 stacking pairs defined. Time for finding SS restraints: 7.23 Creating SS restraints... Processing helix chain 'L' and resid 140 through 161 removed outlier: 4.105A pdb=" N LYS L 144 " --> pdb=" O LYS L 140 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU L 145 " --> pdb=" O ALA L 141 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS L 151 " --> pdb=" O GLU L 147 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU L 152 " --> pdb=" O GLN L 148 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY L 161 " --> pdb=" O ARG L 157 " (cutoff:3.500A) Processing helix chain 'L' and resid 163 through 176 Processing helix chain 'L' and resid 180 through 189 removed outlier: 3.520A pdb=" N GLU L 188 " --> pdb=" O ILE L 184 " (cutoff:3.500A) Processing helix chain 'L' and resid 193 through 214 Proline residue: L 202 - end of helix 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: 3.803A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.725A 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: 3.548A 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: 3.620A 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: 3.673A 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: 3.709A pdb=" N ASP N 240 " --> pdb=" O GLU N 237 " (cutoff:3.500A) removed outlier: 4.162A 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 helix chain 'M' and resid 240 through 247 Processing helix chain 'M' and resid 255 through 268 removed outlier: 3.586A pdb=" N HIS M 262 " --> pdb=" O GLN M 258 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN M 265 " --> pdb=" O SER M 261 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN M 266 " --> pdb=" O HIS M 262 " (cutoff:3.500A) Processing helix chain 'M' and resid 270 through 287 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: 6.573A 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: 7.139A 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: 5.965A 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: 3.502A pdb=" N MET K 169 " --> pdb=" O LYS K 261 " (cutoff:3.500A) removed outlier: 4.309A 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: 6.860A pdb=" N LEU K 191 " --> pdb=" O TYR K 207 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N TYR K 207 " --> pdb=" O LEU K 191 " (cutoff:3.500A) removed outlier: 6.399A 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: 3.502A pdb=" N MET K 169 " --> pdb=" O LYS K 261 " (cutoff:3.500A) removed outlier: 4.309A 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: 3.955A pdb=" N PHE N 229 " --> pdb=" O CYS N 181 " (cutoff:3.500A) removed outlier: 3.601A 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: 6.817A 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: 6.354A pdb=" N TRP N 193 " --> pdb=" O LEU N 205 " (cutoff:3.500A) 611 hydrogen bonds defined for protein. 1734 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 350 hydrogen bonds 700 hydrogen bond angles 0 basepair planarities 139 basepair parallelities 256 stacking parallelities Total time for adding SS restraints: 6.41 Time building geometry restraints manager: 4.76 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: 4862 1.36 - 1.51: 7352 1.51 - 1.67: 5139 1.67 - 1.83: 57 Bond restraints: 17425 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 0.191 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 2.06e+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 1.362 0.161 1.37e-02 5.33e+03 1.38e+02 ... (remaining 17420 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.95: 24738 5.95 - 11.91: 56 11.91 - 17.86: 9 17.86 - 23.82: 1 23.82 - 29.77: 1 Bond angle restraints: 24805 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 110.61 126.90 -16.29 1.25e+00 6.40e-01 1.70e+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 82.93 29.77 3.00e+00 1.11e-01 9.85e+01 angle pdb=" N LYS C 13 " pdb=" CA LYS C 13 " pdb=" C LYS C 13 " ideal model delta sigma weight residual 110.80 128.73 -17.93 2.13e+00 2.20e-01 7.09e+01 angle pdb=" C LYS C 13 " pdb=" N ALA C 14 " pdb=" CA ALA C 14 " ideal model delta sigma weight residual 121.54 134.08 -12.54 1.91e+00 2.74e-01 4.31e+01 angle pdb=" CA GLN B 93 " pdb=" CB GLN B 93 " pdb=" CG GLN B 93 " ideal model delta sigma weight residual 114.10 101.79 12.31 2.00e+00 2.50e-01 3.79e+01 ... (remaining 24800 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.44: 8097 35.44 - 70.87: 1595 70.87 - 106.31: 36 106.31 - 141.74: 0 141.74 - 177.18: 2 Dihedral angle restraints: 9730 sinusoidal: 5861 harmonic: 3869 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 -108.50 -14.10 0 2.50e+00 1.60e-01 3.18e+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 -134.44 11.84 0 2.50e+00 1.60e-01 2.24e+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 -156.78 -23.22 0 5.00e+00 4.00e-02 2.16e+01 ... (remaining 9727 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.137: 2763 0.137 - 0.273: 26 0.273 - 0.410: 6 0.410 - 0.547: 2 0.547 - 0.684: 2 Chirality restraints: 2799 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 1.83 0.68 2.00e-01 2.50e+01 1.17e+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 1.06e+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 0.43 2.00e-01 2.50e+01 4.71e+00 ... (remaining 2796 not shown) Planarity restraints: 2116 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU C 92 " 0.035 2.00e-02 2.50e+03 7.34e-02 5.39e+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 " -0.026 2.00e-02 2.50e+03 5.34e-02 2.85e+01 pdb=" C MET C 51 " 0.092 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 1.27e-01 2.56e+01 pdb=" N PRO N 63 " -0.219 5.00e-02 4.00e+02 pdb=" CA PRO N 63 " 0.068 5.00e-02 4.00e+02 pdb=" CD PRO N 63 " 0.067 