Starting phenix.real_space_refine on Tue Nov 18 15:03:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5wfe_8827/11_2025/5wfe_8827.cif Found real_map, /net/cci-nas-00/data/ceres_data/5wfe_8827/11_2025/5wfe_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_8827/11_2025/5wfe_8827.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5wfe_8827/11_2025/5wfe_8827.map" model { file = "/net/cci-nas-00/data/ceres_data/5wfe_8827/11_2025/5wfe_8827.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5wfe_8827/11_2025/5wfe_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/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: 3.51, 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: 1.24 Conformation dependent library (CDL) restraints added in 554.8 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: 2.21 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: 2.92 Time building geometry restraints manager: 1.68 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=" C ALA F 37 " pdb=" N LYS F 38 " ideal model delta sigma weight residual 1.332 1.297 0.035 1.40e-02 5.10e+03 6.27e+00 bond pdb=" C3' DG I 6 " pdb=" O3' DG I 6 " ideal model delta sigma weight residual 1.422 1.477 -0.055 3.00e-02 1.11e+03 3.31e+00 bond pdb=" C GLN A 90 " pdb=" O GLN A 90 " ideal model delta sigma weight residual 1.233 1.224 0.009 4.80e-03 4.34e+04 3.19e+00 bond pdb=" C3' DC H 37 " pdb=" O3' DC H 37 " ideal model delta sigma weight residual 1.422 1.474 -0.052 3.00e-02 1.11e+03 3.03e+00 ... (remaining 16250 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 22245 1.85 - 3.69: 635 3.69 - 5.54: 35 5.54 - 7.38: 2 7.38 - 9.23: 1 Bond angle restraints: 22918 Sorted by residual: angle pdb=" C ALA F 37 " pdb=" N LYS F 38 " pdb=" CA LYS F 38 " ideal model delta sigma weight residual 121.54 115.20 6.34 1.91e+00 2.74e-01 1.10e+01 angle pdb=" C GLU E 52 " pdb=" CA GLU E 52 " pdb=" CB GLU E 52 " ideal model delta sigma weight residual 114.40 110.60 3.80 1.25e+00 6.40e-01 9.24e+00 angle pdb=" C ALA B 273 " pdb=" N ALA B 274 " pdb=" CA ALA B 274 " ideal model delta sigma weight residual 120.38 124.68 -4.30 1.46e+00 4.69e-01 8.67e+00 angle pdb=" C3' DC H 37 " pdb=" O3' DC H 37 " pdb=" P DG H 38 " ideal model delta sigma weight residual 120.20 124.58 -4.38 1.50e+00 4.44e-01 8.53e+00 angle pdb=" C3' DT J 33 " pdb=" C2' DT J 33 " pdb=" C1' DT J 33 " ideal model delta sigma weight residual 101.60 97.56 4.04 1.50e+00 4.44e-01 7.26e+00 ... (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 - 0.031: 1653 0.031 - 0.062: 664 0.062 - 0.093: 192 0.093 - 0.125: 83 0.125 - 0.156: 10 Chirality restraints: 2602 Sorted by residual: chirality pdb=" P DG H 38 " pdb=" OP1 DG H 38 " pdb=" OP2 DG H 38 " pdb=" O5' DG H 38 " both_signs ideal model delta sigma weight residual True 2.35 -2.50 -0.16 2.00e-01 2.50e+01 6.06e-01 chirality pdb=" CB ILE B 176 " pdb=" CA ILE B 176 " pdb=" CG1 ILE B 176 " pdb=" CG2 ILE B 176 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.68e-01 chirality pdb=" C1' DT J 33 " pdb=" O4' DT J 33 " pdb=" C2' DT J 33 " pdb=" N1 DT J 33 " both_signs ideal model delta sigma weight residual False 2.47 2.32 0.15 2.00e-01 2.50e+01 5.40e-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: 2.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.500 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6676 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16255 Z= 0.183 Angle : 0.661 9.228 22918 Z= 0.395 Chirality : 0.039 0.156 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 covalent geometry : bond 0.00381 (16255) covalent geometry : angle 0.66108 (22918) hydrogen bonds : bond 0.15906 ( 887) hydrogen bonds : angle 7.13707 ( 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 : 0.498 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: 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: 0.8412 (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: 0.7553 (mtm110) REVERT: A 164 ARG cc_start: 0.9005 (mtt180) cc_final: 0.8407 (ptp90) REVERT: A 179 CYS cc_start: 0.8479 (m) cc_final: 0.8130 (p) REVERT: A 192 GLU cc_start: 0.6924 (tt0) cc_final: 0.6690 (tt0) REVERT: A 235 ILE cc_start: 0.8314 (mt) cc_final: 0.8027 (mp) REVERT: A 237 ARG cc_start: 0.8445 (ttp80) cc_final: 0.8231 (tpt-90) REVERT: A 246 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8535 (tp30) REVERT: A 263 LYS cc_start: 0.7593 (mtmt) cc_final: 0.7218 (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: 0.7429 (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: 0.8467 (mp) REVERT: C 55 GLU cc_start: 0.8388 (mt-10) cc_final: 0.8054 (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: 0.8201 (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: 0.7298 (ttm170) REVERT: D 264 LEU cc_start: 0.7297 (mt) cc_final: 0.7078 (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: 0.7405 (m-80) REVERT: F 38 LYS cc_start: 0.6572 (OUTLIER) cc_final: 0.6193 (ptpt) REVERT: K 80 THR cc_start: 0.8072 (p) cc_final: 0.7422 (t) REVERT: K 86 LYS cc_start: 0.9046 (tttp) cc_final: 0.8831 (mtpt) outliers start: 1 outliers final: 0 residues processed: 418 average time/residue: 0.1643 time to fit residues: 93.7374 Evaluate side-chains 226 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 225 time to evaluate : 0.450 ------------------------------------------------------------------------------- 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: 3.