Starting phenix.real_space_refine on Sat Sep 12 09:23:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5wfe_8827/09_2026/5wfe_8827.cif Found real_map, /net/cci-nas-00/data/ceres_data/5wfe_8827/09_2026/5wfe_8827.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5wfe_8827/09_2026/5wfe_8827.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5wfe_8827/09_2026/5wfe_8827.map" model { file = "/net/cci-nas-00/data/ceres_data/5wfe_8827/09_2026/5wfe_8827.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5wfe_8827/09_2026/5wfe_8827.cif" } resolution = 3.64 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.081 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 208 5.49 5 S 40 5.16 5 C 9220 2.51 5 N 2771 2.21 5 O 3284 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15523 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2018 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 14, 'TRANS': 247} Chain breaks: 1 Chain: "B" Number of atoms: 2157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2157 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 17, 'TRANS': 261} Chain: "C" Number of atoms: 1964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1964 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 12, 'TRANS': 243} Chain breaks: 1 Chain: "D" Number of atoms: 2096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2096 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 15, 'TRANS': 256} Chain: "E" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 739 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "F" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 739 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "G" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 578 Classifications: {'DNA': 28} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 27} Chain: "H" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 907 Classifications: {'DNA': 45} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 44} Chain: "I" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1570 Classifications: {'DNA': 77} Link IDs: {'rna3p': 76} Chain: "J" Number of atoms: 1244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1244 Classifications: {'DNA': 60} Link IDs: {'rna3p': 59} Chain: "K" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 769 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 90} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 742 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 88} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 3.50, per 1000 atoms: 0.23 Number of scatterers: 15523 At special positions: 0 Unit cell: (120.91, 128.4, 196.88, 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 40 16.00 P 208 15.00 O 3284 8.00 N 2771 7.00 C 9220 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: 1.32 Conformation dependent library (CDL) restraints added in 594.3 milliseconds 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2652 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 9 sheets defined 54.1% alpha, 14.9% beta 94 base pairs and 161 stacking pairs defined. Time for finding SS restraints: 2.02 Creating SS restraints... Processing helix chain 'A' and resid 62 through 71 Processing helix chain 'A' and resid 80 through 83 Processing helix chain 'A' and resid 95 through 108 Processing helix chain 'A' and resid 108 through 124 Processing helix chain 'A' and resid 133 through 157 Processing helix chain 'A' and resid 175 through 199 Processing helix chain 'A' and resid 213 through 223 removed outlier: 3.756A pdb=" N ILE A 223 " --> pdb=" O ILE A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 239 Processing helix chain 'A' and resid 242 through 259 removed outlier: 3.790A pdb=" N GLU A 246 " --> pdb=" O GLU A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 274 removed outlier: 4.409A pdb=" N ILE A 265 " --> pdb=" O LEU A 261 " (cutoff:3.500A) Proline residue: A 266 - end of helix Processing helix chain 'B' and resid 45 through 47 No H-bonds generated for 'chain 'B' and resid 45 through 47' Processing helix chain 'B' and resid 62 through 71 Processing helix chain 'B' and resid 80 through 82 No H-bonds generated for 'chain 'B' and resid 80 through 82' Processing helix chain 'B' and resid 95 through 108 removed outlier: 4.121A pdb=" N LEU B 99 " --> pdb=" O ARG B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 124 Processing helix chain 'B' and resid 133 through 157 Processing helix chain 'B' and resid 166 through 170 removed outlier: 3.592A pdb=" N ASP B 169 " --> pdb=" O ASP B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 199 Processing helix chain 'B' and resid 213 through 239 removed outlier: 3.984A pdb=" N ILE B 223 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N PHE B 225 " --> pdb=" O ASP B 221 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ASP B 226 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N THR B 227 " --> pdb=" O ILE B 223 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N VAL B 229 " --> pdb=" O PHE B 225 " (cutoff:3.500A) Proline residue: B 230 - end of helix Processing helix chain 'B' and resid 242 through 259 removed outlier: 3.521A pdb=" N GLU B 246 " --> pdb=" O GLU B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 274 removed outlier: 4.136A pdb=" N ILE B 265 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Proline residue: B 266 - end of helix removed outlier: 3.757A pdb=" N ALA B 274 " --> pdb=" O ASP B 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 71 Processing helix chain 'C' and resid 80 through 83 Processing helix chain 'C' and resid 95 through 108 removed outlier: 3.670A pdb=" N LEU C 99 " --> pdb=" O ARG C 95 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP C 108 " --> pdb=" O LYS C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 124 Processing helix chain 'C' and resid 133 through 156 Processing helix chain 'C' and resid 175 through 199 Processing helix chain 'C' and resid 213 through 223 removed outlier: 3.883A pdb=" N ILE C 223 " --> pdb=" O ILE C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 239 Processing helix chain 'C' and resid 242 through 259 removed outlier: 3.630A pdb=" N GLU C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 274 removed outlier: 4.505A pdb=" N ILE C 265 " --> pdb=" O LEU C 261 " (cutoff:3.500A) Proline residue: C 266 - end of helix Processing helix chain 'D' and resid 10 through 14 removed outlier: 3.595A pdb=" N ARG D 14 " --> pdb=" O LEU D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 47 No H-bonds generated for 'chain 'D' and resid 45 through 47' Processing helix chain 'D' and resid 62 through 71 Processing helix chain 'D' and resid 80 through 82 No H-bonds generated for 'chain 'D' and resid 80 through 82' Processing helix chain 'D' and resid 95 through 108 removed outlier: 3.766A pdb=" N ASP D 108 " --> pdb=" O LYS D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 125 Processing helix chain 'D' and resid 133 through 157 removed outlier: 3.536A pdb=" N LEU D 137 " --> pdb=" O SER D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 170 removed outlier: 3.566A pdb=" N ASP