5.00e-02 4.00e+02 ... (remaining 2113 not shown) Histogram of nonbonded interaction distances: 0.57 - 1.44: 3 1.44 - 2.30: 8 2.30 - 3.17: 12600 3.17 - 4.03: 48048 4.03 - 4.90: 81529 Warning: very small nonbonded interaction distances. Nonbonded interactions: 142188 Sorted by model distance: nonbonded pdb=" O TYR L 162 " pdb=" NZ LYS G 13 " model vdw 0.574 3.120 nonbonded pdb=" C TYR L 162 " pdb=" NZ LYS G 13 " model vdw 0.937 3.350 nonbonded pdb=" O TYR L 162 " pdb=" CE LYS G 13 " model vdw 1.305 3.440 nonbonded pdb=" N THR L 163 " pdb=" NZ LYS G 13 " model vdw 1.818 3.200 nonbonded pdb=" O SER H 33 " pdb=" OG SER H 33 " model vdw 2.088 3.040 ... (remaining 142183 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: 0.690 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: 0.020 Extract box with map and model: 0.610 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 43.660 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.090 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:12.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.191 17429 Z= 0.479 Angle : 0.882 29.772 24813 Z= 0.494 Chirality : 0.049 0.684 2799 Planarity : 0.007 0.127 2116 Dihedral : 27.009 177.177 7234 Min Nonbonded Distance : 0.574 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.59 % Favored : 95.33 % Rotamer: Outliers : 0.53 % Allowed : 21.53 % Favored : 77.94 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.21), residues: 1306 helix: -0.09 (0.18), residues: 634 sheet: -0.23 (0.34), residues: 234 loop : -1.31 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP N 58 HIS 0.006 0.002 HIS C 31 PHE 0.029 0.002 PHE A 78 TYR 0.045 0.002 TYR H 41 ARG 0.012 0.000 ARG D 100 Details of bonding type rmsd hydrogen bonds : bond 0.13037 ( 950) hydrogen bonds : angle 5.39350 ( 2434) SS BOND : bond 0.00293 ( 4) SS BOND : angle 1.22539 ( 8) covalent geometry : bond 0.00794 (17425) covalent geometry : angle 0.88203 (24805) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 360 time to evaluate : 1.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 25 ASN cc_start: 0.8364 (m110) cc_final: 0.7835 (m-40) REVERT: H 84 TYR cc_start: 0.8585 (m-10) cc_final: 0.8108 (m-10) outliers start: 6 outliers final: 2 residues processed: 362 average time/residue: 1.4802 time to fit residues: 585.9362 Evaluate side-chains 224 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 222 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain K residue 264 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 8.9990 chunk 116 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 120 optimal weight: 7.9990 chunk 46 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 139 optimal weight: 10.0000 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 31 HIS C 38 ASN C 73 ASN D 85 ASN F 93 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN H 50 HIS K 196 GLN K 234 ASN N 61 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.127835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.080526 restraints weight = 38128.008| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.48 r_work: 0.3064 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17429 Z= 0.154 Angle : 0.606 8.277 24813 Z= 0.342 Chirality : 0.036 0.175 2799 Planarity : 0.005 0.082 2116 Dihedral : 29.526 175.758 4697 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.11 % Allowed : 26.78 % Favored : 70.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.23), residues: 1306 helix: 1.52 (0.20), residues: 647 sheet: -0.02 (0.34), residues: 234 loop : -1.02 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 207 HIS 0.004 0.001 HIS B 75 PHE 0.012 0.001 PHE N 256 TYR 0.020 0.001 TYR B 88 ARG 0.008 0.001 ARG K 176 Details of bonding type rmsd hydrogen bonds : bond 0.03949 ( 950) hydrogen bonds : angle 3.68436 ( 2434) SS BOND : bond 0.00463 ( 4) SS BOND : angle 0.94945 ( 8) covalent geometry : bond 0.00337 (17425) covalent geometry : angle 0.60563 (24805) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 253 time to evaluate : 1.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.6926 (OUTLIER) cc_final: 0.6618 (mt-10) REVERT: B 79 LYS cc_start: 0.8911 (mtmt) cc_final: 0.8654 (mtmt) REVERT: B 85 ASP cc_start: 0.8848 (m-30) cc_final: 0.8626 (m-30) REVERT: C 15 LYS cc_start: 0.8670 (mtpp) cc_final: 0.8207 (pttt) REVERT: C 71 ARG cc_start: 0.8437 (ttp80) cc_final: 0.8183 (ttp80) REVERT: C 76 THR cc_start: 0.9063 (p) cc_final: 0.8718 (t) REVERT: C 95 LYS cc_start: 0.9109 (tttm) cc_final: 0.8813 (tppp) REVERT: C 101 THR cc_start: 0.9112 (OUTLIER) cc_final: 0.8785 (p) REVERT: D 69 ASP cc_start: 0.9101 (t0) cc_final: 0.8829 (t0) REVERT: D 87 ARG cc_start: 0.8424 (mmm-85) cc_final: 0.8150 (mmm-85) REVERT: D 94 GLU cc_start: 0.9024 (mp0) cc_final: 0.8263 (mp0) REVERT: E 73 GLU cc_start: 0.8730 (tt0) cc_final: 0.8196 (tt0) REVERT: E 83 ARG cc_start: 0.7867 (OUTLIER) cc_final: 0.6498 (ptm-80) REVERT: E 90 MET cc_start: 0.8706 (tpp) cc_final: 0.8303 (mmp) REVERT: F 25 ASN cc_start: 0.8581 (m110) cc_final: 0.7970 (m-40) REVERT: G 73 ASN cc_start: 0.8777 (t0) cc_final: 0.8369 (m-40) REVERT: G 91 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8481 (tt0) REVERT: H 47 LYS cc_start: 0.9084 (ttmm) cc_final: 0.8768 (mptp) REVERT: H 52 ASP cc_start: 0.8535 (m-30) cc_final: 0.8009 (t0) REVERT: H 69 ASP cc_start: 0.8690 (t0) cc_final: 0.8456 (t0) REVERT: H 84 TYR cc_start: 0.8985 (m-10) cc_final: 0.8432 (m-10) REVERT: H 114 GLU cc_start: 0.9114 (mm-30) cc_final: 0.8850 (mm-30) REVERT: K 32 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7823 (mm-30) REVERT: K 84 GLU cc_start: 0.9025 (tp30) cc_final: 0.8655 (tp30) REVERT: K 87 LYS cc_start: 0.8845 (ttmm) cc_final: 0.8515 (ttpp) REVERT: K 95 ASP cc_start: 0.8059 (t0) cc_final: 0.7705 (t0) REVERT: K 111 GLU cc_start: 0.9300 (pm20) cc_final: 0.9041 (pm20) REVERT: K 176 ARG cc_start: 0.8823 (mmm-85) cc_final: 0.8152 (tpt-90) REVERT: K 182 LYS cc_start: 0.8424 (tptt) cc_final: 0.8150 (tppt) REVERT: K 237 GLU cc_start: 0.7600 (tm-30) cc_final: 0.7163 (tm-30) REVERT: K 239 ASP cc_start: 0.8483 (t70) cc_final: 0.7925 (t0) REVERT: N 161 LYS cc_start: 0.8758 (tmmm) cc_final: 0.8526 (ttpp) outliers start: 35 outliers final: 9 residues processed: 274 average time/residue: 1.4294 time to fit residues: 429.6561 Evaluate side-chains 225 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 212 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 170 HIS Chi-restraints excluded: chain N residue 235 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 147 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 144 optimal weight: 9.9990 chunk 83 optimal weight: 0.7980 chunk 118 optimal weight: 9.9990 chunk 55 optimal weight: 3.9990 chunk 141 optimal weight: 0.2980 chunk 59 optimal weight: 4.9990 chunk 124 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 143 optimal weight: 1.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN E 39 HIS E 76 GLN G 31 HIS N 57 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.122553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.074907 restraints weight = 37975.038| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.45 r_work: 0.2933 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 17429 Z= 0.217 Angle : 0.628 9.601 24813 Z= 0.353 Chirality : 0.037 0.157 2799 Planarity : 0.005 0.068 2116 Dihedral : 29.609 176.621 4693 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 4.54 % Allowed : 24.56 % Favored : 70.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.23), residues: 1306 helix: 2.17 (0.20), residues: 640 sheet: 0.11 (0.35), residues: 234 loop : -0.91 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 199 HIS 0.006 0.001 HIS F 75 PHE 0.012 0.001 PHE N 256 TYR 0.031 0.002 TYR D 84 ARG 0.007 0.001 ARG G 71 Details of bonding type rmsd hydrogen bonds : bond 0.04271 ( 950) hydrogen bonds : angle 3.56382 ( 2434) SS BOND : bond 0.00546 ( 4) SS BOND : angle 1.08581 ( 8) covalent geometry : bond 0.00491 (17425) covalent geometry : angle 0.62771 (24805) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 226 time to evaluate : 1.436 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.8696 (m-80) cc_final: 0.8453 (m-10) REVERT: A 105 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7475 (tp30) REVERT: A 133 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.7223 (mt-10) REVERT: B 85 ASP cc_start: 0.8900 (m-30) cc_final: 0.8669 (m-30) REVERT: C 61 GLU cc_start: 0.8604 (tp30) cc_final: 0.8369 (tp30) REVERT: C 76 THR cc_start: 0.9233 (p) cc_final: 0.8990 (t) REVERT: C 101 THR cc_start: 0.9185 (m) cc_final: 0.8897 (p) REVERT: D 94 GLU cc_start: 0.9038 (mp0) cc_final: 0.8752 (mp0) REVERT: E 73 GLU cc_start: 0.8774 (tt0) cc_final: 0.8111 (tt0) REVERT: E 83 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.6499 (ptm-80) REVERT: E 123 ASP cc_start: 0.8698 (m-30) cc_final: 0.8251 (m-30) REVERT: F 22 LEU cc_start: 0.8923 (mt) cc_final: 0.8647 (mt) REVERT: F 23 ARG cc_start: 0.8255 (ttp80) cc_final: 0.7897 (ttp-110) REVERT: F 25 ASN cc_start: 0.8446 (m110) cc_final: 0.7768 (m-40) REVERT: G 20 ARG cc_start: 0.8717 (mtt90) cc_final: 0.8350 (mtt90) REVERT: G 73 ASN cc_start: 0.8881 (t0) cc_final: 0.8425 (m-40) REVERT: G 92 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8381 (mt-10) REVERT: H 47 LYS cc_start: 0.9074 (OUTLIER) cc_final: 0.8797 (mptm) REVERT: H 52 ASP cc_start: 0.8611 (m-30) cc_final: 0.7996 (t0) REVERT: H 69 ASP cc_start: 0.9037 (t0) cc_final: 0.8766 (t0) REVERT: H 84 TYR cc_start: 0.9000 (m-10) cc_final: 0.8613 (m-10) REVERT: H 114 GLU cc_start: 0.9089 (mm-30) cc_final: 0.8804 (mm-30) REVERT: K 23 GLU cc_start: 0.7095 (OUTLIER) cc_final: 0.6865 (tp30) REVERT: K 95 ASP cc_start: 0.8166 (t0) cc_final: 0.7793 (t0) REVERT: K 103 MET cc_start: 0.9065 (OUTLIER) cc_final: 0.7970 (tmm) REVERT: K 109 THR cc_start: 0.7865 (m) cc_final: 0.7498 (t) REVERT: K 111 GLU cc_start: 0.9222 (pm20) cc_final: 0.8947 (pm20) REVERT: K 189 SER cc_start: 0.9142 (m) cc_final: 0.8894 (p) outliers start: 51 outliers final: 17 residues processed: 259 average time/residue: 1.5032 time to fit residues: 426.8081 Evaluate side-chains 219 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 196 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 185 CYS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain H residue 47 LYS Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain K residue 23 GLU Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 103 MET Chi-restraints excluded: chain K residue 137 SER Chi-restraints excluded: chain N residue 38 THR Chi-restraints excluded: chain N residue 170 HIS Chi-restraints excluded: chain N residue 235 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 52 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 8 optimal weight: 7.9990 chunk 0 optimal weight: 50.0000 chunk 5 optimal weight: 6.9990 chunk 105 optimal weight: 0.9980 chunk 13 optimal weight: 10.0000 chunk 68 optimal weight: 0.7980 chunk 4 optimal weight: 8.9990 chunk 113 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN B 75 HIS C 38 ASN C 73 ASN E 76 GLN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN K 196 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.123211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.075314 restraints weight = 37905.506| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.78 r_work: 0.2938 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 17429 Z= 0.185 Angle : 0.610 10.138 24813 Z= 0.342 Chirality : 0.037 0.146 2799 Planarity : 0.004 0.059 2116 Dihedral : 29.475 176.335 4693 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.38 % Allowed : 26.69 % Favored : 69.