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS A 278 GLN B 43 HIS 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.113226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.083413 restraints weight = 51811.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.085011 restraints weight = 28139.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.085219 restraints weight = 18965.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.085414 restraints weight = 15585.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.085522 restraints weight = 14997.941| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.086 16255 Z= 0.444 Angle : 0.940 17.476 22918 Z= 0.503 Chirality : 0.050 0.219 2602 Planarity : 0.008 0.120 2209 Dihedral : 28.581 179.985 3941 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 22.26 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.41 % Favored : 95.52 % Rotamer: Outliers : 3.92 % Allowed : 13.04 % Favored : 83.03 % 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: -1.27 (0.20), residues: 1427 helix: 0.01 (0.18), residues: 715 sheet: -0.56 (0.33), residues: 198 loop : -2.11 (0.24), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 164 TYR 0.028 0.003 TYR A 86 PHE 0.033 0.003 PHE C 215 TRP 0.020 0.003 TRP C 160 HIS 0.012 0.002 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.01021 (16255) covalent geometry : angle 0.94006 (22918) hydrogen bonds : bond 0.07486 ( 887) hydrogen bonds : angle 5.57331 ( 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 272 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 226 time to evaluate : 0.510 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: A 86 TYR cc_start: 0.7850 (m-80) cc_final: 0.7609 (m-80) REVERT: B 119 MET cc_start: 0.8092 (mtt) cc_final: 0.7595 (tmm) REVERT: B 187 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7699 (tp) REVERT: B 191 THR cc_start: 0.7770 (OUTLIER) cc_final: 0.7451 (p) REVERT: C 74 LEU cc_start: 0.8802 (tp) cc_final: 0.8423 (pp) REVERT: C 112 ARG cc_start: 0.7298 (ttt-90) cc_final: 0.7060 (ttm-80) REVERT: C 177 ASN cc_start: 0.9358 (m-40) cc_final: 0.8857 (t0) REVERT: C 178 GLN cc_start: 0.8424 (tt0) cc_final: 0.8063 (tp-100) REVERT: D 98 LYS cc_start: 0.8297 (mttt) cc_final: 0.8047 (mttp) REVERT: D 117 ARG cc_start: 0.8988 (mtp85) cc_final: 0.8750 (mmm-85) REVERT: D 188 TYR cc_start: 0.7690 (m-80) cc_final: 0.7406 (m-80) REVERT: D 237 ARG cc_start: 0.7913 (ttp80) cc_final: 0.7686 (tmm-80) REVERT: D 264 LEU cc_start: 0.7516 (mt) cc_final: 0.7065 (mt) REVERT: E 22 TRP cc_start: 0.7906 (m-90) cc_final: 0.7426 (m-10) REVERT: E 42 MET cc_start: 0.9078 (tmm) cc_final: 0.8327 (tmm) REVERT: F 50 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8021 (mm) REVERT: K 5 LYS cc_start: 0.9029 (pptt) cc_final: 0.8712 (pptt) REVERT: K 13 PHE cc_start: 0.8308 (t80) cc_final: 0.7943 (t80) REVERT: K 33 GLU cc_start: 0.8594 (tp30) cc_final: 0.8227 (mm-30) REVERT: K 36 ARG cc_start: 0.9105 (mtp180) cc_final: 0.8682 (mtm180) REVERT: L 21 THR cc_start: 0.8129 (m) cc_final: 0.7917 (p) REVERT: L 27 LYS cc_start: 0.8798 (mttm) cc_final: 0.8526 (mtmm) REVERT: L 28 GLU cc_start: 0.8575 (mm-30) cc_final: 0.8192 (mm-30) outliers start: 46 outliers final: 27 residues processed: 256 average time/residue: 0.1627 time to fit residues: 57.7654 Evaluate side-chains 216 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 186 time to evaluate : 0.420 ------------------------------------------------------------------------------- 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 28 ILE Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 191 THR 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 61 SER Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 120 PHE Chi-restraints excluded: chain D residue 144 ARG Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain K residue 18 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: 9.9990 chunk 98 optimal weight: 9.9990 chunk 51 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 94 optimal weight: 7.9990 chunk 1 optimal weight: 0.9990 chunk 147 optimal weight: 10.0000 chunk 95 optimal weight: 7.9990 chunk 88 optimal weight: 9.9990 chunk 129 optimal weight: 8.9990 chunk 152 optimal weight: 0.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 10 ASN ** L 63 ASN ** 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 = 0.4309 r_free = 0.4309 target = 0.116181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.086320 restraints weight = 51880.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.087485 restraints weight = 26835.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.088102 restraints weight = 18001.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.088143 restraints weight = 15974.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.088214 restraints weight = 15100.588| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 16255 Z= 0.259 Angle : 0.749 13.088 22918 Z= 0.408 Chirality : 0.043 0.205 2602 Planarity : 0.006 0.105 2209 Dihedral : 28.419 176.128 3937 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 18.