D 169 " --> pdb=" O ASP D 166 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TRP D 170 " --> pdb=" O PRO D 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 166 through 170' Processing helix chain 'D' and resid 175 through 199 Processing helix chain 'D' and resid 213 through 239 removed outlier: 3.764A pdb=" N ILE D 223 " --> pdb=" O ILE D 219 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N PHE D 225 " --> pdb=" O ASP D 221 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ASP D 226 " --> pdb=" O ILE D 222 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N THR D 227 " --> pdb=" O ILE D 223 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N VAL D 229 " --> pdb=" O PHE D 225 " (cutoff:3.500A) Proline residue: D 230 - end of helix Processing helix chain 'D' and resid 242 through 259 removed outlier: 3.971A pdb=" N GLU D 246 " --> pdb=" O GLU D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 274 removed outlier: 3.986A pdb=" N LYS D 263 " --> pdb=" O LYS D 259 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILE D 265 " --> pdb=" O LEU D 261 " (cutoff:3.500A) Proline residue: D 266 - end of helix removed outlier: 4.043A pdb=" N ALA D 274 " --> pdb=" O ASP D 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 23 removed outlier: 3.735A pdb=" N ARG E 16 " --> pdb=" O PRO E 12 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N TRP E 22 " --> pdb=" O ARG E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 51 removed outlier: 3.523A pdb=" N ALA E 51 " --> pdb=" O ILE E 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 23 removed outlier: 3.634A pdb=" N ARG F 16 " --> pdb=" O PRO F 12 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N TRP F 22 " --> pdb=" O ARG F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 51 Processing helix chain 'K' and resid 4 through 17 Processing helix chain 'K' and resid 19 through 40 removed outlier: 3.514A pdb=" N VAL K 27 " --> pdb=" O ALA K 23 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE K 34 " --> pdb=" O PHE K 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 84 through 93 removed outlier: 4.225A pdb=" N ASN K 93 " --> pdb=" O SER K 89 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 14 removed outlier: 3.727A pdb=" N ARG L 9 " --> pdb=" O GLU L 5 " (cutoff:3.500A) Processing helix chain 'L' and resid 18 through 39 Processing helix chain 'L' and resid 83 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 20 removed outlier: 5.809A pdb=" N ILE A 18 " --> pdb=" O MET A 53 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N LEU A 75 " --> pdb=" O GLY A 89 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER A 88 " --> pdb=" O GLY B 89 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY B 89 " --> pdb=" O SER A 88 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU B 74 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N VAL B 15 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ILE B 52 " --> pdb=" O VAL B 15 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N MET B 17 " --> pdb=" O ILE B 52 " (cutoff:3.500A) removed outlier: 9.804A pdb=" N LEU B 54 " --> pdb=" O MET B 17 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N PHE B 19 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 35 removed outlier: 7.215A pdb=" N ILE A 25 " --> pdb=" O SER A 61 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N VAL B 27 " --> pdb=" O SER B 61 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N HIS B 43 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N VAL E 89 " --> pdb=" O HIS B 43 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 17 through 20 removed outlier: 6.093A pdb=" N ILE C 18 " --> pdb=" O MET C 53 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N LEU C 75 " --> pdb=" O GLY C 89 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU D 75 " --> pdb=" O SER D 88 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N SER D 16 " --> pdb=" O CYS D 51 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N MET D 53 " --> pdb=" O SER D 16 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N ILE D 18 " --> pdb=" O MET D 53 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 32 through 35 removed outlier: 7.472A pdb=" N ILE C 25 " --> pdb=" O SER C 61 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N VAL D 27 " --> pdb=" O SER D 61 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS D 43 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VAL F 89 " --> pdb=" O HIS D 43 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 24 through 27 removed outlier: 3.707A pdb=" N VAL E 26 " --> pdb=" O VAL E 30 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N VAL E 30 " --> pdb=" O VAL E 26 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N MET E 3 " --> pdb=" O ALA E 61 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 24 through 27 removed outlier: 6.836A pdb=" N VAL F 30 " --> pdb=" O VAL F 26 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N MET F 3 " --> pdb=" O ALA F 61 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 44 through 46 removed outlier: 3.734A pdb=" N ARG K 76 " --> pdb=" O LYS K 57 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 43 through 45 removed outlier: 4.049A pdb=" N LYS L 75 " --> pdb=" O ARG L 56 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 60 through 62 666 hydrogen bonds defined for protein. 1935 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 221 hydrogen bonds 432 hydrogen bond angles 0 basepair planarities 94 basepair parallelities 161 stacking parallelities Total time for adding SS restraints: 2.99 Time building geometry restraints manager: 1.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3566 1.33 - 1.45: 4073 1.45 - 1.57: 8138 1.57 - 1.69: 414 1.69 - 1.81: 64 Bond restraints: 16255 Sorted by residual: bond pdb=" N LYS F 38 " pdb=" CA LYS F 38 " ideal model delta sigma weight residual 1.457 1.407 0.050 1.29e-02 6.01e+03 1.52e+01 bond pdb=" C3' DT I 68 " pdb=" C2' DT I 68 " ideal model delta sigma weight residual 1.516 1.547 -0.031 8.00e-03 1.56e+04 1.47e+01 bond pdb=" C3' DG J 4 " pdb=" C2' DG J 4 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.24e+01 bond pdb=" C1' DT I 79 " pdb=" N1 DT I 79 " ideal model delta sigma weight residual 1.468 1.516 -0.048 1.40e-02 5.10e+03 1.17e+01 bond pdb=" C3' DG I 9 " pdb=" C2' DG I 9 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.12e+01 ... (remaining 16250 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 21864 1.85 - 3.69: 994 3.69 - 5.54: 55 5.54 - 7.38: 4 7.38 - 9.23: 1 Bond angle restraints: 22918 Sorted by residual: angle pdb=" O4' DG I 3 " pdb=" C4' DG I 3 " pdb=" C3' DG I 3 " ideal model delta sigma weight residual 106.00 103.06 2.94 6.00e-01 2.78e+00 2.40e+01 angle pdb=" O4' DA I 15 " pdb=" C4' DA I 15 " pdb=" C3' DA I 15 " ideal model delta sigma weight residual 106.00 103.14 2.86 6.00e-01 2.78e+00 2.28e+01 angle pdb=" O4' DT J 25 " pdb=" C4' DT J 25 " pdb=" C3' DT J 25 " ideal model delta sigma weight residual 106.00 103.16 2.84 6.00e-01 2.78e+00 2.23e+01 angle pdb=" O4' DG I 11 " pdb=" C4' DG I 11 " pdb=" C3' DG