Starting phenix.real_space_refine on Sat Oct 11 21:36:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tnj_41418/10_2025/8tnj_41418.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tnj_41418/10_2025/8tnj_41418.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8tnj_41418/10_2025/8tnj_41418.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tnj_41418/10_2025/8tnj_41418.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tnj_41418/10_2025/8tnj_41418.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tnj_41418/10_2025/8tnj_41418.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2970 atoms to isotropic. 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 S 30 5.16 5 C 5092 2.51 5 N 1368 2.21 5 O 1583 1.98 5 H 7642 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15715 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 5899 Classifications: {'peptide': 382} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 361} Chain breaks: 3 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 62 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 6, 'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 52 Chain: "C" Number of atoms: 3173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 3173 Classifications: {'peptide': 212} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 200} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 3163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 3163 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 200} Chain breaks: 1 Chain: "E" Number of atoms: 1868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1868 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "F" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 1612 Classifications: {'peptide': 107} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Time building chain proxies: 2.92, per 1000 atoms: 0.19 Number of scatterers: 15715 At special positions: 0 Unit cell: (115.02, 127.8, 86.265, 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 30 16.00 O 1583 8.00 N 1368 7.00 C 5092 6.00 H 7642 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 104 " distance=2.03 Simple disulfide: pdb=" SG CYS A 245 " - pdb=" SG CYS A 308 " distance=2.03 Simple disulfide: pdb=" SG CYS A 347 " - pdb=" SG CYS A 403 " distance=2.04 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 89 " distance=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 25 " - pdb=" SG CYS D 99 " distance=2.03 Simple disulfide: pdb=" SG CYS D 151 " - pdb=" SG CYS D 207 " distance=2.03 Simple disulfide: pdb=" SG CYS E 25 " - pdb=" SG CYS E 99 " distance=2.03 Simple disulfide: pdb=" SG CYS F 24 " - pdb=" SG CYS F 89 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.98 Conformation dependent library (CDL) restraints added in 427.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1934 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 24 sheets defined 12.3% alpha, 42.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 200 through 229 removed outlier: 3.559A pdb=" N TRP A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN A 216 " --> pdb=" O LYS A 212 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY A 227 " --> pdb=" O ARG A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 294 removed outlier: 3.517A pdb=" N ILE A 286 " --> pdb=" O THR A 282 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS A 290 " --> pdb=" O ILE A 286 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA A 294 " --> pdb=" O LYS A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 306 removed outlier: 4.122A pdb=" N GLN A 299 " --> pdb=" O ARG A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 319 Processing helix chain 'A' and resid 397 through 399 No H-bonds generated for 'chain 'A' and resid 397 through 399' Processing helix chain 'C' and resid 80 through 84 Processing helix chain 'C' and resid 123 through 130 Processing helix chain 'C' and resid 185 through 191 removed outlier: 3.547A pdb=" N LYS C 190 " --> pdb=" O ALA C 186 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N HIS C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 35 removed outlier: 3.655A pdb=" N TYR D 35 " --> pdb=" O VAL D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 94 removed outlier: 3.542A pdb=" N ASP D 93 " --> pdb=" O ARG D 90 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR D 94 " --> pdb=" O ALA D 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 90 through 94' Processing helix chain 'D' and resid 165 through 169 Processing helix chain 'D' and resid 196 through 200 Processing helix chain 'E' and resid 31 through 35 Processing helix chain 'E' and resid 90 through 94 removed outlier: 3.680A pdb=" N THR E 94 " --> pdb=" O ALA E 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 84 removed outlier: 3.879A pdb=" N PHE F 84 " --> pdb=" O PRO F 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 35 removed outlier: 4.691A pdb=" N PHE A 46 " --> pdb=" O PHE A 94 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N PHE A 94 " --> pdb=" O PHE A 46 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ASN A 48 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N