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.67 % Allowed : 14.75 % Favored : 81.59 % 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: -0.81 (0.21), residues: 1427 helix: 0.51 (0.18), residues: 715 sheet: -0.49 (0.34), residues: 192 loop : -2.02 (0.24), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 76 TYR 0.022 0.002 TYR D 86 PHE 0.022 0.002 PHE C 215 TRP 0.014 0.002 TRP E 44 HIS 0.005 0.001 HIS L 32 Details of bonding type rmsd covalent geometry : bond 0.00591 (16255) covalent geometry : angle 0.74887 (22918) hydrogen bonds : bond 0.05508 ( 887) hydrogen bonds : angle 5.12076 ( 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 258 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 215 time to evaluate : 0.526 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: A 86 TYR cc_start: 0.7808 (m-80) cc_final: 0.7575 (m-80) REVERT: B 119 MET cc_start: 0.7885 (mtt) cc_final: 0.7543 (tmm) REVERT: B 154 LYS cc_start: 0.8384 (mmtm) cc_final: 0.8184 (mmtm) REVERT: B 268 ILE cc_start: 0.7725 (OUTLIER) cc_final: 0.7465 (mp) REVERT: C 74 LEU cc_start: 0.8732 (tp) cc_final: 0.8307 (pp) REVERT: C 177 ASN cc_start: 0.9296 (m-40) cc_final: 0.8833 (t0) REVERT: C 178 GLN cc_start: 0.8372 (tt0) cc_final: 0.8165 (tp-100) REVERT: C 184 THR cc_start: 0.7603 (p) cc_final: 0.7227 (t) REVERT: D 19 PHE cc_start: 0.7780 (m-80) cc_final: 0.6964 (m-10) REVERT: D 98 LYS cc_start: 0.8344 (mttt) cc_final: 0.8091 (mptp) REVERT: D 117 ARG cc_start: 0.8980 (mtp85) cc_final: 0.8654 (mmm-85) REVERT: D 237 ARG cc_start: 0.7837 (ttp80) cc_final: 0.7074 (ttm170) REVERT: D 264 LEU cc_start: 0.7607 (mt) cc_final: 0.7133 (mt) REVERT: E 22 TRP cc_start: 0.7780 (m-90) cc_final: 0.7344 (m-10) REVERT: E 42 MET cc_start: 0.8752 (tmm) cc_final: 0.8324 (tmm) REVERT: E 45 GLU cc_start: 0.7534 (tm-30) cc_final: 0.7333 (tm-30) REVERT: K 5 LYS cc_start: 0.9028 (pptt) cc_final: 0.8613 (pptt) REVERT: K 86 LYS cc_start: 0.8811 (mtmt) cc_final: 0.8441 (mttp) REVERT: L 1 MET cc_start: 0.8329 (OUTLIER) cc_final: 0.7959 (ttt) REVERT: L 27 LYS cc_start: 0.8716 (mttm) cc_final: 0.8466 (mtmm) REVERT: L 28 GLU cc_start: 0.8418 (mm-30) cc_final: 0.8077 (mm-30) outliers start: 43 outliers final: 26 residues processed: 243 average time/residue: 0.1533 time to fit residues: 52.2147 Evaluate side-chains 222 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 194 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 53 MET 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 219 ILE Chi-restraints excluded: chain B residue 268 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 D residue 144 ARG Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 92 LEU 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 Chi-restraints excluded: chain L residue 50 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 153 optimal weight: 2.9990 chunk 19 optimal weight: 0.0980 chunk 133 optimal weight: 7.9990 chunk 61 optimal weight: 0.9990 chunk 101 optimal weight: 0.0670 chunk 64 optimal weight: 20.0000 chunk 45 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 145 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 141 optimal weight: 6.9990 overall best weight: 0.5120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 71 GLN L 13 GLN ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 63 ASN ** 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 = 0.4365 r_free = 0.4365 target = 0.119513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.089672 restraints weight = 52023.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.091410 restraints weight = 27516.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.091911 restraints weight = 16106.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.092232 restraints weight = 14986.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.092327 restraints weight = 14061.960| |-----------------------------------------------------------------------------| r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16255 Z= 0.160 Angle : 0.674 13.611 22918 Z= 0.371 Chirality : 0.041 0.185 2602 Planarity : 0.005 0.081 2209 Dihedral : 28.151 179.554 3937 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.22 % Allowed : 16.97 % Favored : 80.82 % 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 (0.21), residues: 1427 helix: 1.08 (0.18), residues: 719 sheet: -0.48 (0.35), residues: 177 loop : -1.65 (0.25), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 76 TYR 0.027 0.002 TYR A 149 PHE 0.022 0.002 PHE D 19 TRP 0.020 0.002 TRP C 77 HIS 0.008 0.001 HIS L 32 Details of bonding type rmsd covalent geometry : bond 0.00352 (16255) covalent geometry : angle 0.67361 (22918) hydrogen bonds : bond 0.04540 ( 887) hydrogen bonds : angle 4.66192 ( 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 261 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 235 time to evaluate : 0.457 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: A 164 ARG cc_start: 0.7772 (ptp90) cc_final: 0.7452 (ptp90) REVERT: B 119 MET cc_start: 0.7765 (mtt) cc_final: 0.7392 (tmm) REVERT: B 154 LYS cc_start: 0.8326 (mmtm) cc_final: 0.8070 (mmtm) REVERT: C 74 LEU cc_start: 0.8797 (tp) cc_final: 0.8405 (pp) REVERT: C 177 ASN cc_start: 0.9270 (m-40) cc_final: 0.8912 (t0) REVERT: C 184 THR cc_start: 0.7682 (p) cc_final: 0.7270 (t) REVERT: C 191 THR cc_start: 0.8135 (m) cc_final: 0.7861 (p) REVERT: D 98 LYS cc_start: 0.8341 (mttt) cc_final: 0.8132 (mttp) REVERT: D 117 ARG cc_start: 0.8915 (mtp85) cc_final: 