Starting phenix.real_space_refine on Tue Jul 29 22:13:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z0o_14428/07_2025/7z0o_14428.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z0o_14428/07_2025/7z0o_14428.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7z0o_14428/07_2025/7z0o_14428.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z0o_14428/07_2025/7z0o_14428.map" model { file = "/net/cci-nas-00/data/ceres_data/7z0o_14428/07_2025/7z0o_14428.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z0o_14428/07_2025/7z0o_14428.cif" } resolution = 2.8 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= 0.001 sd= 0.019 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 78 5.49 5 S 29 5.16 5 C 7291 2.51 5 N 2111 2.21 5 O 2355 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11864 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 774 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "B" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 610 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 1, 'TRANS': 74} Chain: "C" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 799 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "D" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2436 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 9, 'TRANS': 286} Chain breaks: 5 Chain: "E" Number of atoms: 2518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2518 Classifications: {'peptide': 301} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 290} Chain breaks: 2 Chain: "F" Number of atoms: 1067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1067 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 6, 'TRANS': 126} Chain breaks: 2 Chain: "G" Number of atoms: 681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 681 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "H" Number of atoms: 1380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1380 Classifications: {'peptide': 175} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 166} Chain: "N" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 820 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Chain: "T" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 779 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Time building chain proxies: 8.65, per 1000 atoms: 0.73 Number of scatterers: 11864 At special positions: 0 Unit cell: (74.175, 126.42, 132.225, 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 29 16.00 P 78 15.00 O 2355 8.00 N 2111 7.00 C 7291 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.12 Conformation dependent library (CDL) restraints added in 1.5 seconds 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2430 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 9 sheets defined 64.8% alpha, 6.0% beta 36 base pairs and 74 stacking pairs defined. Time for finding SS restraints: 4.50 Creating SS restraints... Processing helix chain 'A' and resid 48 through 60 Processing helix chain 'A' and resid 64 through 79 Processing helix chain 'A' and resid 86 through 115 removed outlier: 3.695A pdb=" N ALA A 99 " --> pdb=" O GLU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 133 removed outlier: 3.526A pdb=" N ILE A 125 " --> pdb=" O GLN A 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 30 removed outlier: 3.508A pdb=" N ILE B 30 " --> pdb=" O ILE B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 42 removed outlier: 3.662A pdb=" N ILE B 35 " --> pdb=" O THR B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 77 removed outlier: 3.562A pdb=" N SER B 65 " --> pdb=" O SER B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 93 Processing helix chain 'C' and resid 48 through 55 removed outlier: 3.603A pdb=" N ILE C 52 " --> pdb=" O ALA C 48 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE C 55 " --> pdb=" O GLU C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 79 removed outlier: 3.621A pdb=" N ASP C 78 " --> pdb=" O GLU C 74 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N PHE C 79 " --> pdb=" O ILE C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 115 Processing helix chain 'C' and resid 121 through 132 removed outlier: 3.581A pdb=" N ILE C 125 " --> pdb=" O GLN C 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 22 Processing helix chain 'D' and resid 63 through 77 Processing helix chain 'D' and resid 78 through 80 No H-bonds generated for 'chain 'D' and resid 78 through 80' Processing helix chain 'D' and resid 81 through 86 removed outlier: 3.501A pdb=" N TRP D 85 " --> pdb=" O ARG D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 89 No H-bonds generated for 'chain 'D' and resid 87 through 89' Processing helix chain 'D' and resid 93 through 110 Processing helix chain 'D' and resid 128 through 147 Processing helix chain 'D' and resid 148 through 150 No H-bonds generated for 'chain 'D' and resid 148 through 150' Processing helix chain 'D' and resid 164 through 175 removed outlier: 3.893A pdb=" N TRP D 168 " --> pdb=" O ASP D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 179 Processing helix chain 'D' and resid 181 through 185 Processing helix chain 'D' and resid 195 through 218 Processing helix chain 'D' and resid 219 through 224 removed outlier: 4.521A pdb=" N ALA D 223 " --> pdb=" O ALA D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 256 Processing helix chain 'D' and resid 257 through 261 Processing helix chain 'D' and resid 264 through 276 removed outlier: 3.679A pdb=" N VAL D 270 " --> pdb=" O PRO D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 302 Processing helix chain 'D' and resid 340 through 363 Processing helix chain 'E' and resid 36 through 54 removed outlier: 3.566A pdb=" N ASP E 54 " --> pdb=" O SER E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 73 Processing helix chain 'E' and resid 77 through 89 Processing helix chain 'E' and resid 90 through 94 Processing helix chain 'E' and resid 129 through 160 Processing helix chain 'E' and resid 171 through 208 Processing helix chain 'E' and resid 229 through 240 Processing helix chain 'E' and resid 244 through 256 Processing helix chain 'E' and resid 258 through 262 Processing helix chain 'E' and resid 263 through 268 removed outlier: 3.700A pdb=" N ARG E 268 " --> pdb=" O ARG E 265 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 277 Processing helix chain 'E' and resid 286 through 294 Processing helix chain 'E' and resid 301 through 306 removed outlier: 3.529A pdb=" N LYS E 306 " --> pdb=" O GLU E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 340 Processing helix chain 'E' and resid 352 through 356 Processing helix chain 'F' and resid 4 through 9 Processing helix chain 'F' and resid 22 through 31 Processing