I 11 " ideal model delta sigma weight residual 106.00 103.20 2.80 6.00e-01 2.78e+00 2.18e+01 angle pdb=" N3 DT I 51 " pdb=" C4 DT I 51 " pdb=" O4 DT I 51 " ideal model delta sigma weight residual 119.90 122.66 -2.76 6.00e-01 2.78e+00 2.12e+01 ... (remaining 22913 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.61: 8202 34.61 - 69.23: 1031 69.23 - 103.84: 27 103.84 - 138.45: 2 138.45 - 173.07: 6 Dihedral angle restraints: 9268 sinusoidal: 5138 harmonic: 4130 Sorted by residual: dihedral pdb=" CA ARG B 95 " pdb=" C ARG B 95 " pdb=" N SER B 96 " pdb=" CA SER B 96 " ideal model delta harmonic sigma weight residual -180.00 -151.58 -28.42 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" C4' DC I 17 " pdb=" C3' DC I 17 " pdb=" O3' DC I 17 " pdb=" P DA I 18 " ideal model delta sinusoidal sigma weight residual -140.00 33.07 -173.07 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DT H 28 " pdb=" C3' DT H 28 " pdb=" O3' DT H 28 " pdb=" P DG H 29 " ideal model delta sinusoidal sigma weight residual 220.00 48.62 171.38 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 9265 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1785 0.039 - 0.077: 591 0.077 - 0.116: 191 0.116 - 0.155: 28 0.155 - 0.194: 7 Chirality restraints: 2602 Sorted by residual: chirality pdb=" C3' DC H 39 " pdb=" C4' DC H 39 " pdb=" O3' DC H 39 " pdb=" C2' DC H 39 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 9.36e-01 chirality pdb=" C3' DA J 31 " pdb=" C4' DA J 31 " pdb=" O3' DA J 31 " pdb=" C2' DA J 31 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 7.80e-01 chirality pdb=" C3' DA I 45 " pdb=" C4' DA I 45 " pdb=" O3' DA I 45 " pdb=" C2' DA I 45 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 7.31e-01 ... (remaining 2599 not shown) Planarity restraints: 2209 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 166 " 0.047 5.00e-02 4.00e+02 7.16e-02 8.20e+00 pdb=" N PRO A 167 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO A 167 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 167 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 45 " -0.024 2.00e-02 2.50e+03 1.21e-02 4.02e+00 pdb=" N9 DA I 45 " 0.030 2.00e-02 2.50e+03 pdb=" C8 DA I 45 " 0.000 2.00e-02 2.50e+03 pdb=" N7 DA I 45 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DA I 45 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DA I 45 " -0.006 2.00e-02 2.50e+03 pdb=" N6 DA I 45 " -0.001 2.00e-02 2.50e+03 pdb=" N1 DA I 45 " -0.004 2.00e-02 2.50e+03 pdb=" C2 DA I 45 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DA I 45 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DA I 45 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS F 38 " 0.009 2.00e-02 2.50e+03 1.79e-02 3.20e+00 pdb=" C LYS F 38 " -0.031 2.00e-02 2.50e+03 pdb=" O LYS F 38 " 0.012 2.00e-02 2.50e+03 pdb=" N ILE F 39 " 0.010 2.00e-02 2.50e+03 ... (remaining 2206 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 95 2.49 - 3.09: 10815 3.09 - 3.70: 27152 3.70 - 4.30: 37948 4.30 - 4.90: 56901 Nonbonded interactions: 132911 Sorted by model distance: nonbonded pdb=" N3 DT J 29 " pdb=" CB PRO L 64 " model vdw 1.891 3.520 nonbonded pdb=" O2 DC I 32 " pdb=" N2 DG J 41 " model vdw 2.018 2.496 nonbonded pdb=" N2 DG H 38 " pdb=" O2 DC I 10 " model vdw 2.023 2.496 nonbonded pdb=" C2 DT J 29 " pdb=" CB PRO L 64 " model vdw 2.091 3.660 nonbonded pdb=" N7 DG I 57 " pdb=" N4 DC I 58 " model vdw 2.118 3.200 ... (remaining 132906 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' and (resid 16 through 167 or resid 174 through 275)) selection = (chain 'B' and (resid 16 through 167 or resid 174 through 275)) selection = (chain 'C' and resid 16 through 275) selection = (chain 'D' and (resid 16 through 167 or resid 174 through 275)) } ncs_group { reference = chain 'E' selection = chain 'F' } 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 group one per residue 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: 2.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.950 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6685 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 16255 Z= 0.420 Angle : 0.768 9.228 22918 Z= 0.645 Chirality : 0.043 0.194 2602 Planarity : 0.005 0.072 2209 Dihedral : 23.005 173.065 6616 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.63 % Favored : 95.30 % Rotamer: Outliers : 0.09 % Allowed : 0.77 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.19), residues: 1427 helix: -0.66 (0.16), residues: 707 sheet: -0.64 (0.31), residues: 235 loop : -2.08 (0.24), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 40 TYR 0.020 0.002 TYR D 149 PHE 0.021 0.002 PHE B 19 TRP 0.020 0.002 TRP A 77 HIS 0.002 0.001 HIS A 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.42 (16255) covalent geometry : angle 0.76775 / 0.64 (22918) hydrogen bonds : bond 0.15906 / 10.64 ( 887) hydrogen bonds : angle 7.13707 / 5.23 ( 2367) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 417 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.8814 (mmt) cc_final: 0.8332 (mmt) REVERT: A 109 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7741 (mm-30) REVERT: A 110 ASP cc_start: 0.8680 (m-30) cc_final: 0.8411 (t0) REVERT: A 121 GLU cc_start: 0.8054 (tt0) cc_final: 0.7713 (tm-30) REVERT: A 131 ARG cc_start: 0.8117 (mtt180) cc_final: 0.7552 (mtm110) REVERT: A 164 ARG cc_start: 0.9005 (mtt180) cc_final: 0.8408 (ptp90) REVERT: A 179 CYS cc_start: 0.8479 (m) cc_final: 0.8129 (p) REVERT: A 192 GLU cc_start: 0.6924 (tt0) cc_final: 0.6689 (tt0) REVERT: A 235 ILE cc_start: 0.8314 (mt) cc_final: 0.8029 (mp) REVERT: A 237 ARG cc_start: 0.8445 (ttp80) cc_final: 0.8230 (tpt-90) REVERT: A 246 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8518 (tp30) REVERT: A 263 LYS cc_start: 0.7593 (mtmt) cc_final: 0.7217 (mmtt) REVERT: B 108 ASP cc_start: 0.7472 (t0) cc_final: 0.7223 (t70) REVERT: B 119 MET cc_start: 0.8415 (mtt) cc_final: 0.7428 (tmm) REVERT: B 154 LYS cc_start: 0.9132 (tttp) cc_final: 0.8886 (mmtm) REVERT: C 54 LEU cc_start: 0.8702 (mt) cc_final: 0.8468 (mp) REVERT: C 55 GLU cc_start: 0.8388 (mt-10) cc_final: 0.8053 (mt-10) REVERT: C 74 LEU cc_start: 0.8414 (tp) cc_final: 0.8082 (pp) REVERT: C 165 TYR cc_start: 0.7439 (p90) cc_final: 0.6297 (p90) REVERT: C 178 GLN cc_start: 0.8433 (tt0) cc_final: 0.8203 (tp-100) REVERT: D 16 SER cc_start: 0.8971 (t) cc_final: 0.8294 (p) REVERT: D 53 MET cc_start: 0.8547 (mmt) cc_final: 0.8324 (mmm) REVERT: D 98 LYS cc_start: 0.8460 (mttt) cc_final: 0.7944 (mptt) REVERT: D 237 ARG cc_start: 0.7992 (ttp80) cc_final: 0.7297 (ttm170) REVERT: D 264 LEU cc_start: 0.7297 (mt) cc_final: 0.7079 (mt) REVERT: E 45 GLU cc_start: 0.8792 (mm-30) cc_final: 0.8223 (tm-30) REVERT: F 31 TYR cc_start: 0.7746 (m-80) cc_final: 0.7414 (m-80) REVERT: F 38 LYS cc_start: 0.6572 (OUTLIER) cc_final: 0.6194 (ptpt) REVERT: K 80 THR cc_start: 0.8072 (p) cc_final: 0.7482 (t) REVERT: K 86 LYS cc_start: 0.9046 (tttp) cc_final: 0.8769 (mtmt) REVERT: L 72 LEU cc_start: 0.7507 (mt) cc_final: 0.7299 (mt) outliers start: 1 outliers final: 0 residues processed: 418 average time/residue: 0.1561 time to fit residues: 90.7961 Evaluate side-chains 228 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 227 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 38 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 HIS A 278 GLN B 155 GLN B 177 ASN C 90 GLN D 7 ASN K 59 GLN K 85 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.113567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.082171 restraints weight = 52131.