0.8668 (mmm-85) REVERT: D 188 TYR cc_start: 0.7544 (m-80) cc_final: 0.7303 (m-80) REVERT: D 237 ARG cc_start: 0.7812 (ttp80) cc_final: 0.7118 (ttm170) REVERT: D 264 LEU cc_start: 0.7712 (mt) cc_final: 0.7247 (mt) REVERT: E 42 MET cc_start: 0.8923 (tmm) cc_final: 0.8219 (tmm) REVERT: E 45 GLU cc_start: 0.7560 (tm-30) cc_final: 0.7237 (tm-30) REVERT: K 5 LYS cc_start: 0.8892 (pptt) cc_final: 0.8669 (pptt) REVERT: K 86 LYS cc_start: 0.8769 (mtmt) cc_final: 0.8376 (mttp) REVERT: L 1 MET cc_start: 0.8292 (OUTLIER) cc_final: 0.7928 (ttt) REVERT: L 28 GLU cc_start: 0.8448 (mm-30) cc_final: 0.7987 (mm-30) outliers start: 26 outliers final: 12 residues processed: 248 average time/residue: 0.1537 time to fit residues: 53.1413 Evaluate side-chains 210 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 197 time to evaluate : 0.521 ------------------------------------------------------------------------------- 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 213 LEU Chi-restraints excluded: chain B residue 53 MET 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 D residue 28 ILE Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 120 PHE Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 29 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 115 optimal weight: 2.9990 chunk 84 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 18 optimal weight: 0.2980 chunk 58 optimal weight: 9.9990 chunk 22 optimal weight: 0.8980 chunk 30 optimal weight: 0.2980 chunk 127 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 156 optimal weight: 8.9990 chunk 155 optimal weight: 8.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 178 GLN L 16 HIS ** L 63 ASN ** 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 = 0.4364 r_free = 0.4364 target = 0.119589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.089676 restraints weight = 52166.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.091225 restraints weight = 27175.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.091887 restraints weight = 16386.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.092674 restraints weight = 14849.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.092644 restraints weight = 13871.184| |-----------------------------------------------------------------------------| r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.3869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16255 Z= 0.167 Angle : 0.668 13.638 22918 Z= 0.367 Chirality : 0.040 0.160 2602 Planarity : 0.005 0.068 2209 Dihedral : 27.980 177.459 3937 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.39 % Allowed : 18.93 % Favored : 78.69 % 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: 0.11 (0.22), residues: 1427 helix: 1.24 (0.19), residues: 719 sheet: -0.39 (0.36), residues: 177 loop : -1.38 (0.26), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 9 TYR 0.018 0.001 TYR A 149 PHE 0.017 0.002 PHE K 30 TRP 0.033 0.002 TRP E 22 HIS 0.005 0.001 HIS B 43 Details of bonding type rmsd covalent geometry : bond 0.00372 (16255) covalent geometry : angle 0.66811 (22918) hydrogen bonds : bond 0.04547 ( 887) hydrogen bonds : angle 4.54046 ( 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 250 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 222 time to evaluate : 0.482 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: A 164 ARG cc_start: 0.7702 (ptp90) cc_final: 0.7405 (ptp90) REVERT: A 222 ILE cc_start: 0.8856 (mm) cc_final: 0.8646 (mm) REVERT: B 119 MET cc_start: 0.7785 (mtt) cc_final: 0.7378 (tmm) REVERT: C 70 GLN cc_start: 0.8735 (tm-30) cc_final: 0.8352 (tm-30) REVERT: C 74 LEU cc_start: 0.8878 (tp) cc_final: 0.8434 (pp) REVERT: C 177 ASN cc_start: 0.9236 (m-40) cc_final: 0.8897 (t0) REVERT: C 184 THR cc_start: 0.7670 (p) cc_final: 0.7231 (t) REVERT: C 191 THR cc_start: 0.8261 (m) cc_final: 0.8060 (p) REVERT: D 117 ARG cc_start: 0.8952 (mtp85) cc_final: 0.8735 (mmm-85) REVERT: D 120 PHE cc_start: 0.8595 (OUTLIER) cc_final: 0.7498 (m-80) REVERT: D 237 ARG cc_start: 0.7804 (ttp80) cc_final: 0.7014 (ttm170) REVERT: D 264 LEU cc_start: 0.7501 (mt) cc_final: 0.7023 (mt) REVERT: E 45 GLU cc_start: 0.7488 (tm-30) cc_final: 0.7156 (tm-30) REVERT: K 86 LYS cc_start: 0.8796 (mtmt) cc_final: 0.8438 (mtmt) REVERT: L 1 MET cc_start: 0.8251 (OUTLIER) cc_final: 0.7258 (tpp) REVERT: L 9 ARG cc_start: 0.8767 (ttm-80) cc_final: 0.8474 (mtp-110) REVERT: L 28 GLU cc_start: 0.8374 (mm-30) cc_final: 0.8002 (mm-30) REVERT: L 76 TYR cc_start: 0.7426 (m-80) cc_final: 0.6604 (t80) outliers start: 28 outliers final: 16 residues processed: 239 average time/residue: 0.1508 time to fit residues: 51.0746 Evaluate side-chains 221 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 203 time to evaluate : 0.517 ------------------------------------------------------------------------------- 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 175 THR Chi-restraints excluded: chain A residue 213 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 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 80 THR Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 29 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 7 optimal weight: 0.0020 chunk 120 optimal weight: 0.9980 chunk 88 optimal weight: 10.0000 chunk 156 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 26 optimal weight: 0.3980 chunk 154 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 0.1980 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 16 HIS ** L 63 ASN ** 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 = 0.4337 r_free = 0.4337 target = 0.119638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.087577 restraints weight = 53573.