helix chain 'F' and resid 41 through 48 Processing helix chain 'F' and resid 49 through 55 Processing helix chain 'F' and resid 67 through 83 Processing helix chain 'F' and resid 84 through 87 removed outlier: 3.937A pdb=" N ILE F 87 " --> pdb=" O PRO F 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 84 through 87' Processing helix chain 'F' and resid 91 through 109 removed outlier: 3.772A pdb=" N TYR F 109 " --> pdb=" O TRP F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 132 removed outlier: 4.460A pdb=" N CYS F 129 " --> pdb=" O GLY F 125 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE F 132 " --> pdb=" O PRO F 128 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 16 removed outlier: 3.608A pdb=" N MET G 10 " --> pdb=" O ASP G 6 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 37 removed outlier: 3.569A pdb=" N LYS G 33 " --> pdb=" O ARG G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 43 through 58 removed outlier: 3.878A pdb=" N LEU G 57 " --> pdb=" O LYS G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 86 removed outlier: 3.581A pdb=" N GLU G 85 " --> pdb=" O GLU G 81 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE G 86 " --> pdb=" O LEU G 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 81 through 89 Processing helix chain 'H' and resid 128 through 146 Processing helix chain 'H' and resid 173 through 179 removed outlier: 3.945A pdb=" N PHE H 177 " --> pdb=" O GLU H 173 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N HIS H 179 " --> pdb=" O LEU H 175 " (cutoff:3.500A) Processing helix chain 'H' and resid 219 through 236 Proline residue: H 232 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 44 Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.665A pdb=" N ARG A 84 " --> pdb=" O VAL B 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 119 through 120 Processing sheet with id=AA4, first strand: chain 'C' and resid 40 through 41 removed outlier: 4.121A pdb=" N LEU D 187 " --> pdb=" O ARG C 41 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 83 through 85 Processing sheet with id=AA6, first strand: chain 'D' and resid 35 through 37 Processing sheet with id=AA7, first strand: chain 'D' and resid 226 through 228 Processing sheet with id=AA8, first strand: chain 'F' and resid 112 through 114 Processing sheet with id=AA9, first strand: chain 'H' and resid 102 through 106 removed outlier: 3.627A pdb=" N MET H 104 " --> pdb=" O ALA H 113 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR H 111 " --> pdb=" O ILE H 106 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LEU H 67 " --> pdb=" O GLY H 162 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLY H 162 " --> pdb=" O LEU H 67 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ASN H 69 " --> pdb=" O ILE H 160 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N ILE H 160 " --> pdb=" O ASN H 69 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N VAL H 71 " --> pdb=" O GLN H 158 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N THR H 75 " --> pdb=" O ASP H 154 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ASP H 154 " --> pdb=" O THR H 75 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N ILE H 160 " --> pdb=" O GLY H 216 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY H 216 " --> pdb=" O ILE H 160 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ILE H 202 " --> pdb=" O MET H 197 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N MET H 197 " --> pdb=" O ILE H 202 " (cutoff:3.500A) 598 hydrogen bonds defined for protein. 1728 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 82 hydrogen bonds 164 hydrogen bond angles 0 basepair planarities 36 basepair parallelities 74 stacking parallelities Total time for adding SS restraints: 3.89 Time building geometry restraints manager: 3.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3656 1.34 - 1.46: 3057 1.46 - 1.58: 5318 1.58 - 1.70: 154 1.70 - 1.82: 46 Bond restraints: 12231 Sorted by residual: bond pdb=" CG PRO G 62 " pdb=" CD PRO G 62 " ideal model delta sigma weight residual 1.503 1.557 -0.054 3.40e-02 8.65e+02 2.50e+00 bond pdb=" CB PRO G 62 " pdb=" CG PRO G 62 " ideal model delta sigma weight residual 1.492 1.563 -0.071 5.00e-02 4.00e+02 2.03e+00 bond pdb=" CB GLU G 81 " pdb=" CG GLU G 81 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.71e+00 bond pdb=" C1' DT T 76 " pdb=" N1 DT T 76 " ideal model delta sigma weight residual 1.490 1.454 0.036 3.00e-02 1.11e+03 1.45e+00 bond pdb=" C1' DT T 56 " pdb=" N1 DT T 56 " ideal model delta sigma weight residual 1.490 1.454 0.036 3.00e-02 1.11e+03 1.44e+00 ... (remaining 12226 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 16333 1.92 - 3.84: 405 3.84 - 5.76: 62 5.76 - 7.68: 6 7.68 - 9.60: 2 Bond angle restraints: 16808 Sorted by residual: angle pdb=" CA GLN G 43 " pdb=" CB GLN G 43 " pdb=" CG GLN G 43 " ideal model delta sigma weight residual 114.10 121.86 -7.76 2.00e+00 2.50e-01 1.50e+01 angle pdb=" CA GLU G 81 " pdb=" CB GLU G 81 " pdb=" CG GLU G 81 " ideal model delta sigma weight residual 114.10 121.04 -6.94 2.00e+00 2.50e-01 1.20e+01 angle pdb=" CG ARG H 98 " pdb=" CD ARG H 98 " pdb=" NE ARG H 98 " ideal model delta sigma weight residual 112.00 119.54 -7.54 2.20e+00 2.07e-01 1.17e+01 angle pdb=" CA PRO G 62 " pdb=" N PRO G 62 " pdb=" CD PRO G 62 " ideal model delta sigma weight residual 112.00 107.25 4.75 1.40e+00 5.10e-01 1.15e+01 angle pdb=" N GLU E 112 " pdb=" CA GLU E 112 " pdb=" C GLU E 112 " ideal model delta sigma weight residual 114.56 110.32 4.24 1.27e+00 6.20e-01 1.12e+01 ... (remaining 16803 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.08: 6040 18.08 - 36.15: 825 36.15 - 54.22: 364 54.22 - 72.30: 87 72.30 - 90.37: 14 Dihedral angle restraints: 7330 sinusoidal: 3614 harmonic: 3716 Sorted by residual: dihedral pdb=" CA SER D 41 " pdb=" C SER D 41 " pdb=" N ILE D 42 " pdb=" CA ILE D 42 " ideal model delta harmonic sigma weight residual 180.00 -161.44 -18.56 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA LYS F 126 " pdb=" C LYS F 126 " pdb=" N GLY F 127 " pdb=" CA GLY F 127 " ideal model delta harmonic sigma weight residual -180.00 -162.36 -17.64 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CG ARG H 98 " pdb=" CD ARG H 98 " pdb=" NE ARG H 98 " pdb=" CZ ARG H 98 " ideal model delta sinusoidal sigma weight residual 90.00 41.51 48.49 2 1.50e+01 4.44e-03 1.20e+01 ... (remaining 7327 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1303 0.032 - 0.064: 407 0.064 - 0.097: 131 0.097 - 0.129: 52 0.129 - 0.161: 4 Chirality restraints: 1897 Sorted by residual: chirality pdb=" CB ILE D 42 " pdb=" CA ILE D 42 " pdb=" CG1 ILE D 42 " pdb=" CG2 ILE D 42 