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.083934 restraints weight = 28048.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.084144 restraints weight = 18906.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.084301 restraints weight = 16302.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.084399 restraints weight = 15597.118| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.086 16255 Z= 0.407 Angle : 0.986 16.163 22918 Z= 0.526 Chirality : 0.055 0.392 2602 Planarity : 0.008 0.115 2209 Dihedral : 28.769 177.212 3941 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 22.60 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.99 % Favored : 95.87 % Rotamer: Outliers : 4.43 % Allowed : 11.51 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.20), residues: 1427 helix: -0.09 (0.17), residues: 717 sheet: -0.77 (0.32), residues: 200 loop : -2.01 (0.25), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG B 66 TYR 0.043 0.004 TYR A 86 PHE 0.025 0.003 PHE C 215 TRP 0.023 0.003 TRP B 3 HIS 0.012 0.002 HIS B 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00897 / 0.41 (16255) covalent geometry : angle 0.98570 / 0.53 (22918) hydrogen bonds : bond 0.07697 / 5.11 ( 887) hydrogen bonds : angle 5.64769 / 4.10 ( 2367) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 225 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 TYR cc_start: 0.7638 (m-80) cc_final: 0.7368 (m-80) REVERT: B 119 MET cc_start: 0.8065 (mtt) cc_final: 0.7432 (tmm) REVERT: B 191 THR cc_start: 0.7849 (OUTLIER) cc_final: 0.7606 (p) REVERT: C 74 LEU cc_start: 0.8835 (tp) cc_final: 0.8423 (pp) REVERT: C 112 ARG cc_start: 0.7583 (ttt-90) cc_final: 0.7284 (ttm-80) REVERT: C 177 ASN cc_start: 0.9356 (m-40) cc_final: 0.8793 (t0) REVERT: C 178 GLN cc_start: 0.8372 (tt0) cc_final: 0.8040 (tp-100) REVERT: D 98 LYS cc_start: 0.8302 (mttt) cc_final: 0.8039 (mttp) REVERT: D 264 LEU cc_start: 0.7459 (mt) cc_final: 0.7016 (mt) REVERT: F 50 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8020 (mm) REVERT: K 5 LYS cc_start: 0.8987 (pptt) cc_final: 0.8721 (pptt) REVERT: K 13 PHE cc_start: 0.8329 (t80) cc_final: 0.7923 (t80) REVERT: K 33 GLU cc_start: 0.8614 (tp30) cc_final: 0.8180 (mm-30) REVERT: K 36 ARG cc_start: 0.9121 (mtp180) cc_final: 0.8779 (mtm180) REVERT: L 1 MET cc_start: 0.8414 (ttp) cc_final: 0.7921 (ttt) REVERT: L 24 ASP cc_start: 0.8928 (t0) cc_final: 0.8618 (t0) REVERT: L 28 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8200 (mm-30) REVERT: L 29 MET cc_start: 0.7551 (ttp) cc_final: 0.7211 (tmm) outliers start: 52 outliers final: 32 residues processed: 258 average time/residue: 0.1669 time to fit residues: 59.5745 Evaluate side-chains 221 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 187 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain B residue 3 TRP Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 120 PHE Chi-restraints excluded: chain D residue 258 SER Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain K residue 34 ILE Chi-restraints excluded: chain K residue 93 ASN Chi-restraints excluded: chain L residue 26 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 87 optimal weight: 10.0000 chunk 98 optimal weight: 9.9990 chunk 51 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 94 optimal weight: 40.0000 chunk 1 optimal weight: 2.9990 chunk 147 optimal weight: 10.0000 chunk 95 optimal weight: 9.9990 chunk 88 optimal weight: 0.8980 chunk 129 optimal weight: 30.0000 chunk 152 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 10 ASN ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.117525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.088133 restraints weight = 51811.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.089340 restraints weight = 28207.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.089944 restraints weight = 18494.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.090037 restraints weight = 15884.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.090056 restraints weight = 15180.278| |-----------------------------------------------------------------------------| r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16255 Z= 0.213 Angle : 0.773 10.686 22918 Z= 0.426 Chirality : 0.049 0.393 2602 Planarity : 0.006 0.111 2209 Dihedral : 28.582 178.731 3937 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.07 % Allowed : 14.24 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.21), residues: 1427 helix: 0.50 (0.18), residues: 717 sheet: -0.50 (0.32), residues: 211 loop : -1.91 (0.25), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG L 62 TYR 0.017 0.002 TYR K 11 PHE 0.020 0.002 PHE C 215 TRP 0.012 0.002 TRP E 44 HIS 0.005 0.001 HIS L 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.21 (16255) covalent geometry : angle 0.77294 / 0.43 (22918) hydrogen bonds : bond 0.05634 / 3.78 ( 887) hydrogen bonds : angle 5.17440 / 3.75 ( 2367) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 221 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 3 TRP cc_start: 0.7170 (OUTLIER) cc_final: 0.6543 (m100) REVERT: B 119 MET cc_start: 0.7627 (mtt) cc_final: 0.7383 (tmm) REVERT: B 140 ILE cc_start: 0.8564 (OUTLIER) cc_final: 0.8359 (tt) REVERT: C 74 LEU cc_start: 0.8735 (tp) cc_final: 0.8385 (pp) REVERT: C 177 ASN cc_start: 0.9240 (m-40) cc_final: 0.8779 (t0) REVERT: C 191 THR cc_start: 0.8571 (m) cc_final: 0.8285 (p) REVERT: D 61 SER cc_start: 0.8684 (OUTLIER) cc_final: 0.8287 (p) REVERT: D 98 LYS cc_start: 0.8357 (mttt) cc_final: 0.8113 (mptp) REVERT: D 110 ASP cc_start: 0.6313 (m-30) cc_final: 0.5572 (p0) REVERT: D 264 LEU cc_start: 0.7432 (mt) cc_final: 0.6995 (mt) REVERT: E 22 TRP cc_start: 0.7674 (m-90) cc_final: 0.7184 (m-10) REVERT: E 45 GLU cc_start: 0.7465 (tm-30) cc_final: 0.7264 (tm-30) REVERT: K 5 LYS cc_start: 0.8974 (pptt) cc_final: 0.8704 (pptt) REVERT: K 86 LYS cc_start: 0.8787 (mtmt) cc_final: 0.8464 (mtmt) REVERT: L 1 MET cc_start: 0.8182 (OUTLIER) cc_final: 0.7872 (ttt) REVERT: L 27 LYS cc_start: 0.8805 (mttm) cc_final: 0.8490 (mtmm) REVERT: L 28 GLU cc_start: 0.8426 (mm-30) cc_final: 0.8071 (mm-30) outliers start: 36 outliers final: 18 residues processed: 243 average time/residue: 0.1515 time to fit residues: 52.2827 Evaluate side-chains 215 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 193 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain B residue 3 TRP Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 120 PHE Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain K residue 85 GLN Chi-restraints excluded: chain L residue 1 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 153 optimal weight: 4.9990 chunk 19 optimal weight: 0.2980 chunk 133 optimal weight: 20.0000 chunk 61 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 64 optimal weight: 20.0000 chunk 45 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 145 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 141 optimal weight: 10.0000 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 178 GLN C 178 GLN ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.118586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.088907 restraints weight = 51775.