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.090976 restraints weight = 29178.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.091222 restraints weight = 13836.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.091877 restraints weight = 12906.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.091858 restraints weight = 11782.579| |-----------------------------------------------------------------------------| r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.4100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16255 Z= 0.161 Angle : 0.664 14.620 22918 Z= 0.362 Chirality : 0.040 0.214 2602 Planarity : 0.004 0.060 2209 Dihedral : 27.831 178.088 3937 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.13 % Allowed : 19.52 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.30 (0.22), residues: 1427 helix: 1.33 (0.19), residues: 719 sheet: -0.21 (0.35), residues: 192 loop : -1.24 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 248 TYR 0.019 0.001 TYR K 11 PHE 0.027 0.002 PHE D 19 TRP 0.020 0.002 TRP E 22 HIS 0.011 0.001 HIS L 16 Details of bonding type rmsd covalent geometry : bond 0.00356 (16255) covalent geometry : angle 0.66435 (22918) hydrogen bonds : bond 0.04339 ( 887) hydrogen bonds : angle 4.43118 ( 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 244 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 219 time to evaluate : 0.518 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: A 164 ARG cc_start: 0.7884 (ptp90) cc_final: 0.7461 (ptp90) REVERT: A 237 ARG cc_start: 0.7793 (ttp80) cc_final: 0.7580 (ttp80) REVERT: B 119 MET cc_start: 0.8014 (mtt) cc_final: 0.7326 (tmm) REVERT: B 154 LYS cc_start: 0.8272 (mmtm) cc_final: 0.8027 (mmtm) REVERT: C 53 MET cc_start: 0.7090 (mmp) cc_final: 0.6615 (mmp) REVERT: C 74 LEU cc_start: 0.8867 (tp) cc_final: 0.8365 (pp) REVERT: C 156 TYR cc_start: 0.6618 (m-10) cc_final: 0.6251 (m-80) REVERT: C 177 ASN cc_start: 0.9341 (m-40) cc_final: 0.8943 (t0) REVERT: C 184 THR cc_start: 0.7625 (p) cc_final: 0.7178 (t) REVERT: D 25 ILE cc_start: 0.7857 (OUTLIER) cc_final: 0.7535 (tp) REVERT: D 61 SER cc_start: 0.8508 (t) cc_final: 0.7725 (p) REVERT: D 117 ARG cc_start: 0.9018 (mtp85) cc_final: 0.8760 (mmm-85) REVERT: D 237 ARG cc_start: 0.7819 (ttp80) cc_final: 0.7018 (ttm170) REVERT: D 264 LEU cc_start: 0.7409 (mt) cc_final: 0.6956 (mt) REVERT: E 45 GLU cc_start: 0.7629 (tm-30) cc_final: 0.7268 (tm-30) REVERT: F 53 GLU cc_start: 0.7725 (tm-30) cc_final: 0.7469 (tm-30) REVERT: K 18 LEU cc_start: 0.8228 (mp) cc_final: 0.7907 (pt) REVERT: K 73 ILE cc_start: 0.7683 (OUTLIER) cc_final: 0.7358 (tt) REVERT: K 86 LYS cc_start: 0.8842 (mtmt) cc_final: 0.8494 (mtmt) REVERT: L 1 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.7851 (ttt) REVERT: L 9 ARG cc_start: 0.9006 (ttm-80) cc_final: 0.8686 (ttm-80) REVERT: L 27 LYS cc_start: 0.8531 (mtmm) cc_final: 0.8159 (ptpp) REVERT: L 76 TYR cc_start: 0.7853 (m-80) cc_final: 0.6939 (t80) outliers start: 25 outliers final: 15 residues processed: 236 average time/residue: 0.1489 time to fit residues: 49.4847 Evaluate side-chains 213 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 195 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 213 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 D residue 25 ILE Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain K residue 34 ILE Chi-restraints excluded: chain K residue 73 ILE Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 29 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 78 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 chunk 148 optimal weight: 6.9990 chunk 113 optimal weight: 0.3980 chunk 71 optimal weight: 0.5980 chunk 151 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 chunk 27 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 118 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 63 ASN ** 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 = 0.4351 r_free = 0.4351 target = 0.120704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.092146 restraints weight = 52595.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.092764 restraints weight = 28463.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.093897 restraints weight = 17098.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.095226 restraints weight = 13656.