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.47e-01 chirality pdb=" CA GLN G 43 " pdb=" N GLN G 43 " pdb=" C GLN G 43 " pdb=" CB GLN G 43 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.18e-01 chirality pdb=" C1' DC T 55 " pdb=" O4' DC T 55 " pdb=" C2' DC T 55 " pdb=" N1 DC T 55 " both_signs ideal model delta sigma weight residual False 2.47 2.33 0.14 2.00e-01 2.50e+01 5.13e-01 ... (remaining 1894 not shown) Planarity restraints: 1854 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE H 168 " -0.033 5.00e-02 4.00e+02 4.95e-02 3.91e+00 pdb=" N PRO H 169 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO H 169 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO H 169 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG G 61 " 0.031 5.00e-02 4.00e+02 4.58e-02 3.36e+00 pdb=" N PRO G 62 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO G 62 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO G 62 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 28 " 0.008 2.00e-02 2.50e+03 1.66e-02 2.75e+00 pdb=" CD GLN B 28 " -0.029 2.00e-02 2.50e+03 pdb=" OE1 GLN B 28 " 0.011 2.00e-02 2.50e+03 pdb=" NE2 GLN B 28 " 0.010 2.00e-02 2.50e+03 ... (remaining 1851 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 687 2.73 - 3.27: 11598 3.27 - 3.82: 20751 3.82 - 4.36: 25016 4.36 - 4.90: 40566 Nonbonded interactions: 98618 Sorted by model distance: nonbonded pdb=" OG SER G 42 " pdb=" OE1 GLN G 43 " model vdw 2.189 3.040 nonbonded pdb=" O THR H 111 " pdb=" OH TYR H 139 " model vdw 2.231 3.040 nonbonded pdb=" OD1 ASP C 107 " pdb=" NZ LYS D 275 " model vdw 2.254 3.120 nonbonded pdb=" OG SER E 95 " pdb=" OD1 ASN F 88 " model vdw 2.255 3.040 nonbonded pdb=" O ASN G 5 " pdb=" OG SER G 8 " model vdw 2.276 3.040 ... (remaining 98613 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 'C' and resid 40 through 133) } 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: 4.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 33.400 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 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:12.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 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 : 0.004 0.071 12231 Z= 0.160 Angle : 0.663 9.596 16808 Z= 0.400 Chirality : 0.038 0.161 1897 Planarity : 0.004 0.053 1854 Dihedral : 19.644 90.375 4900 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.42 % Allowed : 19.54 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.08 (0.23), residues: 1222 helix: 1.45 (0.19), residues: 740 sheet: 0.07 (0.76), residues: 47 loop : -0.40 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 85 HIS 0.003 0.001 HIS E 58 PHE 0.010 0.001 PHE H 177 TYR 0.008 0.001 TYR E 230 ARG 0.014 0.000 ARG E 265 Details of bonding type rmsd hydrogen bonds : bond 0.24592 ( 680) hydrogen bonds : angle 6.76182 ( 1892) covalent geometry : bond 0.00384 (12231) covalent geometry : angle 0.66335 (16808) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 279 time to evaluate : 1.287 Fit side-chains REVERT: A 98 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.6709 (mp0) REVERT: A 109 ASN cc_start: 0.7773 (t0) cc_final: 0.7200 (t0) REVERT: A 117 ARG cc_start: 0.7746 (mtm110) cc_final: 0.7431 (mtm180) REVERT: A 124 ASP cc_start: 0.7903 (m-30) cc_final: 0.7663 (m-30) REVERT: B 63 LEU cc_start: 0.7628 (tp) cc_final: 0.7420 (tp) REVERT: C 49 LEU cc_start: 0.8131 (mt) cc_final: 0.7888 (mt) REVERT: C 50 ARG cc_start: 0.7235 (ttm170) cc_final: 0.6964 (tpp80) REVERT: D 16 GLU cc_start: 0.7052 (mt-10) cc_final: 0.6837 (mt-10) REVERT: D 19 GLU cc_start: 0.6901 (tp30) cc_final: 0.6653 (tp30) REVERT: D 78 SER cc_start: 0.7169 (OUTLIER) cc_final: 0.6766 (p) REVERT: D 126 GLU cc_start: 0.7060 (tt0) cc_final: 0.6818 (tt0) REVERT: D 135 GLU cc_start: 0.6927 (tt0) cc_final: 0.6726 (tt0) REVERT: D 143 MET cc_start: 0.7399 (mtm) cc_final: 0.7146 (mtm) REVERT: D 162 LEU cc_start: 0.7930 (mt) cc_final: 0.7699 (mt) REVERT: D 169 LYS cc_start: 0.7945 (mttt) cc_final: 0.7592 (mttm) REVERT: D 183 GLU cc_start: 0.7613 (pt0) cc_final: 0.7297 (pm20) REVERT: D 277 GLU cc_start: 0.7159 (mt-10) cc_final: 0.6803 (mt-10) REVERT: D 354 GLU cc_start: 0.7223 (tt0) cc_final: 0.6847 (tt0) REVERT: E 68 LEU cc_start: 0.7988 (mm) cc_final: 0.7785 (mt) REVERT: E 74 GLU cc_start: 0.6326 (tt0) cc_final: 0.6093 (tt0) REVERT: E 75 LYS cc_start: 0.7683 (ttpp) cc_final: 0.7483 (tmtm) REVERT: E 80 GLU cc_start: 0.7659 (mp0) cc_final: 0.7459 (mp0) REVERT: E 94 THR cc_start: 0.7391 (p) cc_final: 0.7123 (m) REVERT: E 127 GLU cc_start: 0.7898 (tt0) cc_final: 0.7331 (tt0) REVERT: E 134 MET cc_start: 0.6615 (mtm) cc_final: 0.6387 (pp-130) REVERT: E 143 GLU cc_start: 0.6805 (mm-30) cc_final: 0.6475 (mm-30) REVERT: E 181 LYS cc_start: 0.7278 (mttp) cc_final: 0.6955 (OUTLIER) REVERT: E 192 LYS cc_start: 0.7497 (tttt) cc_final: 0.6718 (tttp) REVERT: E 196 GLU cc_start: 0.6771 (mt-10) cc_final: 0.6186 (mt-10) REVERT: E 198 GLU cc_start: 0.6754 (mm-30) cc_final: 0.6444 (mm-30) REVERT: E 240 MET cc_start: 0.7815 (mtm) cc_final: 0.7573 (mtp) REVERT: E 241 ASN cc_start: 0.7596 (m110) cc_final: 0.7390 (m110) REVERT: E 261 LYS cc_start: 0.7560 (mmpt) cc_final: 0.7237 (mmtp) REVERT: E 271 LYS cc_start: 0.7487 (mmtp) cc_final: 0.7114 (mmtp) REVERT: E 273 ILE cc_start: 0.7962 (mm) cc_final: 0.7737 (mm) REVERT: E 275 LYS cc_start: 0.7533 (mmpt) cc_final: 0.7220 (mmpt) REVERT: E 276 LYS cc_start: 0.7505 (ttmm) cc_final: 0.7285 (ttmm) REVERT: E 293 LYS cc_start: 0.7500 (mtmt) cc_final: 0.7086 (mtmp) REVERT: E 302 GLU cc_start: 0.6546 (pp20) cc_final: 0.6132 (pp20) REVERT: E 317 LYS cc_start: 0.7584 (mttt) cc_final: 0.7286 (mtpt) REVERT: E 327 GLU cc_start: 0.6659 (mm-30) cc_final: 0.6313 (mm-30) REVERT: E 341 TYR cc_start: 0.6529 (p90) cc_final: 0.5929 (p90) REVERT: F 77 GLN cc_start: 0.8127 (mm-40) cc_final: 0.7557 (mm-40) REVERT: F 81 ASN cc_start: 0.7542 (m-40) cc_final: 0.7168 (m-40) REVERT: F 109 TYR cc_start: 0.8122 (m-80) cc_final: 0.7713 (m-80) REVERT: F 130 GLU cc_start: 0.6901 (mp0) cc_final: 0.6202 (mp0) REVERT: G 18 MET cc_start: 0.5063 (ptp) cc_final: 0.4658 (ptp) REVERT: G 78 LEU cc_start: 0.7574 (mt) cc_final: 0.7366 (mp) outliers start: 16 outliers final: 7 residues processed: 290 average time/residue: 1.5632 time to fit residues: 482.5075 Evaluate side-chains 261 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 253 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 181 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 0.3980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 116 optimal weight: 20.