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.24), residues: 1306 helix: 2.41 (0.20), residues: 644 sheet: 0.18 (0.35), residues: 234 loop : -0.91 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 69 HIS 0.005 0.001 HIS F 75 PHE 0.011 0.001 PHE N 256 TYR 0.036 0.001 TYR D 84 ARG 0.009 0.001 ARG G 71 Details of bonding type rmsd hydrogen bonds : bond 0.03720 ( 950) hydrogen bonds : angle 3.47829 ( 2434) SS BOND : bond 0.00273 ( 4) SS BOND : angle 0.84371 ( 8) covalent geometry : bond 0.00417 (17425) covalent geometry : angle 0.60991 (24805) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 219 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8204 (pm20) REVERT: A 79 LYS cc_start: 0.8429 (tptm) cc_final: 0.8046 (tmtt) REVERT: A 105 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7511 (tp30) REVERT: A 133 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7235 (mt-10) REVERT: B 79 LYS cc_start: 0.9166 (mtmt) cc_final: 0.8778 (mtmt) REVERT: B 85 ASP cc_start: 0.8843 (m-30) cc_final: 0.8642 (m-30) REVERT: D 44 LYS cc_start: 0.9140 (OUTLIER) cc_final: 0.8754 (mtmm) REVERT: D 69 ASP cc_start: 0.9089 (t0) cc_final: 0.8738 (t0) REVERT: D 94 GLU cc_start: 0.9027 (mp0) cc_final: 0.8729 (mp0) REVERT: E 73 GLU cc_start: 0.8834 (tt0) cc_final: 0.8285 (tt0) REVERT: E 83 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.6522 (ptm-80) REVERT: E 90 MET cc_start: 0.8759 (tpp) cc_final: 0.8177 (mmp) REVERT: E 123 ASP cc_start: 0.8718 (m-30) cc_final: 0.8368 (m-30) REVERT: F 23 ARG cc_start: 0.8196 (ttp80) cc_final: 0.7821 (ptp-110) REVERT: F 25 ASN cc_start: 0.8411 (m110) cc_final: 0.7792 (m-40) REVERT: G 20 ARG cc_start: 0.8686 (mtt90) cc_final: 0.8220 (mtm-85) REVERT: G 73 ASN cc_start: 0.8851 (t0) cc_final: 0.8481 (m-40) REVERT: H 47 LYS cc_start: 0.9053 (ttmm) cc_final: 0.8830 (mptm) REVERT: H 52 ASP cc_start: 0.8593 (m-30) cc_final: 0.7981 (t0) REVERT: H 69 ASP cc_start: 0.9068 (t0) cc_final: 0.8788 (t0) REVERT: H 84 TYR cc_start: 0.8951 (m-10) cc_final: 0.8569 (m-10) REVERT: H 114 GLU cc_start: 0.9033 (mm-30) cc_final: 0.8726 (mm-30) REVERT: K 23 GLU cc_start: 0.6965 (OUTLIER) cc_final: 0.6624 (tp30) REVERT: K 95 ASP cc_start: 0.8235 (t0) cc_final: 0.7820 (t0) REVERT: K 109 THR cc_start: 0.8027 (m) cc_final: 0.7794 (t) REVERT: K 111 GLU cc_start: 0.9224 (pm20) cc_final: 0.8790 (pm20) REVERT: K 189 SER cc_start: 0.9210 (m) cc_final: 0.8975 (p) REVERT: K 214 ASP cc_start: 0.8835 (OUTLIER) cc_final: 0.8566 (m-30) outliers start: 38 outliers final: 14 residues processed: 243 average time/residue: 1.6251 time to fit residues: 431.5425 Evaluate side-chains 222 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 201 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 185 CYS Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain K residue 23 GLU Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 214 ASP Chi-restraints excluded: chain N residue 38 THR Chi-restraints excluded: chain N residue 170 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 140 optimal weight: 4.9990 chunk 11 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 chunk 114 optimal weight: 9.9990 chunk 131 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 135 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 32 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 125 GLN C 38 ASN C 73 ASN D 96 GLN E 76 GLN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 164 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.121827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.073546 restraints weight = 38519.570| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.46 r_work: 0.2906 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 17429 Z= 0.223 Angle : 0.635 10.688 24813 Z= 0.354 Chirality : 0.038 0.160 2799 Planarity : 0.004 0.054 2116 Dihedral : 29.521 176.810 4693 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.36 % Allowed : 26.87 % Favored : 68.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.24), residues: 1306 helix: 2.45 (0.20), residues: 643 sheet: 0.69 (0.38), residues: 198 loop : -1.16 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 69 HIS 0.005 0.001 HIS F 75 PHE 0.009 0.001 PHE N 256 TYR 0.033 0.002 TYR D 84 ARG 0.009 0.001 ARG G 71 Details of bonding type rmsd hydrogen bonds : bond 0.03980 ( 950) hydrogen bonds : angle 3.49430 ( 2434) SS BOND : bond 0.00409 ( 4) SS BOND : angle 0.79330 ( 8) covalent geometry : bond 0.00509 (17425) covalent geometry : angle 0.63489 (24805) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 208 time to evaluate : 1.