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.095256 restraints weight = 11889.326| |-----------------------------------------------------------------------------| r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.4309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16255 Z= 0.156 Angle : 0.660 13.281 22918 Z= 0.358 Chirality : 0.039 0.184 2602 Planarity : 0.004 0.080 2209 Dihedral : 27.701 178.064 3937 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.22 % Allowed : 20.20 % Favored : 77.58 % 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: 0.44 (0.22), residues: 1427 helix: 1.44 (0.19), residues: 719 sheet: -0.15 (0.34), residues: 209 loop : -1.18 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 9 TYR 0.018 0.001 TYR C 149 PHE 0.023 0.002 PHE D 19 TRP 0.019 0.001 TRP C 77 HIS 0.003 0.001 HIS B 43 Details of bonding type rmsd covalent geometry : bond 0.00344 (16255) covalent geometry : angle 0.65996 (22918) hydrogen bonds : bond 0.04305 ( 887) hydrogen bonds : angle 4.35422 ( 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 233 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 207 time to evaluate : 0.366 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 164 ARG cc_start: 0.7792 (ptp90) cc_final: 0.7441 (ptp90) REVERT: A 237 ARG cc_start: 0.7735 (ttp80) cc_final: 0.7519 (ttp80) REVERT: B 119 MET cc_start: 0.8013 (mtt) cc_final: 0.7331 (tmm) REVERT: B 154 LYS cc_start: 0.8305 (mmtm) cc_final: 0.8024 (mmtm) REVERT: C 74 LEU cc_start: 0.8900 (tp) cc_final: 0.8456 (pp) REVERT: C 156 TYR cc_start: 0.6501 (m-10) cc_final: 0.6140 (m-80) REVERT: C 177 ASN cc_start: 0.9357 (m-40) cc_final: 0.8957 (t0) REVERT: D 25 ILE cc_start: 0.7761 (OUTLIER) cc_final: 0.7362 (tp) REVERT: D 61 SER cc_start: 0.8511 (t) cc_final: 0.7649 (p) REVERT: D 117 ARG cc_start: 0.9099 (mtp85) cc_final: 0.8718 (mmm-85) REVERT: D 237 ARG cc_start: 0.7810 (ttp80) cc_final: 0.7034 (ttm170) REVERT: D 264 LEU cc_start: 0.7364 (mt) cc_final: 0.6915 (mt) REVERT: E 45 GLU cc_start: 0.7613 (tm-30) cc_final: 0.7245 (tm-30) REVERT: F 53 GLU cc_start: 0.7715 (tm-30) cc_final: 0.7417 (tm-30) REVERT: K 11 TYR cc_start: 0.6800 (t80) cc_final: 0.6175 (t80) REVERT: K 73 ILE cc_start: 0.7617 (OUTLIER) cc_final: 0.7276 (tt) REVERT: K 86 LYS cc_start: 0.8794 (mtmt) cc_final: 0.8544 (mttp) REVERT: K 90 ARG cc_start: 0.7975 (mtp180) cc_final: 0.7662 (ptm160) REVERT: K 92 GLU cc_start: 0.6363 (pp20) cc_final: 0.6082 (pp20) REVERT: L 1 MET cc_start: 0.8412 (OUTLIER) cc_final: 0.8079 (ttt) REVERT: L 28 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7844 (mm-30) REVERT: L 73 GLU cc_start: 0.8764 (mp0) cc_final: 0.8436 (pm20) outliers start: 26 outliers final: 17 residues processed: 226 average time/residue: 0.1456 time to fit residues: 46.0817 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 : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 213 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 27 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 73 ILE Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 29 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 70 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 chunk 148 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 157 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 137 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 13 GLN ** L 63 ASN ** 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 = 0.4405 r_free = 0.4405 target = 0.121646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.093127 restraints weight = 54170.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.095255 restraints weight = 27907.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.095561 restraints weight = 17523.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.096061 restraints weight = 15142.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.096066 restraints weight = 14005.575| |-----------------------------------------------------------------------------| r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.4404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16255 Z= 0.169 Angle : 0.667 14.093 22918 Z= 0.362 Chirality : 0.040 0.194 2602 Planarity : 0.004 0.059 2209 Dihedral : 27.627 178.367 3937 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.96 % Allowed : 20.72 % Favored : 77.32 % 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: 0.44 (0.22), residues: 1427 helix: 1.47 (0.19), residues: 719 sheet: -0.31 (0.35), residues: 189 loop : -1.14 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG L 9 TYR 0.015 0.001 TYR K 11 PHE 0.023 0.002 PHE D 19 TRP 0.016 0.002 TRP C 77 HIS 0.004 0.001 HIS L 32 Details of bonding type rmsd covalent geometry : bond 0.00382 (16255) covalent geometry : angle 0.66665 (22918) hydrogen bonds : bond 0.04385 ( 887) hydrogen bonds : angle 4.32025 ( 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 225 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 202 time to evaluate : 0.486 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: A 164 ARG cc_start: 0.7579 (ptp90) cc_final: 0.7306 (ptp90) REVERT: B 119 MET cc_start: 0.7714 (mtt) cc_final: 0.7362 (tmm) REVERT: B 154 LYS cc_start: 0.8189 (mmtm) cc_final: 0.7924 (mmtm) REVERT: C 74 LEU cc_start: 0.8917 (tp) cc_final: 0.8684 (pp) REVERT: C 156 TYR cc_start: 0.6521 (m-10) cc_final: 0.6163 (m-80) REVERT: C 177 ASN cc_start: 0.9212 (m-40) cc_final: 0.8905 (t0) REVERT: D 25 ILE cc_start: 0.7646 (OUTLIER) cc_final: 0.7369 (tp) REVERT: D 61 SER cc_start: 0.8500 (t) cc_final: 0.7832 (p) REVERT: D 117 ARG cc_start: 0.8895 (mtp85) cc_final: 0.8613 (mmm-85) REVERT: D 237 ARG cc_start: 0.7842 (ttp80) cc_final: 0.7051 (ttm170) REVERT: D 264 LEU cc_start: 0.7490 (mt) cc_final: 0.7021 (mt) REVERT: E 45 GLU cc_start: 0.7505 (tm-30) cc_final: 0.7236 (tm-30) REVERT: E 53 GLU cc_start: 0.7748 (pm20) cc_final: 0.7513 (pm20) REVERT: F 53 GLU cc_start: 0.7423 (tm-30) cc_final: 0.7219 (tm-30) REVERT: K 73 ILE