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 248 GLN D 355 ASN D 356 GLN F 114 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.161599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.131885 restraints weight = 14100.789| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 1.44 r_work: 0.3464 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 12231 Z= 0.201 Angle : 0.596 9.417 16808 Z= 0.336 Chirality : 0.042 0.193 1897 Planarity : 0.004 0.041 1854 Dihedral : 20.249 65.736 2285 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 4.17 % Allowed : 20.43 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.61 (0.23), residues: 1222 helix: 1.93 (0.18), residues: 751 sheet: -0.49 (0.65), residues: 63 loop : -0.25 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP D 85 HIS 0.005 0.001 HIS G 54 PHE 0.014 0.002 PHE D 70 TYR 0.014 0.002 TYR E 230 ARG 0.006 0.001 ARG D 225 Details of bonding type rmsd hydrogen bonds : bond 0.05816 ( 680) hydrogen bonds : angle 4.41564 ( 1892) covalent geometry : bond 0.00455 (12231) covalent geometry : angle 0.59590 (16808) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 242 time to evaluate : 1.256 Fit side-chains REVERT: A 98 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7543 (mp0) REVERT: A 109 ASN cc_start: 0.8493 (t0) cc_final: 0.8135 (t0) REVERT: A 117 ARG cc_start: 0.8158 (mtm110) cc_final: 0.7885 (mtm180) REVERT: B 32 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.8351 (mmtt) REVERT: D 130 GLU cc_start: 0.7975 (mp0) cc_final: 0.7649 (mp0) REVERT: D 135 GLU cc_start: 0.7813 (tt0) cc_final: 0.7605 (tt0) REVERT: D 344 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.6948 (mp0) REVERT: E 127 GLU cc_start: 0.8055 (tt0) cc_final: 0.7819 (tt0) REVERT: E 143 GLU cc_start: 0.7371 (mm-30) cc_final: 0.7128 (mm-30) REVERT: E 187 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7320 (pp20) REVERT: E 192 LYS cc_start: 0.8462 (tttt) cc_final: 0.8210 (tttp) REVERT: E 200 ASP cc_start: 0.8063 (m-30) cc_final: 0.7812 (m-30) REVERT: E 275 LYS cc_start: 0.7892 (mmpt) cc_final: 0.7627 (mmpt) REVERT: E 302 GLU cc_start: 0.7073 (pp20) cc_final: 0.6825 (pp20) REVERT: E 320 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7797 (ttt90) REVERT: F 130 GLU cc_start: 0.7671 (mp0) cc_final: 0.7219 (mp0) REVERT: G 18 MET cc_start: 0.6038 (ptp) cc_final: 0.5759 (ptp) REVERT: G 81 GLU cc_start: 0.7451 (tm-30) cc_final: 0.7224 (tm-30) REVERT: H 103 ILE cc_start: 0.7801 (OUTLIER) cc_final: 0.7591 (mm) REVERT: H 199 LYS cc_start: 0.5753 (OUTLIER) cc_final: 0.5482 (pptt) outliers start: 47 outliers final: 16 residues processed: 271 average time/residue: 1.4283 time to fit residues: 414.4804 Evaluate side-chains 264 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 241 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain D residue 65 GLU Chi-restraints excluded: chain D residue 137 LYS Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 320 ARG Chi-restraints excluded: chain F residue 65 ASP Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain H residue 199 LYS Chi-restraints excluded: chain H residue 223 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 52 optimal weight: 3.9990 chunk 33 optimal weight: 0.3980 chunk 3 optimal weight: 0.7980 chunk 99 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 55 optimal weight: 4.9990 chunk 63 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 64 optimal weight: 0.1980 chunk 69 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 248 GLN D 294 HIS D 356 GLN E 337 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.162835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.133168 restraints weight = 14240.096| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 1.45 r_work: 0.3465 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12231 Z= 0.167 Angle : 0.551 8.911 16808 Z= 0.309 Chirality : 0.040 0.190 1897 Planarity : 0.004 0.040 1854 Dihedral : 20.318 61.746 2276 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 4.09 % Allowed : 21.31 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.83 (0.23), residues: 1222 helix: 2.19 (0.18), residues: 743 sheet: -0.34 (0.65), residues: 68 loop : -0.30 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 85 HIS 0.004 0.001 HIS D 353 PHE 0.013 0.001 PHE F 90 TYR 0.011 0.001 TYR H 195 ARG 0.006 0.000 ARG C 64 Details of bonding type rmsd hydrogen bonds : bond 0.04931 ( 680) hydrogen bonds : angle 4.10153 ( 1892) covalent geometry : bond 0.00375 (12231) covalent geometry : angle 0.55072 (16808) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 240 time to evaluate : 1.147 Fit side-chains REVERT: A 98 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7486 (mp0) REVERT: A 109 ASN cc_start: 0.8495 (t0) cc_final: 0.8139 (t160) REVERT: A 117 ARG cc_start: 0.8156 (mtm110) cc_final: 0.7888 (mtm180) REVERT: B 32 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8336 (mmtt) REVERT: D 203 GLU cc_start: 0.7839 (tt0) cc_final: 0.7608 (tt0) REVERT: D 344 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.6766 (mp0) REVERT: E 127 GLU cc_start: 0.8055 (tt0) cc_final: 0.7776 (tt0) REVERT: E 143 GLU cc_start: 0.7312 (mm-30) cc_final: 0.7077 (mm-30) REVERT: E 183 ASP cc_start: 0.7865 (m-30) cc_final: 0.7576 (m-30) REVERT: E 187 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7231 (pp20) REVERT: E 192 LYS cc_start: 0.8481 (tttt) cc_final: 0.8249 (tptp) REVERT: E 275 LYS cc_start: 0.7919 (mmpt) cc_final: 0.7634 (mmpt) REVERT: E 302 GLU cc_start: 0.7030 (pp20) cc_final: 0.6760 (pp20) REVERT: E 320 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7753 (ttt90) REVERT: E 341 TYR cc_start: 0.7268 (p90) cc_final: 0.6594 (p90) REVERT: F 130 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7194 (mp0) REVERT: G 81 GLU cc_start: 0.7539 (tm-30) cc_final: 0.7259 (tm-30) outliers start: 46 outliers final: 22 residues processed: 265 average time/residue: 1.4838 time to fit residues: 419.8836 Evaluate side-chains 252 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 224 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain D residue 4 GLN Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 137 LYS Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 285 LYS Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 249 MET Chi-restraints excluded: chain E residue 288 LYS Chi-restraints excluded: chain E residue 320 ARG Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain H residue 95 ASN Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 198 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 120 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 52 optimal weight: 0.0370 chunk 87 optimal weight: 0.0980 chunk 65 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 71 optimal weight: 0.4980 chunk 39 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 overall best weight: 