THR A 92 " --> pdb=" O ASN A 48 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N TYR A 50 " --> pdb=" O TYR A 90 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N TYR A 90 " --> pdb=" O TYR A 50 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N SER A 52 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N LEU A 88 " --> pdb=" O SER A 52 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE A 54 " --> pdb=" O PHE A 86 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 35 removed outlier: 4.691A pdb=" N PHE A 46 " --> pdb=" O PHE A 94 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N PHE A 94 " --> pdb=" O PHE A 46 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ASN A 48 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N THR A 92 " --> pdb=" O ASN A 48 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N TYR A 50 " --> pdb=" O TYR A 90 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N TYR A 90 " --> pdb=" O TYR A 50 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N SER A 52 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N LEU A 88 " --> pdb=" O SER A 52 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE A 54 " --> pdb=" O PHE A 86 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR A 87 " --> pdb=" O SER A 79 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER A 79 " --> pdb=" O TYR A 87 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 68 through 69 removed outlier: 3.877A pdb=" N ALA A 103 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 190 through 191 removed outlier: 6.796A pdb=" N GLY A 170 " --> pdb=" O PHE A 177 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ARG A 179 " --> pdb=" O THR A 168 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N THR A 168 " --> pdb=" O ARG A 179 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ASP A 181 " --> pdb=" O PHE A 166 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N PHE A 166 " --> pdb=" O ASP A 181 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N MET A 149 " --> pdb=" O CYS A 245 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ARG A 255 " --> pdb=" O ASP A 246 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ASN A 258 " --> pdb=" O ALA A 269 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ALA A 269 " --> pdb=" O ASN A 258 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N PHE A 260 " --> pdb=" O TYR A 267 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 330 through 337 removed outlier: 3.603A pdb=" N HIS A 336 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR A 344 " --> pdb=" O HIS A 336 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N PHE A 385 " --> pdb=" O GLY A 351 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 330 through 337 removed outlier: 3.603A pdb=" N HIS A 336 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR A 344 " --> pdb=" O HIS A 336 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N PHE A 385 " --> pdb=" O GLY A 351 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 357 through 363 removed outlier: 3.840A pdb=" N THR A 360 " --> pdb=" O HIS A 404 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N HIS A 404 " --> pdb=" O THR A 360 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 6 through 8 Processing sheet with id=AA9, first strand: chain 'C' and resid 11 through 15 removed outlier: 6.454A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 117 through 120 removed outlier: 3.906A pdb=" N VAL C 135 " --> pdb=" O PHE C 120 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N SER C 133 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N LEU C 183 " --> pdb=" O SER C 133 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N VAL C 135 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N LEU C 181 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N LEU C 137 " --> pdb=" O SER C 179 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N SER C 179 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N ASN C 139 " --> pdb=" O LEU C 177 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LEU C 177 " --> pdb=" O ASN C 139 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 146 through 152 removed outlier: 3.728A pdb=" N VAL C 198 " --> pdb=" O VAL C 207 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 6 through 8 Processing sheet with id=AB4, first strand: chain 'D' and resid 13 through 14 removed outlier: 6.128A pdb=" N GLY D 13 " --> pdb=" O THR D 121 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N ILE D 37 " --> pdb=" O SER D 53 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N SER D 53 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N TRP D 39 " --> pdb=" O VAL D 51 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 21 through 24 removed outlier: 3.949A pdb=" N LEU D 23 " --> pdb=" O LEU D 84 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU D 84 " --> pdb=" O LEU D 23 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 103 through 104 Processing sheet with id=AB7, first strand: chain 'D' and resid 134 through 135 removed outlier: 6.000A pdb=" N TYR D 187 " --> pdb=" O