cc_start: 0.7186 (OUTLIER) cc_final: 0.6884 (tt) REVERT: K 90 ARG cc_start: 0.7847 (mtp180) cc_final: 0.7607 (ptm160) REVERT: K 92 GLU cc_start: 0.6208 (pp20) cc_final: 0.5895 (pp20) REVERT: L 1 MET cc_start: 0.7996 (OUTLIER) cc_final: 0.7718 (ttt) REVERT: L 27 LYS cc_start: 0.8417 (mtmm) cc_final: 0.8069 (mtmm) REVERT: L 28 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7703 (mm-30) REVERT: L 73 GLU cc_start: 0.8618 (mp0) cc_final: 0.8294 (pm20) outliers start: 23 outliers final: 17 residues processed: 217 average time/residue: 0.1545 time to fit residues: 47.2288 Evaluate side-chains 211 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 191 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 213 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 27 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain K residue 73 ILE Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 29 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 77 optimal weight: 2.9990 chunk 24 optimal weight: 0.0670 chunk 126 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 135 optimal weight: 8.9990 chunk 98 optimal weight: 0.5980 chunk 43 optimal weight: 7.9990 chunk 84 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.6922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 63 ASN ** 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 = 0.4382 r_free = 0.4382 target = 0.120323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.089728 restraints weight = 51879.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.091297 restraints weight = 29166.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.091828 restraints weight = 17208.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.092203 restraints weight = 14607.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.092212 restraints weight = 13287.037| |-----------------------------------------------------------------------------| r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.4576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16255 Z= 0.155 Angle : 0.671 14.962 22918 Z= 0.362 Chirality : 0.040 0.207 2602 Planarity : 0.004 0.056 2209 Dihedral : 27.540 179.173 3937 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.88 % Allowed : 21.23 % Favored : 76.90 % 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: 0.51 (0.22), residues: 1427 helix: 1.54 (0.19), residues: 718 sheet: -0.33 (0.35), residues: 189 loop : -1.09 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG L 9 TYR 0.015 0.001 TYR C 101 PHE 0.023 0.002 PHE D 19 TRP 0.021 0.002 TRP C 77 HIS 0.003 0.001 HIS B 43 Details of bonding type rmsd covalent geometry : bond 0.00345 (16255) covalent geometry : angle 0.67082 (22918) hydrogen bonds : bond 0.04306 ( 887) hydrogen bonds : angle 4.26923 ( 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 229 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 207 time to evaluate : 0.537 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: A 164 ARG cc_start: 0.7591 (ptp90) cc_final: 0.7288 (ptp90) REVERT: B 119 MET cc_start: 0.7726 (mtt) cc_final: 0.7349 (tmm) REVERT: B 154 LYS cc_start: 0.8223 (mmtm) cc_final: 0.7932 (mmtm) REVERT: C 74 LEU cc_start: 0.8902 (tp) cc_final: 0.8675 (pp) REVERT: C 156 TYR cc_start: 0.6503 (m-10) cc_final: 0.6144 (m-80) REVERT: C 177 ASN cc_start: 0.9281 (m-40) cc_final: 0.8937 (t0) REVERT: C 211 LYS cc_start: 0.7556 (mptt) cc_final: 0.7272 (mppt) REVERT: D 25 ILE cc_start: 0.7765 (OUTLIER) cc_final: 0.7495 (tp) REVERT: D 61 SER cc_start: 0.8377 (t) cc_final: 0.7614 (p) REVERT: D 117 ARG cc_start: 0.8927 (mtp85) cc_final: 0.8696 (mmm-85) REVERT: D 237 ARG cc_start: 0.7772 (ttp80) cc_final: 0.7005 (ttm170) REVERT: D 264 LEU cc_start: 0.7446 (mt) cc_final: 0.6984 (mt) REVERT: E 45 GLU cc_start: 0.7662 (tm-30) cc_final: 0.7360 (tm-30) REVERT: F 42 MET cc_start: 0.9244 (tmm) cc_final: 0.8940 (tmm) REVERT: K 42 GLU cc_start: 0.8428 (tp30) cc_final: 0.8227 (tm-30) REVERT: K 73 ILE cc_start: 0.7432 (OUTLIER) cc_final: 0.7035 (tt) REVERT: K 90 ARG cc_start: 0.7711 (mtp180) cc_final: 0.7405 (ptm160) REVERT: L 1 MET cc_start: 0.8214 (OUTLIER) cc_final: 0.7227 (ttt) REVERT: L 27 LYS cc_start: 0.8451 (mtmm) cc_final: 0.8239 (tppt) REVERT: L 46 ARG cc_start: 0.8714 (mmt180) cc_final: 0.8372 (mmt-90) REVERT: L 73 GLU cc_start: 0.8708 (mp0) cc_final: 0.8379 (pm20) outliers start: 22 outliers final: 14 residues processed: 222 average time/residue: 0.1547 time to fit residues: 48.3680 Evaluate side-chains 208 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 191 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 213 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 27 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain K residue 73 ILE Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 29 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 30 optimal weight: 0.9990 chunk 95 optimal weight: 6.9990 chunk 125 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 132 optimal weight: 8.9990 chunk 15 optimal weight: 0.0070 chunk 11 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 116 optimal weight: 0.6980 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 GLN ** L 63 ASN ** 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 = 0.4387 r_free = 0.4387 target = 0.120682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.091081 restraints weight = 52172.