0.3858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 248 GLN D 356 GLN E 337 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.164757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.135204 restraints weight = 14010.686| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 1.43 r_work: 0.3491 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12231 Z= 0.141 Angle : 0.517 8.928 16808 Z= 0.289 Chirality : 0.038 0.157 1897 Planarity : 0.004 0.039 1854 Dihedral : 20.360 59.670 2276 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 4.44 % Allowed : 20.60 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.97 (0.24), residues: 1222 helix: 2.32 (0.18), residues: 743 sheet: -0.33 (0.66), residues: 68 loop : -0.29 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 148 HIS 0.004 0.001 HIS D 353 PHE 0.011 0.001 PHE D 70 TYR 0.012 0.001 TYR H 195 ARG 0.008 0.000 ARG C 64 Details of bonding type rmsd hydrogen bonds : bond 0.04340 ( 680) hydrogen bonds : angle 3.90008 ( 1892) covalent geometry : bond 0.00309 (12231) covalent geometry : angle 0.51675 (16808) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 228 time to evaluate : 1.357 Fit side-chains revert: symmetry clash REVERT: A 109 ASN cc_start: 0.8448 (t0) cc_final: 0.8105 (t160) REVERT: A 117 ARG cc_start: 0.8122 (mtm110) cc_final: 0.7903 (mtm180) REVERT: B 32 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8338 (mmtt) REVERT: D 203 GLU cc_start: 0.7824 (tt0) cc_final: 0.7609 (tt0) REVERT: D 344 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.6733 (mp0) REVERT: E 127 GLU cc_start: 0.8048 (tt0) cc_final: 0.7840 (tt0) REVERT: E 143 GLU cc_start: 0.7281 (mm-30) cc_final: 0.7020 (mm-30) REVERT: E 183 ASP cc_start: 0.7894 (m-30) cc_final: 0.7535 (m-30) REVERT: E 187 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.7122 (pp20) REVERT: E 192 LYS cc_start: 0.8495 (tttt) cc_final: 0.8273 (tptp) REVERT: E 198 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7327 (mm-30) REVERT: E 275 LYS cc_start: 0.7945 (mmpt) cc_final: 0.7652 (mmpt) REVERT: E 302 GLU cc_start: 0.7002 (pp20) cc_final: 0.6742 (pp20) REVERT: E 341 TYR cc_start: 0.7247 (p90) cc_final: 0.6527 (p90) REVERT: F 130 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7105 (mp0) REVERT: G 81 GLU cc_start: 0.7589 (tm-30) cc_final: 0.7245 (tm-30) REVERT: H 160 ILE cc_start: 0.4656 (OUTLIER) cc_final: 0.4261 (pp) outliers start: 50 outliers final: 30 residues processed: 254 average time/residue: 1.6936 time to fit residues: 461.3468 Evaluate side-chains 254 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 219 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain D residue 4 GLN Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 137 LYS Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 285 LYS Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 249 MET Chi-restraints excluded: chain E residue 288 LYS Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain H residue 95 ASN Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain H residue 223 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 112 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 356 GLN E 169 ASN E 337 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.162542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.132416 restraints weight = 14007.114| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 1.45 r_work: 0.3450 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 12231 Z= 0.226 Angle : 0.568 5.408 16808 Z= 0.319 Chirality : 0.042 0.181 1897 Planarity : 0.004 0.047 1854 Dihedral : 20.381 59.960 2276 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 5.33 % Allowed : 20.78 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.69 (0.23), residues: 1222 helix: 2.09 (0.18), residues: 743 sheet: -0.40 (0.68), residues: 62 loop : -0.39 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP D 85 HIS 0.008 0.001 HIS E 135 PHE 0.018 0.002 PHE D 70 TYR 0.014 0.002 TYR E 230 ARG 0.010 0.001 ARG C 64 Details of bonding type rmsd hydrogen bonds : bond 0.05291 ( 680) hydrogen bonds : angle 4.12690 ( 1892) covalent geometry : bond 0.00526 (12231) covalent geometry : angle 0.56830 (16808) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 233 time to evaluate : 1.207 Fit side-chains revert: symmetry clash REVERT: A 109 ASN cc_start: 0.8524 (t0) cc_final: 0.8154 (t160) REVERT: A 117 ARG cc_start: 0.8149 (mtm110) cc_final: 0.7924 (mtm180) REVERT: B 41 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.7793 (mtt180) REVERT: D 130 GLU cc_start: 0.8052 (mp0) cc_final: 0.7735 (mp0) REVERT: D 203 GLU cc_start: 0.7890 (tt0) cc_final: 0.7677 (tt0) REVERT: D 344 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.6731 (mp0) REVERT: E 127 GLU cc_start: 0.8069 (tt0) cc_final: 0.7851 (tt0) REVERT: E 143 GLU cc_start: 0.7343 (mm-30) cc_final: 0.7119 (mm-30) REVERT: E 183 ASP cc_start: 0.7961 (m-30) cc_final: 0.7643 (m-30) REVERT: E 187 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7219 (pp20) REVERT: E 192 LYS cc_start: 0.8488 (tttt) cc_final: 0.8235 (tptp) REVERT: E 198 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7319 (mm-30) REVERT: E 275 LYS cc_start: 0.7956 (mmpt) cc_final: 0.7684 (mmpt) REVERT: E 302 GLU cc_start: 0.6950 (pp20) cc_final: 0.6701 (pp20) REVERT: E 320 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7776 (ttt90) REVERT: E 341 TYR cc_start: 0.7342 (p90) cc_final: 0.6678 (p90) REVERT: F 130 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7105 (mp0) REVERT: G 81 GLU cc_start: 0.7620 (tm-30) cc_final: 0.7296 (tm-30) REVERT: H 160 ILE cc_start: 0.4968 (OUTLIER) cc_final: 0.4588 (pp) outliers start: 60 outliers final: 36 residues processed: 259 average time/residue: 1.9649 time to fit residues: 543.6111 Evaluate side-chains 270 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 228 time to evaluate : 3.