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.8248 (pm20) REVERT: A 79 LYS cc_start: 0.8619 (tptm) cc_final: 0.8219 (tmtt) REVERT: A 105 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7551 (tp30) REVERT: A 133 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7104 (mt-10) REVERT: B 85 ASP cc_start: 0.8924 (m-30) cc_final: 0.8720 (m-30) REVERT: D 94 GLU cc_start: 0.9018 (mp0) cc_final: 0.8723 (mp0) REVERT: E 63 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.7789 (mmp80) REVERT: E 73 GLU cc_start: 0.8843 (tt0) cc_final: 0.8219 (tt0) REVERT: E 83 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.6678 (ptm-80) REVERT: E 94 GLU cc_start: 0.8992 (mm-30) cc_final: 0.8749 (mt-10) REVERT: E 107 THR cc_start: 0.9302 (t) cc_final: 0.9096 (t) REVERT: F 23 ARG cc_start: 0.8347 (ttp80) cc_final: 0.8042 (ptp-110) REVERT: F 25 ASN cc_start: 0.8398 (m110) cc_final: 0.7779 (m-40) REVERT: G 20 ARG cc_start: 0.8645 (mtt90) cc_final: 0.8185 (mtm-85) REVERT: G 73 ASN cc_start: 0.8930 (t0) cc_final: 0.8543 (m-40) REVERT: H 47 LYS cc_start: 0.9047 (OUTLIER) cc_final: 0.8816 (mptm) REVERT: H 52 ASP cc_start: 0.8661 (m-30) cc_final: 0.8047 (t0) REVERT: H 69 ASP cc_start: 0.9134 (t0) cc_final: 0.8828 (t0) REVERT: H 84 TYR cc_start: 0.9009 (m-10) cc_final: 0.8537 (m-10) REVERT: H 94 GLU cc_start: 0.9175 (OUTLIER) cc_final: 0.8253 (mp0) REVERT: H 114 GLU cc_start: 0.9085 (mm-30) cc_final: 0.8783 (mm-30) REVERT: K 23 GLU cc_start: 0.7068 (OUTLIER) cc_final: 0.6713 (tp30) REVERT: K 95 ASP cc_start: 0.8250 (t0) cc_final: 0.7823 (t0) REVERT: K 103 MET cc_start: 0.8828 (ttt) cc_final: 0.8187 (ttp) REVERT: N 214 ASP cc_start: 0.8640 (p0) cc_final: 0.8349 (p0) outliers start: 49 outliers final: 20 residues processed: 240 average time/residue: 1.6024 time to fit residues: 421.7253 Evaluate side-chains 224 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 196 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 185 CYS Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 47 LYS Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 94 GLU Chi-restraints excluded: chain K residue 23 GLU Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 137 SER Chi-restraints excluded: chain N residue 38 THR Chi-restraints excluded: chain N residue 41 LYS Chi-restraints excluded: chain N residue 170 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 110 optimal weight: 0.8980 chunk 107 optimal weight: 6.9990 chunk 84 optimal weight: 0.8980 chunk 2 optimal weight: 10.0000 chunk 119 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 98 optimal weight: 0.7980 chunk 101 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 chunk 139 optimal weight: 0.6980 chunk 96 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.124168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.077270 restraints weight = 38349.363| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.44 r_work: 0.2979 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.4009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17429 Z= 0.140 Angle : 0.603 10.837 24813 Z= 0.336 Chirality : 0.036 0.161 2799 Planarity : 0.004 0.050 2116 Dihedral : 29.285 176.351 4693 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.20 % Allowed : 28.65 % Favored : 68.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.24), residues: 1306 helix: 2.72 (0.20), residues: 640 sheet: 0.15 (0.36), residues: 234 loop : -0.93 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 69 HIS 0.010 0.001 HIS A 39 PHE 0.010 0.001 PHE N 256 TYR 0.047 0.001 TYR D 84 ARG 0.011 0.001 ARG G 71 Details of bonding type rmsd hydrogen bonds : bond 0.03398 ( 950) hydrogen bonds : angle 3.33793 ( 2434) SS BOND : bond 0.00204 ( 4) SS BOND : angle 0.71701 ( 8) covalent geometry : bond 0.00309 (17425) covalent geometry : angle 0.60271 (24805) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 233 time to evaluate : 1.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 192 LEU cc_start: 0.6055 (pt) cc_final: 0.5552 (pt) REVERT: L 197 MET cc_start: 0.3153 (mmm) cc_final: 0.2813 (mpt) REVERT: A 59 GLU cc_start: 0.8401 (pp20) cc_final: 0.8195 (pm20) REVERT: A 105 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7546 (tp30) REVERT: A 133 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.7188 (mt-10) REVERT: B 77 LYS cc_start: 0.9238 (OUTLIER) cc_final: 0.9020 (mttp) REVERT: B 88 TYR cc_start: 0.8989 (m-80) cc_final: 0.8697 (m-80) REVERT: C 95 LYS cc_start: 0.9201 (tttm) cc_final: 0.8859 (tppp) REVERT: D 69 ASP cc_start: 0.9119 (t0) cc_final: 0.8777 (t0) REVERT: D 94 GLU cc_start: 0.8962 (mp0) cc_final: 0.8672 (mp0) REVERT: E 73 GLU cc_start: 0.8853 (tt0) cc_final: 0.8202 (tt0) REVERT: E 83 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.6687 (ptm-80) REVERT: E 90 MET cc_start: 0.8696 (tpp) cc_final: 0.8156 (mmp) REVERT: F 23 ARG cc_start: 0.8324 (ttp80) cc_final: 0.8047 (ptp-110) REVERT: F 25 ASN cc_start: 0.8387 (m110) cc_final: 0.7726 (m-40) REVERT: F 95 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.7863 (mtp85) REVERT: G 51 MET cc_start: 0.8872 (mmm) cc_final: 0.8505 (tpt) REVERT: G 73 ASN cc_start: 0.8930 (t0) cc_final: 0.8545 (m-40) REVERT: H 47 LYS cc_start: 0.9018 (ttmm) cc_final: 0.8787 (mptt) REVERT: H 50 HIS cc_start: 0.8989 (OUTLIER) cc_final: 0.8467 (m170) REVERT: H 52 ASP cc_start: 0.8382 (m-30) cc_final: 0.8029 (t70) REVERT: H 69 ASP cc_start: 0.9008 (t0) cc_final: 0.8784 (t0) REVERT: H 84 TYR cc_start: 0.8947 (m-10) cc_final: 0.8493 (m-10) REVERT: H 94 GLU cc_start: 0.9148 (OUTLIER) cc_final: 0.8245 (mp0) REVERT: H 114 GLU cc_start: 0.9004 (mm-30) cc_final: 0.8684 (mm-30) REVERT: H 125 SER cc_start: 0.8520 (m) cc_final: 0.8255 (p) REVERT: K 95 ASP cc_start: 0.8232 (t0) cc_final: 0.7795 (t0) REVERT: K 189 SER cc_start: 0.9226 (m) cc_final: 0.9022 (p) REVERT: K 240 ASP cc_start: 0.8988 (m-30) cc_final: 0.8762 (m-30) REVERT: K 251 GLU cc_start: 0.8355 (mp0) cc_final: 0.8096 (mp0) REVERT: N 214 ASP cc_start: 0.8641 (p0) cc_final: 0.8302 (p0) outliers start: 36 outliers final: 15 residues processed: 256 average time/residue: 1.4419 time to fit residues: 405.3345 Evaluate side-chains 232 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 210 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 185 CYS Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain H residue 94 GLU Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain N residue 38 THR Chi-restraints excluded: chain N residue 170 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 0 optimal