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.091776 restraints weight = 29617.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.092490 restraints weight = 20672.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.092883 restraints weight = 16346.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.093082 restraints weight = 14217.621| |-----------------------------------------------------------------------------| r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.4752 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= 0.161 Angle : 0.703 16.369 22918 Z= 0.377 Chirality : 0.040 0.218 2602 Planarity : 0.005 0.076 2209 Dihedral : 27.468 179.237 3937 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.96 % Allowed : 21.74 % 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: 0.57 (0.22), residues: 1427 helix: 1.54 (0.19), residues: 716 sheet: -0.15 (0.34), residues: 209 loop : -1.07 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG L 62 TYR 0.018 0.001 TYR K 11 PHE 0.017 0.002 PHE D 19 TRP 0.017 0.001 TRP C 77 HIS 0.003 0.001 HIS B 43 Details of bonding type rmsd covalent geometry : bond 0.00363 (16255) covalent geometry : angle 0.70252 (22918) hydrogen bonds : bond 0.04352 ( 887) hydrogen bonds : angle 4.25860 ( 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 225 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 202 time to evaluate : 0.499 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: A 164 ARG cc_start: 0.7650 (ptp90) cc_final: 0.7366 (ptp90) REVERT: A 237 ARG cc_start: 0.7765 (ttm-80) cc_final: 0.7560 (ttm110) REVERT: B 119 MET cc_start: 0.7795 (mtt) cc_final: 0.7362 (tmm) REVERT: B 154 LYS cc_start: 0.8147 (mmtm) cc_final: 0.7850 (mmtm) REVERT: C 74 LEU cc_start: 0.8828 (tp) cc_final: 0.8539 (pp) REVERT: C 156 TYR cc_start: 0.6388 (m-10) cc_final: 0.6031 (m-80) REVERT: C 177 ASN cc_start: 0.9281 (m-40) cc_final: 0.8947 (t0) REVERT: C 211 LYS cc_start: 0.7602 (mptt) cc_final: 0.7303 (mppt) REVERT: D 61 SER cc_start: 0.8366 (t) cc_final: 0.7575 (p) REVERT: D 117 ARG cc_start: 0.8924 (mtp85) cc_final: 0.8703 (mmm-85) REVERT: D 237 ARG cc_start: 0.7771 (ttp80) cc_final: 0.7002 (ttm170) REVERT: D 264 LEU cc_start: 0.7417 (mt) cc_final: 0.6969 (mt) REVERT: E 45 GLU cc_start: 0.7672 (tm-30) cc_final: 0.7294 (tm-30) REVERT: E 53 GLU cc_start: 0.7905 (pm20) cc_final: 0.7671 (pp20) REVERT: F 1 MET cc_start: 0.7761 (mmm) cc_final: 0.7456 (mmm) REVERT: F 42 MET cc_start: 0.9238 (tmm) cc_final: 0.8937 (tmm) REVERT: L 1 MET cc_start: 0.8265 (OUTLIER) cc_final: 0.7902 (ttt) REVERT: L 23 GLU cc_start: 0.8536 (tp30) cc_final: 0.8279 (tm-30) REVERT: L 46 ARG cc_start: 0.8699 (mmt180) cc_final: 0.8364 (mmt-90) REVERT: L 73 GLU cc_start: 0.8720 (mp0) cc_final: 0.8405 (pm20) outliers start: 23 outliers final: 16 residues processed: 217 average time/residue: 0.1450 time to fit residues: 44.4358 Evaluate side-chains 216 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 199 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 213 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 27 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 29 MET Chi-restraints excluded: chain L residue 39 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 84 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 7 optimal weight: 0.0870 chunk 117 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 91 optimal weight: 7.9990 chunk 46 optimal weight: 0.3980 chunk 36 optimal weight: 0.9990 chunk 64 optimal weight: 20.0000 chunk 83 optimal weight: 0.8980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 GLN ** L 63 ASN ** 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 = 0.4389 r_free = 0.4389 target = 0.120802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.090891 restraints weight = 51849.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.091621 restraints weight = 29096.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.092389 restraints weight = 19058.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.093076 restraints weight = 15632.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.093169 restraints weight = 13795.004| |-----------------------------------------------------------------------------| r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.4849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 16255 Z= 0.160 Angle : 0.695 15.752 22918 Z= 0.375 Chirality : 0.040 0.236 2602 Planarity : 0.004 0.046 2209 Dihedral : 27.394 179.825 3937 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.71 % Allowed : 22.17 % Favored : 76.13 % 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: 0.62 (0.22), residues: 1427 helix: 1.57 (0.19), residues: 718 sheet: -0.17 (0.35), residues: 211 loop : -1.01 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 41 TYR 0.020 0.001 TYR K 11 PHE 0.019 0.001 PHE D 19 TRP 0.021 0.002 TRP C 77 HIS 0.003 0.001 HIS B 43 Details of bonding type rmsd covalent geometry : bond 0.00360 (16255) covalent geometry : angle 0.69533 (22918) hydrogen bonds : bond 0.04273 ( 887) hydrogen bonds : angle 4.21268 ( 2367) =============================================================================== Job complete usr+sys time: 3474.06 seconds wall clock time: 60 minutes 22.23 seconds (3622.23 seconds total)