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain B residue 41 ARG Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain D residue 4 GLN Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 137 LYS Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 285 LYS Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 137 SER Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 249 MET Chi-restraints excluded: chain E residue 288 LYS Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain E residue 320 ARG Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 95 ASN Chi-restraints excluded: chain H residue 129 GLU Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 199 LYS Chi-restraints excluded: chain H residue 223 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 3 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 72 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 111 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 356 GLN E 337 GLN F 81 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.162700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.132500 restraints weight = 14048.023| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 1.46 r_work: 0.3452 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12231 Z= 0.224 Angle : 0.571 5.402 16808 Z= 0.321 Chirality : 0.042 0.159 1897 Planarity : 0.004 0.047 1854 Dihedral : 20.414 59.829 2276 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 5.15 % Allowed : 21.23 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.59 (0.23), residues: 1222 helix: 2.03 (0.18), residues: 737 sheet: -0.38 (0.68), residues: 62 loop : -0.46 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP D 85 HIS 0.006 0.001 HIS G 54 PHE 0.020 0.002 PHE D 70 TYR 0.014 0.002 TYR E 230 ARG 0.009 0.000 ARG C 64 Details of bonding type rmsd hydrogen bonds : bond 0.05259 ( 680) hydrogen bonds : angle 4.14220 ( 1892) covalent geometry : bond 0.00520 (12231) covalent geometry : angle 0.57068 (16808) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 228 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 109 ASN cc_start: 0.8531 (t0) cc_final: 0.8168 (t160) REVERT: A 117 ARG cc_start: 0.8127 (mtm110) cc_final: 0.7914 (mtm180) REVERT: B 32 LYS cc_start: 0.8641 (mmtm) cc_final: 0.8364 (mmtt) REVERT: B 41 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.7784 (mtt180) REVERT: D 105 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7813 (ttp-170) REVERT: D 130 GLU cc_start: 0.8032 (mp0) cc_final: 0.7721 (mp0) REVERT: D 203 GLU cc_start: 0.7826 (tt0) cc_final: 0.7621 (tt0) REVERT: D 344 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.6747 (mp0) REVERT: E 143 GLU cc_start: 0.7337 (mm-30) cc_final: 0.7117 (mm-30) REVERT: E 183 ASP cc_start: 0.7971 (m-30) cc_final: 0.7645 (m-30) REVERT: E 187 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7200 (pp20) REVERT: E 192 LYS cc_start: 0.8466 (tttt) cc_final: 0.8222 (tptp) REVERT: E 198 GLU cc_start: 0.7716 (mm-30) cc_final: 0.7304 (mm-30) REVERT: E 275 LYS cc_start: 0.7943 (mmpt) cc_final: 0.7674 (mmpt) REVERT: E 302 GLU cc_start: 0.6915 (pp20) cc_final: 0.6686 (pp20) REVERT: E 320 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7756 (ttt90) REVERT: E 341 TYR cc_start: 0.7384 (p90) cc_final: 0.6715 (p90) REVERT: G 38 ILE cc_start: 0.8242 (pt) cc_final: 0.8007 (mt) REVERT: G 81 GLU cc_start: 0.7588 (tm-30) cc_final: 0.7264 (tm-30) REVERT: H 91 ASN cc_start: 0.7704 (m-40) cc_final: 0.7406 (m110) REVERT: H 160 ILE cc_start: 0.5160 (OUTLIER) cc_final: 0.4819 (pp) outliers start: 58 outliers final: 41 residues processed: 259 average time/residue: 1.6236 time to fit residues: 449.5663 Evaluate side-chains 275 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 228 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain B residue 41 ARG Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain D residue 4 GLN Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 105 ARG Chi-restraints excluded: chain D residue 137 LYS Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 285 LYS Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 137 SER Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 288 LYS Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain E residue 320 ARG Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 95 ASN Chi-restraints excluded: chain H residue 121 MET Chi-restraints excluded: chain H residue 129 GLU Chi-restraints excluded: chain H residue 158 GLN Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 212 ILE Chi-restraints excluded: chain H residue 223 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 102 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 38 optimal weight: 0.4980 chunk 89 optimal weight: 0.9990 chunk 6 optimal weight: 0.0980 chunk 120 optimal weight: 0.5980 chunk 68 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 119 optimal weight: 4.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 356 GLN E 337 GLN F 81 ASN H 68 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.163966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.133881 restraints weight = 14159.499| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 1.46 r_work: 0.3470 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12231 Z= 0.169 Angle : 0.537 5.267 16808 Z= 0.302 Chirality : 0.039 0.164 1897 Planarity : 0.004 0.043 1854 Dihedral : 20.402 59.955 2276 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 5.06 % Allowed : 21.85 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.76 (0.24), residues: 1222 helix: 2.19 (0.18), residues: 737 sheet: -0.41 (0.67), residues: 62 loop : -0.43 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 85 HIS 0.004 0.001 HIS D 353 PHE 0.016 0.002 PHE D 70 TYR 0.013 0.001 TYR E 230 ARG 0.007 0.000 ARG C 64 Details of bonding type rmsd hydrogen bonds : bond 0.04706 ( 680) hydrogen bonds : angle 4.01633 ( 1892) covalent geometry : bond 0.00383 (12231) covalent geometry : angle 0.53716 (16808) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 228 time to evaluate : 1.430 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 109 ASN cc_start: 0.8476 (t0) cc_final: 0.8127 (t160) REVERT: D 130 GLU cc_start: 0.8009 (mp0) cc_final: 0.7642 (mp0) REVERT: D 135 GLU cc_start: 0.7752 (tt0) cc_final: 0.7472 (tt0) REVERT: D 203 GLU cc_start: 0.7836 (tt0) cc_final: 0.7626 (tt0) REVERT: D 344 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.6754 (mp0) REVERT: E 143 GLU cc_start: 0.7326 (mm-30) cc_final: 0.7099 (mm-30) REVERT: E 183 ASP cc_start: 0.7960 (m-30) cc_final: 0.7598 (m-30) REVERT: E 187 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.7153 (pp20) REVERT: E 192 LYS cc_start: 0.8487 (tttt) cc_final: 0.8247 (tptp) REVERT: E 198 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7323 (mm-30) REVERT: E 275 LYS cc_start: 0.7980 (mmtt) cc_final: 0.7703 (mmpt) REVERT: E 302 GLU cc_start: 0.6922 (pp20) cc_final: 0.6693 (pp20) REVERT: E 320 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7716 (ttt90) REVERT: E 341 TYR cc_start: 0.7366 (p90) cc_final: 0.6667 (p90) REVERT: G 81 GLU cc_start: 0.7615 (tm-30) cc_final: 0.7278 (tm-30) REVERT: H 91 ASN cc_start: 0.7686 (m-40) cc_final: 0.7382 (m110) REVERT: H 160 ILE cc_start: 0.4950 (OUTLIER) cc_final: 0.4553 (pp) outliers start: 57 outliers final: 43 residues processed: 256 average time/residue: 2.2198 time to fit residues: 608.9614 Evaluate side-chains 274 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 227 time to evaluate : 2.