weight: 40.0000 chunk 92 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 1 optimal weight: 30.0000 chunk 134 optimal weight: 0.9990 chunk 131 optimal weight: 0.9990 chunk 149 optimal weight: 7.9990 chunk 72 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 ASN C 73 ASN ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN G 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.124826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.078005 restraints weight = 38493.119| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.78 r_work: 0.2992 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.4178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17429 Z= 0.143 Angle : 0.604 9.618 24813 Z= 0.337 Chirality : 0.036 0.144 2799 Planarity : 0.004 0.048 2116 Dihedral : 29.179 177.506 4693 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.11 % Allowed : 29.54 % Favored : 67.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.24), residues: 1306 helix: 2.72 (0.20), residues: 643 sheet: 0.21 (0.37), residues: 228 loop : -0.79 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 199 HIS 0.008 0.001 HIS A 39 PHE 0.010 0.001 PHE N 256 TYR 0.040 0.001 TYR D 84 ARG 0.012 0.001 ARG G 71 Details of bonding type rmsd hydrogen bonds : bond 0.03374 ( 950) hydrogen bonds : angle 3.28931 ( 2434) SS BOND : bond 0.00187 ( 4) SS BOND : angle 0.65478 ( 8) covalent geometry : bond 0.00315 (17425) covalent geometry : angle 0.60441 (24805) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 228 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 192 LEU cc_start: 0.6143 (pt) cc_final: 0.5641 (pt) REVERT: L 197 MET cc_start: 0.3215 (mmm) cc_final: 0.2790 (mpt) REVERT: A 79 LYS cc_start: 0.8660 (mmmt) cc_final: 0.8301 (tmtt) REVERT: A 105 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7579 (tp30) REVERT: B 88 TYR cc_start: 0.9060 (m-80) cc_final: 0.8794 (m-80) REVERT: C 15 LYS cc_start: 0.8758 (ptpp) cc_final: 0.8038 (pptt) REVERT: C 95 LYS cc_start: 0.9198 (tttm) cc_final: 0.8891 (tppp) REVERT: D 69 ASP cc_start: 0.9120 (t0) cc_final: 0.8772 (t0) REVERT: D 94 GLU cc_start: 0.8918 (mp0) cc_final: 0.8638 (mp0) REVERT: E 73 GLU cc_start: 0.8892 (tt0) cc_final: 0.8316 (tt0) REVERT: E 90 MET cc_start: 0.8634 (tpp) cc_final: 0.8131 (mmp) REVERT: F 23 ARG cc_start: 0.8361 (ttp80) cc_final: 0.8142 (ptp-110) REVERT: F 25 ASN cc_start: 0.8412 (m110) cc_final: 0.7843 (m-40) REVERT: G 73 ASN cc_start: 0.8959 (t0) cc_final: 0.8575 (m-40) REVERT: H 41 TYR cc_start: 0.8231 (m-80) cc_final: 0.7924 (m-80) REVERT: H 47 LYS cc_start: 0.9021 (ttmm) cc_final: 0.8799 (mptt) REVERT: H 50 HIS cc_start: 0.8919 (OUTLIER) cc_final: 0.8299 (m170) REVERT: H 52 ASP cc_start: 0.8268 (m-30) cc_final: 0.7930 (t70) REVERT: H 69 ASP cc_start: 0.8991 (t0) cc_final: 0.8767 (t0) REVERT: H 84 TYR cc_start: 0.8950 (m-10) cc_final: 0.8520 (m-10) REVERT: H 114 GLU cc_start: 0.8955 (mm-30) cc_final: 0.8658 (mm-30) REVERT: K 95 ASP cc_start: 0.8203 (t0) cc_final: 0.7761 (t0) REVERT: K 103 MET cc_start: 0.8633 (ttt) cc_final: 0.7946 (ttp) REVERT: K 214 ASP cc_start: 0.8734 (OUTLIER) cc_final: 0.8455 (m-30) REVERT: K 237 GLU cc_start: 0.7770 (mp0) cc_final: 0.7393 (mp0) REVERT: K 251 GLU cc_start: 0.8299 (mp0) cc_final: 0.8094 (mp0) REVERT: N 214 ASP cc_start: 0.8637 (p0) cc_final: 0.8305 (p0) outliers start: 35 outliers final: 15 residues processed: 247 average time/residue: 1.4830 time to fit residues: 403.1692 Evaluate side-chains 227 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 209 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 185 CYS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 214 ASP Chi-restraints excluded: chain N residue 38 THR Chi-restraints excluded: chain N residue 170 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 54 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 chunk 151 optimal weight: 50.0000 chunk 73 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 136 optimal weight: 6.9990 chunk 91 optimal weight: 0.8980 chunk 130 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 13 optimal weight: 10.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN C 73 ASN ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN G 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.122005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.074596 restraints weight = 38422.564| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.74 r_work: 0.2924 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.4218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 17429 Z= 0.213 Angle : 0.653 9.487 24813 Z= 0.359 Chirality : 0.037 0.148 2799 Planarity : 0.005 0.054 2116 Dihedral : 29.380 178.137 4693 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.47 % Allowed : 29.98 % Favored : 66.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.24), residues: 1306 helix: 2.57 (0.20), residues: 641 sheet: 0.60 (0.36), residues: 222 loop : -1.10 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 199 HIS 0.005 0.001 HIS F 75 PHE 0.008 0.001 PHE E 104 TYR 0.050 0.002 TYR D 84 ARG 0.014 0.001 ARG G 71 Details of bonding type rmsd hydrogen bonds : bond 0.03918 ( 950) hydrogen bonds : angle 3.42444 ( 2434) SS BOND : bond 0.00401 ( 4) SS BOND : angle 0.78633 ( 8) covalent geometry : bond 0.00486 (17425) covalent geometry : angle 0.65273 (24805) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 207 time to evaluate : 1.