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.090925 restraints weight = 27379.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.091214 restraints weight = 16631.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.091334 restraints weight = 15865.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.091390 restraints weight = 14872.912| |-----------------------------------------------------------------------------| r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 16255 Z= 0.174 Angle : 0.739 12.069 22918 Z= 0.405 Chirality : 0.048 0.388 2602 Planarity : 0.006 0.084 2209 Dihedral : 28.432 178.038 3937 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.90 % Allowed : 15.69 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.21), residues: 1427 helix: 0.87 (0.18), residues: 716 sheet: -0.63 (0.34), residues: 186 loop : -1.64 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 131 TYR 0.022 0.002 TYR L 76 PHE 0.019 0.002 PHE C 215 TRP 0.011 0.002 TRP C 160 HIS 0.004 0.001 HIS L 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.17 (16255) covalent geometry : angle 0.73912 / 0.41 (22918) hydrogen bonds : bond 0.05187 / 3.52 ( 887) hydrogen bonds : angle 4.92084 / 3.57 ( 2367) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 224 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.7324 (mmm) cc_final: 0.7078 (tpp) REVERT: B 3 TRP cc_start: 0.7031 (OUTLIER) cc_final: 0.6283 (m100) REVERT: B 119 MET cc_start: 0.7726 (mtt) cc_final: 0.7397 (tmm) REVERT: B 154 LYS cc_start: 0.8150 (mmtm) cc_final: 0.7890 (mmtm) REVERT: C 74 LEU cc_start: 0.8774 (tp) cc_final: 0.8375 (pp) REVERT: C 177 ASN cc_start: 0.9225 (m-40) cc_final: 0.8878 (t0) REVERT: C 191 THR cc_start: 0.8408 (m) cc_final: 0.8125 (p) REVERT: D 61 SER cc_start: 0.8541 (OUTLIER) cc_final: 0.8169 (p) REVERT: D 98 LYS cc_start: 0.8358 (mttt) cc_final: 0.8128 (mttp) REVERT: D 110 ASP cc_start: 0.6615 (m-30) cc_final: 0.5944 (p0) REVERT: D 120 PHE cc_start: 0.8493 (OUTLIER) cc_final: 0.7267 (m-80) REVERT: D 264 LEU cc_start: 0.7639 (mt) cc_final: 0.7204 (mt) REVERT: D 269 GLU cc_start: 0.8883 (mt-10) cc_final: 0.8561 (mp0) REVERT: E 42 MET cc_start: 0.8865 (tmm) cc_final: 0.8415 (tmm) REVERT: E 45 GLU cc_start: 0.7501 (tm-30) cc_final: 0.7259 (tm-30) REVERT: K 5 LYS cc_start: 0.8962 (pptt) cc_final: 0.8666 (pptt) REVERT: K 86 LYS cc_start: 0.8733 (mtmt) cc_final: 0.8417 (mtmt) REVERT: K 90 ARG cc_start: 0.7935 (mtp180) cc_final: 0.7633 (mtp180) REVERT: L 1 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.7941 (ttt) REVERT: L 28 GLU cc_start: 0.8418 (mm-30) cc_final: 0.8022 (mm-30) REVERT: L 33 MET cc_start: 0.7940 (mpp) cc_final: 0.7690 (mpp) outliers start: 34 outliers final: 21 residues processed: 243 average time/residue: 0.1410 time to fit residues: 49.4134 Evaluate side-chains 223 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 198 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain B residue 3 TRP Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 120 PHE Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 85 GLN Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 26 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 115 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 18 optimal weight: 0.0980 chunk 58 optimal weight: 7.9990 chunk 22 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 127 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 chunk 156 optimal weight: 8.9990 chunk 155 optimal weight: 6.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.118618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.088658 restraints weight = 52169.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.090174 restraints weight = 27219.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.090645 restraints weight = 16963.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.090785 restraints weight = 15754.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.090860 restraints weight = 14846.491| |-----------------------------------------------------------------------------| r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16255 Z= 0.178 Angle : 0.722 11.832 22918 Z= 0.395 Chirality : 0.047 0.386 2602 Planarity : 0.005 0.073 2209 Dihedral : 28.270 178.344 3937 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.64 % Allowed : 17.82 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.21), residues: 1427 helix: 1.00 (0.18), residues: 719 sheet: -0.29 (0.34), residues: 206 loop : -1.49 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 36 TYR 0.027 0.002 TYR A 149 PHE 0.017 0.002 PHE C 215 TRP 0.032 0.002 TRP E 22 HIS 0.006 0.001 HIS L 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.18 (16255) covalent geometry : angle 0.72189 / 0.40 (22918) hydrogen bonds : bond 0.05023 / 3.41 ( 887) hydrogen bonds : angle 4.77030 / 3.44 ( 2367) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 214 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 3 TRP cc_start: 0.6970 (OUTLIER) cc_final: 0.6024 (m100) REVERT: B 119 MET cc_start: 0.7812 (mtt) cc_final: 0.7513 (tmm) REVERT: C 74 LEU cc_start: 0.8886 (tp) cc_final: 0.8401 (pp) REVERT: C 177 ASN cc_start: 0.9258 (m-40) cc_final: 0.8895 (t0) REVERT: C 191 THR cc_start: 0.8521 (m) cc_final: 0.8289 (p) REVERT: D 110 ASP cc_start: 0.7017 (m-30) cc_final: 0.6364 (p0) REVERT: D 120 PHE cc_start: 0.8527 (OUTLIER) cc_final: 0.7452 (m-80) REVERT: D 264 LEU cc_start: 0.7738 (mt) cc_final: 0.7285 (mt) REVERT: D 269 GLU cc_start: 0.8887 (mt-10) cc_final: 0.8600 (mp0) REVERT: E 42 MET cc_start: 0.8902 (tmm) cc_final: 0.8295 (tmm) REVERT: E 45 GLU cc_start: 0.7613 (tm-30) cc_final: 0.7291 (tm-30) REVERT: F 53 GLU cc_start: 0.7547 (tm-30) cc_final: 0.7328 (tm-30) REVERT: K 86 LYS cc_start: 0.8755 (mtmt) cc_final: 0.8467 (mtmt) REVERT: L 27 LYS cc_start: 0.8753 (mttm) cc_final: 0.8536 (mtmm) REVERT: L 28 GLU cc_start: 0.8448 (mm-30) cc_final: 0.8012 (mm-30) REVERT: L 29 MET cc_start: 0.7357 (tmm) cc_final: 0.6948 (tmm) outliers start: 31 outliers final: 21 residues processed: 233 average time/residue: 0.1387 time to fit residues: 46.5936 Evaluate side-chains 216 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 193 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain B residue 3 TRP Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 120 PHE Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain L residue 50 SER Chi-restraints excluded: chain L residue 66 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 7 optimal weight: 0.3980 chunk 120 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 156 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 chunk 45 optimal weight: 0.7980 chunk 26 optimal weight: 0.4980 chunk 154 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.119812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.090077 restraints weight = 52260.