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain D residue 4 GLN Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 137 LYS Chi-restraints excluded: chain D residue 151 GLU Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 285 LYS Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 137 SER Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 249 MET Chi-restraints excluded: chain E residue 288 LYS Chi-restraints excluded: chain E residue 320 ARG Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain H residue 68 GLN Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 95 ASN Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 158 GLN Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 212 ILE Chi-restraints excluded: chain H residue 223 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 73 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 79 optimal weight: 0.6980 chunk 41 optimal weight: 0.2980 chunk 65 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 chunk 118 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN D 356 GLN E 337 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.164083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.133861 restraints weight = 14086.688| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 1.46 r_work: 0.3470 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12231 Z= 0.175 Angle : 0.547 7.093 16808 Z= 0.305 Chirality : 0.040 0.160 1897 Planarity : 0.004 0.044 1854 Dihedral : 20.404 59.842 2275 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 5.60 % Allowed : 21.23 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.75 (0.23), residues: 1222 helix: 2.18 (0.18), residues: 737 sheet: -0.37 (0.67), residues: 62 loop : -0.43 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 85 HIS 0.005 0.001 HIS D 353 PHE 0.016 0.002 PHE D 70 TYR 0.013 0.001 TYR E 230 ARG 0.007 0.000 ARG C 64 Details of bonding type rmsd hydrogen bonds : bond 0.04745 ( 680) hydrogen bonds : angle 4.01827 ( 1892) covalent geometry : bond 0.00398 (12231) covalent geometry : angle 0.54750 (16808) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 228 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 109 ASN cc_start: 0.8485 (t0) cc_final: 0.8122 (t160) REVERT: B 41 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.7766 (mtt180) REVERT: D 105 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7874 (ttp-170) REVERT: D 130 GLU cc_start: 0.8010 (mp0) cc_final: 0.7638 (mp0) REVERT: D 135 GLU cc_start: 0.7733 (tt0) cc_final: 0.7489 (tt0) REVERT: D 203 GLU cc_start: 0.7857 (tt0) cc_final: 0.7651 (tt0) REVERT: D 344 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.6767 (mp0) REVERT: E 143 GLU cc_start: 0.7333 (mm-30) cc_final: 0.7114 (mm-30) REVERT: E 183 ASP cc_start: 0.7937 (m-30) cc_final: 0.7653 (m-30) REVERT: E 187 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7155 (pp20) REVERT: E 192 LYS cc_start: 0.8490 (tttt) cc_final: 0.8252 (tptp) REVERT: E 198 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7330 (mm-30) REVERT: E 275 LYS cc_start: 0.7985 (mmtt) cc_final: 0.7711 (mmpt) REVERT: E 302 GLU cc_start: 0.6918 (pp20) cc_final: 0.6692 (pp20) REVERT: E 320 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7727 (ttt90) REVERT: E 341 TYR cc_start: 0.7375 (p90) cc_final: 0.6688 (p90) REVERT: G 38 ILE cc_start: 0.8182 (pt) cc_final: 0.7848 (mt) REVERT: G 81 GLU cc_start: 0.7621 (tm-30) cc_final: 0.7288 (tm-30) REVERT: H 91 ASN cc_start: 0.7693 (m-40) cc_final: 0.7383 (m110) REVERT: H 160 ILE cc_start: 0.4871 (OUTLIER) cc_final: 0.4492 (pp) outliers start: 63 outliers final: 44 residues processed: 259 average time/residue: 1.6816 time to fit residues: 464.4658 Evaluate side-chains 277 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 227 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain B residue 41 ARG Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain D residue 4 GLN Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 105 ARG Chi-restraints excluded: chain D residue 137 LYS Chi-restraints excluded: chain D residue 151 GLU Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 285 LYS Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 137 SER Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 203 GLN Chi-restraints excluded: chain E residue 249 MET Chi-restraints excluded: chain E residue 288 LYS Chi-restraints excluded: chain E residue 320 ARG Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 95 ASN Chi-restraints excluded: chain H residue 129 GLU Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 158 GLN Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 212 ILE Chi-restraints excluded: chain H residue 223 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 81 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 112 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 115 optimal weight: 7.9990 chunk 93 optimal weight: 0.0870 chunk 48 optimal weight: 0.3980 chunk 10 optimal weight: 0.2980 chunk 43 optimal weight: 0.5980 chunk 99 optimal weight: 2.9990 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN D 356 GLN E 337 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.164737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.134632 restraints weight = 14071.139| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 1.46 r_work: 0.3483 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12231 Z= 0.147 Angle : 0.540 7.586 16808 Z= 0.300 Chirality : 0.039 0.158 1897 Planarity : 0.004 0.043 1854 Dihedral : 20.398 60.105 2275 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 4.97 % Allowed : 22.20 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.85 (0.24), residues: 1222 helix: 2.26 (0.18), residues: 737 sheet: -0.35 (0.67), residues: 62 loop : -0.37 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 148 HIS 0.005 0.001 HIS D 353 PHE 0.013 0.001 PHE D 70 TYR 0.012 0.001 TYR E 230 ARG 0.009 0.000 ARG A 117 Details of bonding type rmsd hydrogen bonds : bond 0.04535 ( 680) hydrogen bonds : angle 3.97862 ( 1892) covalent geometry : bond 0.00325 (12231) covalent geometry : angle 0.54030 (16808) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 226 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 109 ASN cc_start: 0.8463 (t0) cc_final: 0.8118 (t160) REVERT: B 32 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.8258 (mttt) REVERT: D 105 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7882 (ttp-170) REVERT: D 130 GLU cc_start: 0.7992 (mp0) cc_final: 0.7623 (mp0) REVERT: D 203 GLU cc_start: 0.7836 (tt0) cc_final: 0.7632 (tt0) REVERT: D 344 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.6748 (mp0) REVERT: E 143 GLU cc_start: 0.7325 (mm-30) cc_final: 0.7109 (mm-30) REVERT: E 183 ASP cc_start: 0.7922 (m-30) cc_final: 0.7645 (m-30) REVERT: E 187 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.7129 (pp20) REVERT: E 192 LYS cc_start: 0.8489 (tttt) cc_final: 0.8255 (tptp) REVERT: E 198 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7294 (mm-30) REVERT: E 275 LYS cc_start: 0.7997 (mmtt) cc_final: 0.7717 (mmpt) REVERT: E 302 GLU cc_start: 0.6914 (pp20) cc_final: 0.6684 (pp20) REVERT: E 341 TYR cc_start: 0.7347 (p90) cc_final: 0.6612 (p90) REVERT: G 38 ILE cc_start: 0.8138 (pt) cc_final: 0.7788 (mt) REVERT: G 81 GLU cc_start: 0.7609 (tm-30) cc_final: 0.7276 (tm-30) REVERT: H 91 ASN cc_start: 0.7681 (m-40) cc_final: 0.7375 (m110) REVERT: H 160 ILE cc_start: 0.4890 (OUTLIER) cc_final: 0.4489 (pp) outliers start: 56 outliers final: 44 residues processed: 257 average time/residue: 1.5101 time to fit residues: 415.5447 Evaluate side-chains 272 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 223 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain D residue 4 GLN Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 105 ARG Chi-restraints excluded: chain D residue 137 LYS Chi-restraints excluded: chain D residue 151 GLU Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 285 LYS Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 137 SER Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 203 GLN Chi-restraints excluded: chain E residue 249 MET Chi-restraints excluded: chain E residue 288 LYS Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 95 ASN Chi-restraints excluded: chain H residue 129 GLU Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 158 GLN Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 212 ILE Chi-restraints excluded: chain H residue 223 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 26 optimal weight: 0.8980 chunk 61 optimal weight: 0.0970 chunk 78 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 86 optimal weight: 0.1980 chunk 45 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 94 optimal weight: 0.7980 chunk 127 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN D 356 GLN E 337 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.164892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.134876 restraints weight = 13965.843| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 1.45 r_work: 0.3483 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12231 Z= 0.155 Angle : 0.538 7.349 16808 Z= 0.299 Chirality : 0.039 0.162 1897 Planarity : 0.004 0.043 1854 Dihedral : 20.391 60.947 2275 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 4.71 % Allowed : 22.02 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.86 (0.24), residues: 1222 helix: 2.26 (0.18), residues: 738 sheet: -0.29 (0.67), residues: 62 loop : -0.37 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 148 HIS 0.006 0.001 HIS D 353 PHE 0.014 0.001 PHE D 70 TYR 0.013 0.001 TYR E 230 ARG 0.007 0.000 ARG A 117 Details of bonding type rmsd hydrogen bonds : bond 0.04520 ( 680) hydrogen bonds : angle 3.94137 ( 1892) covalent geometry : bond 0.00348 (12231) covalent geometry : angle 0.53845 (16808) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 226 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 109 ASN cc_start: 0.8468 (t0) cc_final: 0.8124 (t160) REVERT: D 105 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7864 (ttp-170) REVERT: D 203 GLU cc_start: 0.7806 (tt0) cc_final: 0.7583 (tt0) REVERT: D 344 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.6735 (mp0) REVERT: E 143 GLU cc_start: 0.7355 (mm-30) cc_final: 0.7145 (mm-30) REVERT: E 183 ASP cc_start: 0.7921 (m-30) cc_final: 0.7628 (m-30) REVERT: E 187 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.7128 (pp20) REVERT: E 192 LYS cc_start: 0.8489 (tttt) cc_final: 0.8269 (tptp) REVERT: E 198 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7298 (mm-30) REVERT: E 275 LYS cc_start: 0.7986 (mmtt) cc_final: 0.7714 (mmpt) REVERT: E 302 GLU cc_start: 0.6916 (pp20) cc_final: 0.6688 (pp20) REVERT: E 341 TYR cc_start: 0.7339 (p90) cc_final: 0.6631 (p90) REVERT: G 38 ILE cc_start: 0.8123 (pt) cc_final: 0.7799 (mt) REVERT: G 81 GLU cc_start: 0.7613 (tm-30) cc_final: 0.7269 (tm-30) REVERT: H 91 ASN cc_start: 0.7667 (m-40) cc_final: 0.7361 (m110) REVERT: H 160 ILE cc_start: 0.4963 (OUTLIER) cc_final: 0.4551 (pp) outliers start: 53 outliers final: 44 residues processed: 257 average time/residue: 1.4988 time to fit residues: 411.3890 Evaluate side-chains 275 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 227 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain D residue 4 GLN Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 105 ARG Chi-restraints excluded: chain D residue 137 LYS Chi-restraints excluded: chain D residue 151 GLU Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 285 LYS Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 137 SER Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 203 GLN Chi-restraints excluded: chain E residue 249 MET Chi-restraints excluded: chain E residue 288 LYS Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 95 ASN Chi-restraints excluded: chain H residue 129 GLU Chi-restraints excluded: chain H residue 158 GLN Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 199 LYS Chi-restraints excluded: chain H residue 212 ILE Chi-restraints excluded: chain H residue 223 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 90 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 119 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 115 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN D 356 GLN E 337 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.163599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.133568 restraints weight = 13936.235| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 1.44 r_work: 0.3466 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 12231 Z= 0.204 Angle : 0.574 7.320 16808 Z= 0.318 Chirality : 0.041 0.160 1897 Planarity : 0.004 0.048 1854 Dihedral : 20.393 60.717 2275 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 4.80 % Allowed : 22.29 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.66 (0.23), residues: 1222 helix: 2.09 (0.18), residues: 737 sheet: -0.36 (0.67), residues: 62 loop : -0.42 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP D 85 HIS 0.005 0.001 HIS G 54 PHE 0.018 0.002 PHE D 70 TYR 0.016 0.002 TYR C 100 ARG 0.018 0.000 ARG A 117 Details of bonding type rmsd hydrogen bonds : bond 0.05032 ( 680) hydrogen bonds : angle 4.07732 ( 1892) covalent geometry : bond 0.00470 (12231) covalent geometry : angle 0.57352 (16808) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11631.08 seconds wall clock time: 207 minutes 24.56 seconds (12444.56 seconds total)