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 192 LEU cc_start: 0.5925 (pt) cc_final: 0.5552 (pt) REVERT: L 197 MET cc_start: 0.3259 (mmm) cc_final: 0.2740 (mpt) REVERT: A 79 LYS cc_start: 0.8725 (mmmt) cc_final: 0.8328 (tmtt) REVERT: A 105 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7605 (tp30) REVERT: C 91 GLU cc_start: 0.8338 (pt0) cc_final: 0.8017 (pt0) REVERT: C 95 LYS cc_start: 0.9203 (tttm) cc_final: 0.8908 (tppp) REVERT: D 64 ASN cc_start: 0.8769 (OUTLIER) cc_final: 0.8501 (t0) REVERT: D 94 GLU cc_start: 0.8933 (mp0) cc_final: 0.8701 (mp0) REVERT: E 73 GLU cc_start: 0.8920 (tt0) cc_final: 0.8242 (tt0) REVERT: E 90 MET cc_start: 0.8770 (tpp) cc_final: 0.8228 (mmp) REVERT: F 23 ARG cc_start: 0.8401 (ttp80) cc_final: 0.8175 (ptp-110) REVERT: F 25 ASN cc_start: 0.8424 (m110) cc_final: 0.7791 (m-40) REVERT: F 95 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.7993 (mtp85) REVERT: G 73 ASN cc_start: 0.8945 (t0) cc_final: 0.8585 (m-40) REVERT: H 41 TYR cc_start: 0.8262 (m-80) cc_final: 0.7904 (m-80) REVERT: H 47 LYS cc_start: 0.9054 (OUTLIER) cc_final: 0.8819 (mptt) REVERT: H 52 ASP cc_start: 0.8491 (m-30) cc_final: 0.8137 (t70) REVERT: H 69 ASP cc_start: 0.9106 (t0) cc_final: 0.8788 (t0) REVERT: H 84 TYR cc_start: 0.9014 (m-10) cc_final: 0.8630 (m-10) REVERT: H 94 GLU cc_start: 0.9134 (mp0) cc_final: 0.8887 (mp0) REVERT: H 114 GLU cc_start: 0.9052 (mm-30) cc_final: 0.8742 (mm-30) REVERT: K 23 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.7061 (tp30) REVERT: K 95 ASP cc_start: 0.8192 (t0) cc_final: 0.7747 (t0) REVERT: K 237 GLU cc_start: 0.7848 (mp0) cc_final: 0.7585 (mp0) REVERT: N 214 ASP cc_start: 0.8686 (p0) cc_final: 0.8444 (p0) outliers start: 39 outliers final: 15 residues processed: 231 average time/residue: 1.4309 time to fit residues: 362.7305 Evaluate side-chains 220 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 200 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 185 CYS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 64 ASN Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain H residue 47 LYS Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain K residue 23 GLU Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain N residue 38 THR Chi-restraints excluded: chain N residue 170 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 40 optimal weight: 0.6980 chunk 89 optimal weight: 4.9990 chunk 137 optimal weight: 7.9990 chunk 56 optimal weight: 0.6980 chunk 124 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 21 optimal weight: 6.9990 chunk 102 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN E 76 GLN G 38 ASN H 50 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.124144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.077102 restraints weight = 38631.956| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.71 r_work: 0.2978 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.4362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17429 Z= 0.153 Angle : 0.634 12.702 24813 Z= 0.349 Chirality : 0.036 0.164 2799 Planarity : 0.004 0.057 2116 Dihedral : 29.198 178.272 4693 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.76 % Allowed : 30.69 % Favored : 66.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.24), residues: 1306 helix: 2.64 (0.20), residues: 644 sheet: 0.18 (0.36), residues: 234 loop : -0.95 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 199 HIS 0.004 0.001 HIS G 31 PHE 0.009 0.001 PHE N 256 TYR 0.057 0.001 TYR B 88 ARG 0.014 0.001 ARG G 71 Details of bonding type rmsd hydrogen bonds : bond 0.03483 ( 950) hydrogen bonds : angle 3.37508 ( 2434) SS BOND : bond 0.00200 ( 4) SS BOND : angle 0.73553 ( 8) covalent geometry : bond 0.00341 (17425) covalent geometry : angle 0.63436 (24805) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 219 time to evaluate : 1.411 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 192 LEU cc_start: 0.6052 (pt) cc_final: 0.5593 (pt) REVERT: L 197 MET cc_start: 0.3176 (mmm) cc_final: 0.2753 (mpt) REVERT: A 79 LYS cc_start: 0.8657 (mmmt) cc_final: 0.8281 (tmtt) REVERT: A 105 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7590 (tp30) REVERT: C 91 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.8033 (pt0) REVERT: C 95 LYS cc_start: 0.9192 (tttm) cc_final: 0.8918 (tppp) REVERT: D 64 ASN cc_start: 0.8681 (OUTLIER) cc_final: 0.8355 (t0) REVERT: D 94 GLU cc_start: 0.8894 (mp0) cc_final: 0.8670 (mp0) REVERT: E 73 GLU cc_start: 0.8907 (tt0) cc_final: 0.8313 (tt0) REVERT: E 90 MET cc_start: 0.8718 (tpp) cc_final: 0.8158 (mmp) REVERT: E 133 GLU cc_start: 0.8327 (mp0) cc_final: 0.7638 (mt-10) REVERT: F 25 ASN cc_start: 0.8414 (m110) cc_final: 0.7841 (m-40) REVERT: F 63 GLU cc_start: 0.8461 (pt0) cc_final: 0.8093 (mt-10) REVERT: F 95 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.7877 (mtp85) REVERT: G 73 ASN cc_start: 0.8939 (t0) cc_final: 0.8571 (m-40) REVERT: H 39 SER cc_start: 0.9074 (m) cc_final: 0.8838 (p) REVERT: H 41 TYR cc_start: 0.8124 (m-80) cc_final: 0.7904 (m-80) REVERT: H 47 LYS cc_start: 0.9048 (ttmm) cc_final: 0.8835 (mptt) REVERT: H 52 ASP cc_start: 0.8302 (m-30) cc_final: 0.7995 (t70) REVERT: H 69 ASP cc_start: 0.9020 (t0) cc_final: 0.8778 (t0) REVERT: H 84 TYR cc_start: 0.9005 (m-10) cc_final: 0.8600 (m-10) REVERT: H 94 GLU cc_start: 0.9151 (OUTLIER) cc_final: 0.8877 (mp0) REVERT: H 114 GLU cc_start: 0.8952 (mm-30) cc_final: 0.8667 (mm-30) REVERT: K 23 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.7127 (tp30) REVERT: K 95 ASP cc_start: 0.8130 (t0) cc_final: 0.7687 (t0) REVERT: K 176 ARG cc_start: 0.8674 (mmm-85) cc_final: 0.7978 (tpt-90) REVERT: K 251 GLU cc_start: 0.8290 (mp0) cc_final: 0.8069 (mp0) REVERT: N 214 ASP cc_start: 0.8666 (p0) cc_final: 0.8406 (p0) outliers start: 31 outliers final: 17 residues processed: 237 average time/residue: 1.3925 time to fit residues: 363.4361 Evaluate side-chains 229 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 206 