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.091668 restraints weight = 28707.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.091982 restraints weight = 17061.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.092220 restraints weight = 16088.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.092308 restraints weight = 15328.654| |-----------------------------------------------------------------------------| r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16255 Z= 0.157 Angle : 0.712 15.643 22918 Z= 0.390 Chirality : 0.046 0.383 2602 Planarity : 0.005 0.064 2209 Dihedral : 28.138 176.864 3937 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.56 % Allowed : 18.93 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.22), residues: 1427 helix: 1.15 (0.18), residues: 719 sheet: -0.29 (0.34), residues: 208 loop : -1.34 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 9 TYR 0.019 0.002 TYR L 76 PHE 0.033 0.002 PHE D 19 TRP 0.043 0.002 TRP E 22 HIS 0.004 0.001 HIS L 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.16 (16255) covalent geometry : angle 0.71218 / 0.39 (22918) hydrogen bonds : bond 0.04701 / 3.21 ( 887) hydrogen bonds : angle 4.63605 / 3.36 ( 2367) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 217 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 3 TRP cc_start: 0.6914 (OUTLIER) cc_final: 0.5871 (m100) REVERT: B 119 MET cc_start: 0.7747 (mtt) cc_final: 0.7411 (tmm) REVERT: B 154 LYS cc_start: 0.8136 (mmtm) cc_final: 0.7870 (mmtm) REVERT: C 70 GLN cc_start: 0.8646 (tm-30) cc_final: 0.8229 (tm-30) REVERT: C 74 LEU cc_start: 0.8896 (tp) cc_final: 0.8414 (pp) REVERT: C 156 TYR cc_start: 0.6737 (m-10) cc_final: 0.6426 (m-80) REVERT: C 177 ASN cc_start: 0.9248 (m-40) cc_final: 0.8885 (t0) REVERT: C 184 THR cc_start: 0.7645 (p) cc_final: 0.7254 (t) REVERT: D 110 ASP cc_start: 0.6970 (m-30) cc_final: 0.6317 (p0) REVERT: D 120 PHE cc_start: 0.8312 (OUTLIER) cc_final: 0.7365 (m-80) REVERT: D 264 LEU cc_start: 0.7535 (mt) cc_final: 0.7092 (mt) REVERT: D 269 GLU cc_start: 0.8904 (mt-10) cc_final: 0.8586 (mp0) REVERT: E 45 GLU cc_start: 0.7565 (tm-30) cc_final: 0.7250 (tm-30) REVERT: F 1 MET cc_start: 0.7735 (mmm) cc_final: 0.7448 (mmm) REVERT: F 53 GLU cc_start: 0.7488 (tm-30) cc_final: 0.7205 (tm-30) REVERT: K 86 LYS cc_start: 0.8783 (mtmt) cc_final: 0.8456 (mtmt) REVERT: K 92 GLU cc_start: 0.6204 (pp20) cc_final: 0.6000 (pp20) REVERT: L 29 MET cc_start: 0.7261 (tmm) cc_final: 0.7040 (tmm) REVERT: L 73 GLU cc_start: 0.8754 (mp0) cc_final: 0.8474 (pm20) outliers start: 30 outliers final: 19 residues processed: 236 average time/residue: 0.1368 time to fit residues: 46.9242 Evaluate side-chains 215 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 194 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain B residue 3 TRP Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 120 PHE Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 85 GLN Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 66 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 78 optimal weight: 0.0670 chunk 52 optimal weight: 0.5980 chunk 148 optimal weight: 8.9990 chunk 113 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 68 optimal weight: 0.4980 chunk 118 optimal weight: 0.9980 overall best weight: 0.8320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.118550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.087359 restraints weight = 50704.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.088415 restraints weight = 29182.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.088799 restraints weight = 18135.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.089357 restraints weight = 16145.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.089415 restraints weight = 14334.490| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.4025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16255 Z= 0.154 Angle : 0.701 12.331 22918 Z= 0.385 Chirality : 0.046 0.383 2602 Planarity : 0.005 0.061 2209 Dihedral : 28.043 177.432 3937 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.73 % Allowed : 20.55 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.22), residues: 1427 helix: 1.31 (0.19), residues: 719 sheet: -0.14 (0.36), residues: 190 loop : -1.30 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG L 9 TYR 0.016 0.002 TYR A 149 PHE 0.024 0.002 PHE D 19 TRP 0.050 0.002 TRP E 22 HIS 0.004 0.001 HIS L 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.15 (16255) covalent geometry : angle 0.70071 / 0.38 (22918) hydrogen bonds : bond 0.04705 / 3.20 ( 887) hydrogen bonds : angle 4.53550 / 3.28 ( 2367) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 211 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 3 TRP cc_start: 0.7055 (OUTLIER) cc_final: 0.5926 (m100) REVERT: B 11 LEU cc_start: 0.7597 (OUTLIER) cc_final: 0.7272 (tt) REVERT: B 119 MET cc_start: 0.8058 (mtt) cc_final: 0.7391 (tmm) REVERT: B 154 LYS cc_start: 0.8204 (mmtm) cc_final: 0.7953 (mmtm) REVERT: C 74 LEU cc_start: 0.8887 (tp) cc_final: 0.8441 (pp) REVERT: C 156 TYR cc_start: 0.6729 (m-10) cc_final: 0.6374 (m-80) REVERT: C 177 ASN cc_start: 0.9381 (m-40) cc_final: 0.8932 (t0) REVERT: C 184 THR cc_start: 0.7699 (p) cc_final: 0.7295 (t) REVERT: D 98 LYS cc_start: 0.8017 (mttp) cc_final: 0.7535 (mptt) REVERT: D 110 ASP cc_start: 0.7093 (m-30) cc_final: 0.6432 (p0) REVERT: D 120 PHE cc_start: 0.8176 (OUTLIER) cc_final: 0.7457 (m-80) REVERT: D 264 LEU cc_start: 0.7508 (mt) cc_final: 0.7077 (mt) REVERT: D 269 GLU cc_start: 0.8927 (mt-10) cc_final: 0.8611 (mp0) REVERT: E 42 MET cc_start: 0.9062 (tmm) cc_final: 0.8838 (tmm) REVERT: E 45 GLU cc_start: 0.7798 (tm-30) cc_final: 0.7455 (tm-30) REVERT: F 1 MET cc_start: 0.7786 (mmm) cc_final: 0.7530 (mmm) REVERT: F 53 GLU cc_start: 0.7566 (tm-30) cc_final: 0.7189 (tm-30) REVERT: K 28 GLU cc_start: 0.8942 (tm-30) cc_final: 0.8733 (tm-30) REVERT: K 32 GLU cc_start: 0.9033 (tm-30) cc_final: 0.8597 (pp20) REVERT: K 86 LYS cc_start: 0.8813 (mtmt) cc_final: 0.8475 (mtmt) REVERT: K 92 GLU cc_start: 0.6389 (pp20) cc_final: 0.6029 (pp20) REVERT: L 1 MET cc_start: 0.7933 (tpp) cc_final: 0.7582 (tpp) REVERT: L 27 LYS cc_start: 0.8532 (mtmm) cc_final: 0.8000 (ptpp) REVERT: L 42 ARG cc_start: 0.6619 (OUTLIER) cc_final: 0.6385 (ptm-80) REVERT: L 73 GLU cc_start: 0.8883 (mp0) cc_final: 0.8647 (pm20) outliers start: 32 outliers final: 16 residues processed: 234 average time/residue: 0.1406 time to fit residues: 47.9888 Evaluate side-chains 220 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 200 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain B residue 3 TRP Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 120 PHE Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 42 ARG Chi-restraints excluded: chain L residue 66 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 70 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 148 optimal weight: 2.9990 chunk 1 optimal weight: 0.4980 chunk 118 optimal weight: 0.1980 chunk 157 optimal weight: 20.0000 chunk 19 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 137 optimal weight: 20.0000 chunk 28 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.118914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.088435 restraints weight = 51355.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.089234 restraints weight = 29103.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.089644 restraints weight = 18166.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.090213 restraints weight = 16301.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.090304 restraints weight = 14492.340| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.4174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16255 Z= 0.150 Angle : 0.708 13.745 22918 Z= 0.387 Chirality : 0.046 0.382 2602 Planarity : 0.005 0.053 2209 Dihedral : 27.920 176.871 3937 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.13 % Allowed : 21.57 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.22), residues: 1427 helix: 1.31 (0.18), residues: 720 sheet: -0.18 (0.35), residues: 196 loop : -1.20 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 9 TYR 0.020 0.001 TYR C 149 PHE 0.023 0.002 PHE D 19 TRP 0.028 0.002 TRP E 22 HIS 0.005 0.001 HIS L 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.15 (16255) covalent geometry : angle 0.70761 / 0.39 (22918) hydrogen bonds : bond 0.04605 / 3.14 ( 887) hydrogen bonds : angle 4.49365 / 3.24 ( 2367) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 205 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 GLU cc_start: 0.7510 (tm-30) cc_final: 0.7259 (tt0) REVERT: B 3 TRP cc_start: 0.6890 (OUTLIER) cc_final: 0.5843 (m100) REVERT: B 11 LEU cc_start: 0.7590 (OUTLIER) cc_final: 0.7270 (tt) REVERT: B 119 MET cc_start: 0.7988 (mtt) cc_final: 0.7377 (tmm) REVERT: B 154 LYS cc_start: 0.8260 (mmtm) cc_final: 0.8000 (mmtm) REVERT: C 74 LEU cc_start: 0.8917 (tp) cc_final: 0.8484 (pp) REVERT: C 156 TYR cc_start: 0.6674 (m-10) cc_final: 0.6317 (m-80) REVERT: C 177 ASN cc_start: 0.9362 (m-40) cc_final: 0.8933 (t0) REVERT: C 184 THR cc_start: 0.7679 (p) cc_final: 0.7262 (t) REVERT: C 211 LYS cc_start: 0.7337 (mptt) cc_final: 0.7087 (mppt) REVERT: D 25 ILE cc_start: 0.7962 (mm) cc_final: 0.7583 (tp) REVERT: D 61 SER cc_start: 0.8612 (t) cc_final: 0.7730 (p) REVERT: D 98 LYS cc_start: 0.8060 (mttp) cc_final: 0.7558 (mptt) REVERT: D 110 ASP cc_start: 0.7073 (m-30) cc_final: 0.6417 (p0) REVERT: D 120 PHE cc_start: 0.8285 (OUTLIER) cc_final: 0.7574 (m-80) REVERT: D 264 LEU cc_start: 0.7574 (mt) cc_final: 0.7132 (mt) REVERT: D 269 GLU cc_start: 0.8895 (mt-10) cc_final: 0.8584 (mp0) REVERT: E 45 GLU cc_start: 0.7785 (tm-30) cc_final: 0.7431 (tm-30) REVERT: E 53 GLU cc_start: 0.7368 (tm-30) cc_final: 0.7096 (tm-30) REVERT: F 1 MET cc_start: 0.7762 (mmm) cc_final: 0.7488 (mmm) REVERT: F 53 GLU cc_start: 0.7494 (tm-30) cc_final: 0.7130 (tm-30) REVERT: K 11 TYR cc_start: 0.6850 (t80) cc_final: 0.6349 (t80) REVERT: K 28 GLU cc_start: 0.8961 (tm-30) cc_final: 0.8735 (tm-30) REVERT: K 32 GLU cc_start: 0.9018 (OUTLIER) cc_final: 0.8621 (pp20) REVERT: K 73 ILE cc_start: 0.7564 (OUTLIER) cc_final: 0.7321 (tt) REVERT: K 86 LYS cc_start: 0.8816 (mtmt) cc_final: 0.8479 (mtmt) REVERT: K 92 GLU cc_start: 0.6395 (pp20) cc_final: 0.6070 (pp20) REVERT: L 1 MET cc_start: 0.8170 (tpp) cc_final: 0.7688 (tpp) REVERT: L 23 GLU cc_start: 0.8415 (tt0) cc_final: 0.7945 (pt0) REVERT: L 28 GLU cc_start: 0.8319 (mm-30) cc_final: 0.7878 (mm-30) REVERT: L 33 MET cc_start: 0.7865 (mpp) cc_final: 0.7438 (mpp) REVERT: L 73 GLU cc_start: 0.8847 (mp0) cc_final: 0.8615 (pm20) REVERT: L 76 TYR cc_start: 0.7719 (m-80) cc_final: 0.6777 (t80) outliers start: 25 outliers final: 16 residues processed: 224 average time/residue: 0.1328 time to fit residues: 43.1674 Evaluate side-chains 215 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 194 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain B residue 3 TRP Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 164 ARG Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 120 PHE Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain K residue 32 GLU Chi-restraints excluded: chain K residue 73 ILE Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain L residue 42 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 77 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 126 optimal weight: 9.9990 chunk 61 optimal weight: 9.9990 chunk 135 optimal weight: 30.0000 chunk 98 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.117161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.086219 restraints weight = 50799.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.087577 restraints weight = 25340.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.088232 restraints weight = 17174.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.088333 restraints weight = 14632.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.088452 restraints weight = 14176.410| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.4286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16255 Z= 0.207 Angle : 0.736 13.780 22918 Z= 0.400 Chirality : 0.046 0.384 2602 Planarity : 0.005 0.051 2209 Dihedral : 27.872 177.703 3937 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.30 % Allowed : 21.06 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.22), residues: 1427 helix: 1.21 (0.19), residues: 719 sheet: -0.24 (0.36), residues: 184 loop : -1.26 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 9 TYR 0.017 0.002 TYR A 149 PHE 0.021 0.002 PHE D 19 TRP 0.039 0.002 TRP E 22 HIS 0.006 0.001 HIS L 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.21 (16255) covalent geometry : angle 0.73575 / 0.40 (22918) hydrogen bonds : bond 0.05118 / 3.44 ( 887) hydrogen bonds : angle 4.58926 / 3.30 ( 2367) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 193 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 3 TRP cc_start: 0.7169 (OUTLIER) cc_final: 0.5953 (m100) REVERT: B 11 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7360 (tt) REVERT: B 119 MET cc_start: 0.8065 (mtt) cc_final: 0.7461 (tmm) REVERT: C 74 LEU cc_start: 0.8939 (tp) cc_final: 0.8548 (pp) REVERT: C 156 TYR cc_start: 0.6683 (m-10) cc_final: 0.6306 (m-80) REVERT: C 177 ASN cc_start: 0.9336 (m-40) cc_final: 0.8935 (t0) REVERT: C 184 THR cc_start: 0.7702 (p) cc_final: 0.7285 (t) REVERT: D 25 ILE cc_start: 0.8030 (OUTLIER) cc_final: 0.7699 (tp) REVERT: D 61 SER cc_start: 0.8738 (t) cc_final: 0.7851 (p) REVERT: D 98 LYS cc_start: 0.8073 (mttp) cc_final: 0.7553 (mptt) REVERT: D 110 ASP cc_start: 0.7004 (m-30) cc_final: 0.6389 (p0) REVERT: D 120 PHE cc_start: 0.8257 (OUTLIER) cc_final: 0.7587 (m-80) REVERT: D 264 LEU cc_start: 0.7646 (mt) cc_final: 0.7194 (mt) REVERT: D 269 GLU cc_start: 0.8820 (mt-10) cc_final: 0.8614 (mp0) REVERT: E 45 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7466 (tm-30) REVERT: E 53 GLU cc_start: 0.7484 (tm-30) cc_final: 0.7238 (tm-30) REVERT: F 1 MET cc_start: 0.7750 (mmm) cc_final: 0.7498 (mmm) REVERT: F 53 GLU cc_start: 0.7586 (tm-30) cc_final: 