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 185 CYS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 64 ASN Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 94 GLU Chi-restraints excluded: chain K residue 23 GLU Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain N residue 38 THR Chi-restraints excluded: chain N residue 170 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 141 optimal weight: 4.9990 chunk 86 optimal weight: 0.0870 chunk 13 optimal weight: 10.0000 chunk 56 optimal weight: 0.9980 chunk 89 optimal weight: 5.9990 chunk 123 optimal weight: 0.0970 chunk 16 optimal weight: 10.0000 chunk 68 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 ASN C 73 ASN C 104 GLN E 76 GLN H 50 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.125692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.078866 restraints weight = 38734.106| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.77 r_work: 0.3016 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.4564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17429 Z= 0.142 Angle : 0.640 9.969 24813 Z= 0.350 Chirality : 0.036 0.180 2799 Planarity : 0.004 0.059 2116 Dihedral : 29.073 179.088 4693 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.22 % Allowed : 31.85 % Favored : 65.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.24), residues: 1306 helix: 2.61 (0.20), residues: 644 sheet: 0.22 (0.36), residues: 234 loop : -0.94 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 199 HIS 0.011 0.001 HIS A 39 PHE 0.009 0.001 PHE N 256 TYR 0.046 0.001 TYR D 84 ARG 0.017 0.001 ARG C 71 Details of bonding type rmsd hydrogen bonds : bond 0.03383 ( 950) hydrogen bonds : angle 3.33771 ( 2434) SS BOND : bond 0.00143 ( 4) SS BOND : angle 0.64546 ( 8) covalent geometry : bond 0.00314 (17425) covalent geometry : angle 0.63967 (24805) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 222 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 192 LEU cc_start: 0.6085 (pt) cc_final: 0.5671 (pt) REVERT: L 197 MET cc_start: 0.3034 (mmm) cc_final: 0.2660 (mpt) REVERT: A 79 LYS cc_start: 0.8544 (mmmt) cc_final: 0.8064 (tmtt) REVERT: B 88 TYR cc_start: 0.8887 (m-80) cc_final: 0.8488 (m-80) REVERT: C 91 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.8040 (pt0) REVERT: C 95 LYS cc_start: 0.9178 (tttm) cc_final: 0.8934 (tppp) REVERT: D 69 ASP cc_start: 0.9120 (t0) cc_final: 0.8747 (t0) REVERT: D 94 GLU cc_start: 0.8884 (mp0) cc_final: 0.8660 (mp0) REVERT: E 73 GLU cc_start: 0.8909 (tt0) cc_final: 0.8272 (tt0) REVERT: E 83 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.6698 (ptm-80) REVERT: E 90 MET cc_start: 0.8650 (tpp) cc_final: 0.8168 (mmp) REVERT: E 133 GLU cc_start: 0.8323 (mp0) cc_final: 0.7610 (mt-10) REVERT: F 25 ASN cc_start: 0.8405 (m110) cc_final: 0.7796 (m-40) REVERT: F 63 GLU cc_start: 0.8455 (pt0) cc_final: 0.8092 (mt-10) REVERT: F 93 GLN cc_start: 0.8959 (mt0) cc_final: 0.8514 (mp10) REVERT: G 73 ASN cc_start: 0.8960 (t0) cc_final: 0.8575 (m-40) REVERT: H 41 TYR cc_start: 0.8123 (m-80) cc_final: 0.7802 (m-80) REVERT: H 52 ASP cc_start: 0.8157 (m-30) cc_final: 0.7839 (t70) REVERT: H 69 ASP cc_start: 0.8947 (t0) cc_final: 0.8691 (t0) REVERT: H 84 TYR cc_start: 0.8987 (m-10) cc_final: 0.8490 (m-10) REVERT: H 94 GLU cc_start: 0.9144 (OUTLIER) cc_final: 0.8874 (mp0) REVERT: H 114 GLU cc_start: 0.8933 (mm-30) cc_final: 0.8629 (mm-30) REVERT: K 95 ASP cc_start: 0.8152 (t0) cc_final: 0.7703 (t0) REVERT: K 176 ARG cc_start: 0.8645 (mmm-85) cc_final: 0.8005 (tpt-90) REVERT: K 251 GLU cc_start: 0.8154 (mp0) cc_final: 0.7905 (mp0) REVERT: N 214 ASP cc_start: 0.8643 (p0) cc_final: 0.8356 (p0) outliers start: 25 outliers final: 12 residues processed: 236 average time/residue: 1.4466 time to fit residues: 374.2902 Evaluate side-chains 221 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 206 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 185 CYS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain H residue 94 GLU Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain N residue 38 THR Chi-restraints excluded: chain N residue 170 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 112 optimal weight: 6.9990 chunk 31 optimal weight: 20.0000 chunk 121 optimal weight: 7.9990 chunk 152 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 27 optimal weight: 30.0000 chunk 21 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN C 38 ASN C 73 ASN ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.122016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.073939 restraints weight = 38749.209| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.51 r_work: 0.2921 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.4477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 17429 Z= 0.227 Angle : 0.688 9.909 24813 Z= 0.375 Chirality : 0.039 0.188 2799 Planarity : 0.005 0.057 2116 Dihedral : 29.340 179.239 4693 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.58 % Allowed : 31.94 % Favored : 65.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.24), residues: 1306 helix: 2.37 (0.20), residues: 645 sheet: 0.78 (0.38), residues: 198 loop : -1.23 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 199 HIS 0.006 0.001 HIS F 75 PHE 0.008 0.001 PHE F 61 TYR 0.058 0.002 TYR D 84 ARG 0.014 0.001 ARG G 71 Details of bonding type rmsd hydrogen bonds : bond 0.04012 ( 950) hydrogen bonds : angle 3.51922 ( 2434) SS BOND : bond 0.00444 ( 4) SS BOND : angle 0.83888 ( 8) covalent geometry : bond 0.00519 (17425) covalent geometry : angle 0.68810 (24805) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14816.64 seconds wall clock time: 252 minutes 20.25 seconds (15140.25 seconds total)