0.7179 (tm-30) REVERT: K 28 GLU cc_start: 0.8952 (tm-30) cc_final: 0.8709 (tm-30) REVERT: K 32 GLU cc_start: 0.8998 (OUTLIER) cc_final: 0.8559 (pp20) REVERT: K 73 ILE cc_start: 0.7491 (OUTLIER) cc_final: 0.7259 (tt) REVERT: K 86 LYS cc_start: 0.8843 (mtmt) cc_final: 0.8558 (mtmt) REVERT: L 24 ASP cc_start: 0.8905 (t0) cc_final: 0.8647 (m-30) REVERT: L 28 GLU cc_start: 0.8280 (mm-30) cc_final: 0.7941 (mm-30) REVERT: L 33 MET cc_start: 0.7863 (mpp) cc_final: 0.7491 (mpp) REVERT: L 73 GLU cc_start: 0.8826 (mp0) cc_final: 0.8605 (pm20) REVERT: L 76 TYR cc_start: 0.7683 (m-80) cc_final: 0.6776 (t80) outliers start: 27 outliers final: 18 residues processed: 212 average time/residue: 0.1292 time to fit residues: 40.0947 Evaluate side-chains 210 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 186 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain B residue 3 TRP Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 120 PHE Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain K residue 32 GLU Chi-restraints excluded: chain K residue 73 ILE Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 42 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 30 optimal weight: 0.8980 chunk 95 optimal weight: 7.9990 chunk 125 optimal weight: 10.0000 chunk 31 optimal weight: 0.5980 chunk 105 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 132 optimal weight: 30.0000 chunk 15 optimal weight: 3.9990 chunk 11 optimal weight: 9.9990 chunk 8 optimal weight: 0.9990 chunk 116 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.118586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.087520 restraints weight = 51266.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.088987 restraints weight = 30375.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.089387 restraints weight = 19374.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.089752 restraints weight = 18439.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.090040 restraints weight = 15887.033| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.4389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16255 Z= 0.156 Angle : 0.709 14.979 22918 Z= 0.388 Chirality : 0.046 0.382 2602 Planarity : 0.005 0.045 2209 Dihedral : 27.795 175.450 3937 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.88 % Allowed : 21.65 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.22), residues: 1427 helix: 1.29 (0.19), residues: 718 sheet: -0.23 (0.35), residues: 206 loop : -1.28 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 9 TYR 0.039 0.002 TYR D 217 PHE 0.019 0.002 PHE D 19 TRP 0.035 0.002 TRP E 22 HIS 0.004 0.001 HIS D 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.16 (16255) covalent geometry : angle 0.70944 / 0.39 (22918) hydrogen bonds : bond 0.04633 / 3.14 ( 887) hydrogen bonds : angle 4.52067 / 3.25 ( 2367) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 195 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 11 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7513 (tt) REVERT: B 119 MET cc_start: 0.7948 (mtt) cc_final: 0.7359 (tmm) REVERT: C 17 MET cc_start: 0.8787 (mmm) cc_final: 0.8487 (tpt) REVERT: C 74 LEU cc_start: 0.8889 (tp) cc_final: 0.8452 (pp) REVERT: C 156 TYR cc_start: 0.6689 (m-10) cc_final: 0.6291 (m-80) REVERT: C 177 ASN cc_start: 0.9370 (m-40) cc_final: 0.8953 (t0) REVERT: C 184 THR cc_start: 0.7680 (p) cc_final: 0.7259 (t) REVERT: C 211 LYS cc_start: 0.7362 (mptt) cc_final: 0.7106 (mppt) REVERT: D 25 ILE cc_start: 0.7939 (mm) cc_final: 0.7605 (tp) REVERT: D 61 SER cc_start: 0.8624 (t) cc_final: 0.7786 (p) REVERT: D 98 LYS cc_start: 0.8089 (mttp) cc_final: 0.7600 (mptt) REVERT: D 110 ASP cc_start: 0.7020 (m-30) cc_final: 0.6434 (p0) REVERT: D 120 PHE cc_start: 0.8176 (OUTLIER) cc_final: 0.7554 (m-80) REVERT: D 264 LEU cc_start: 0.7681 (mt) cc_final: 0.7242 (mt) REVERT: E 45 GLU cc_start: 0.7813 (tm-30) cc_final: 0.7494 (tm-30) REVERT: E 53 GLU cc_start: 0.7405 (tm-30) cc_final: 0.7154 (tm-30) REVERT: F 1 MET cc_start: 0.7758 (mmm) cc_final: 0.7517 (mmm) REVERT: F 42 MET cc_start: 0.9229 (tmm) cc_final: 0.8901 (tmm) REVERT: F 53 GLU cc_start: 0.7502 (tm-30) cc_final: 0.7159 (tm-30) REVERT: K 18 LEU cc_start: 0.7955 (pt) cc_final: 0.7657 (tp) REVERT: K 28 GLU cc_start: 0.8982 (tm-30) cc_final: 0.8746 (tm-30) REVERT: K 32 GLU cc_start: 0.9016 (OUTLIER) cc_final: 0.8553 (pp20) REVERT: K 73 ILE cc_start: 0.7477 (OUTLIER) cc_final: 0.7160 (tt) REVERT: K 86 LYS cc_start: 0.8822 (mtmt) cc_final: 0.8525 (mtmt) REVERT: L 28 GLU cc_start: 0.8373 (mm-30) cc_final: 0.7921 (mm-30) REVERT: L 33 MET cc_start: 0.7908 (mpp) cc_final: 0.7519 (mpp) REVERT: L 73 GLU cc_start: 0.8847 (mp0) cc_final: 0.8630 (pm20) REVERT: L 76 TYR cc_start: 0.7771 (m-80) cc_final: 0.6851 (t80) outliers start: 22 outliers final: 16 residues processed: 211 average time/residue: 0.1350 time to fit residues: 41.3818 Evaluate side-chains 214 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 194 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain B residue 3 TRP Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 120 PHE Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain K residue 32 GLU Chi-restraints excluded: chain K residue 73 ILE Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain L residue 29 MET Chi-restraints excluded: chain L residue 42 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 84 optimal weight: 0.9990 chunk 124 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 7 optimal weight: 0.1980 chunk 117 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 64 optimal weight: 8.9990 chunk 83 optimal weight: 4.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.117821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.087067 restraints weight = 50882.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.088420 restraints weight = 26145.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.089004 restraints weight = 17899.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.089093 restraints weight = 15083.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.089271 restraints weight = 14247.486| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.4489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16255 Z= 0.180 Angle : 0.740 19.064 22918 Z= 0.400 Chirality : 0.046 0.383 2602 Planarity : 0.005 0.053 2209 Dihedral : 27.761 176.304 3937 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.13 % Allowed : 21.40 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.22), residues: 1427 helix: 1.22 (0.19), residues: 718 sheet: -0.32 (0.35), residues: 212 loop : -1.30 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 9 TYR 0.031 0.002 TYR D 217 PHE 0.019 0.002 PHE K 31 TRP 0.039 0.002 TRP E 22 HIS 0.004 0.001 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.18 (16255) covalent geometry : angle 0.74008 / 0.40 (22918) hydrogen bonds : bond 0.04902 / 3.31 ( 887) hydrogen bonds : angle 4.54828 / 3.27 ( 2367) =============================================================================== Job complete usr+sys time: 3445.68 seconds wall clock time: 59 minutes 58.23 seconds (3598.23 seconds total)