ASP D 155 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL D 192 " --> pdb=" O HIS D 175 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 134 through 135 removed outlier: 6.000A pdb=" N TYR D 187 " --> pdb=" O ASP D 155 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 205 through 211 removed outlier: 4.619A pdb=" N TYR D 205 " --> pdb=" O VAL D 222 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS D 220 " --> pdb=" O CYS D 207 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 8 through 10 Processing sheet with id=AC2, first strand: chain 'E' and resid 13 through 15 removed outlier: 6.535A pdb=" N GLY E 13 " --> pdb=" O THR E 127 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLN E 42 " --> pdb=" O VAL E 96 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER E 36 " --> pdb=" O TYR E 102 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ARG E 41 " --> pdb=" O TRP E 50 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N TRP E 50 " --> pdb=" O ARG E 41 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER E 60 " --> pdb=" O SER E 55 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 13 through 15 removed outlier: 6.535A pdb=" N GLY E 13 " --> pdb=" O THR E 127 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N TYR E 119 " --> pdb=" O ARG E 101 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N SER E 103 " --> pdb=" O MET E 117 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N MET E 117 " --> pdb=" O SER E 103 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 5 through 8 removed outlier: 3.696A pdb=" N SER F 8 " --> pdb=" O THR F 23 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR F 23 " --> pdb=" O SER F 8 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 11 through 13 removed outlier: 3.615A pdb=" N GLU F 106 " --> pdb=" O LEU F 12 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN F 39 " --> pdb=" O THR F 86 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N TRP F 36 " --> pdb=" O LEU F 48 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 90 through 91 removed outlier: 3.700A pdb=" N THR F 98 " --> pdb=" O GLN F 91 " (cutoff:3.500A) 333 hydrogen bonds defined for protein. 816 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.42 Time building geometry restraints manager: 1.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 7641 1.03 - 1.23: 39 1.23 - 1.42: 3626 1.42 - 1.62: 4579 1.62 - 1.82: 41 Bond restraints: 15926 Sorted by residual: bond pdb=" N GLU D 4 " pdb=" H GLU D 4 " ideal model delta sigma weight residual 0.860 0.960 -0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" N GLU E 4 " pdb=" H GLU E 4 " ideal model delta sigma weight residual 0.860 0.960 -0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" N ASP C 2 " pdb=" H ASP C 2 " ideal model delta sigma weight residual 0.860 0.960 -0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" N ILE A 25 " pdb=" CA ILE A 25 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.52e+00 bond pdb=" N ILE A 25 " pdb=" H ILE A 25 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.21e+00 ... (remaining 15921 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 27479 1.20 - 2.40: 997 2.40 - 3.60: 75 3.60 - 4.81: 11 4.81 - 6.01: 3 Bond angle restraints: 28565 Sorted by residual: angle pdb=" CA PRO A 413 " pdb=" N PRO A 413 " pdb=" CD PRO A 413 " ideal model delta sigma weight residual 112.00 108.20 3.80 1.40e+00 5.10e-01 7.36e+00 angle pdb=" N ILE F 3 " pdb=" CA ILE F 3 " pdb=" C ILE F 3 " ideal model delta sigma weight residual 106.32 110.08 -3.76 1.61e+00 3.86e-01 5.45e+00 angle pdb=" CA TYR C 50 " pdb=" CB TYR C 50 " pdb=" CG TYR C 50 " ideal model delta sigma weight residual 113.90 117.60 -3.70 1.80e+00 3.09e-01 4.22e+00 angle pdb=" CA TYR E 113 " pdb=" CB TYR E 113 " pdb=" CG TYR E 113 " ideal model delta sigma weight residual 113.90 117.57 -3.67 1.80e+00 3.09e-01 4.17e+00 angle pdb=" CA SER F 29 " pdb=" C SER F 29 " pdb=" N VAL F 30 " ideal model delta sigma weight residual 114.76 117.08 -2.32 1.14e+00 7.69e-01 4.15e+00 ... (remaining 28560 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 6829 17.79 - 35.58: 586 35.58 - 53.37: 194 53.37 - 71.16: 57 71.16 - 88.95: 21 Dihedral angle restraints: 7687 sinusoidal: 4028 harmonic: 3659 Sorted by residual: dihedral pdb=" CB CYS C 24 " pdb=" SG CYS C 24 " pdb=" SG CYS C 89 " pdb=" CB CYS C 89 " ideal model delta sinusoidal sigma weight residual 93.00 56.90 36.10 1 1.00e+01 1.00e-02 1.84e+01 dihedral pdb=" CA PHE C 98 " pdb=" C PHE C 98 " pdb=" N THR C 99 " pdb=" CA THR C 99 " ideal model delta harmonic sigma weight residual -180.00 -160.12 -19.88 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA VAL A 393 " pdb=" C VAL A 393 " pdb=" N PRO A 394 " pdb=" CA PRO A 394 " ideal model delta harmonic sigma weight residual 180.00 160.47 19.53 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 7684 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 733 0.031 - 0.062: 348 0.062 - 0.094: 61 0.094 - 0.125: 72 0.125 - 0.156: 8 Chirality restraints: 1222 Sorted by residual: chirality pdb=" CA ILE C 49 " pdb=" N ILE C 49 " pdb=" C ILE C 49 " pdb=" CB ILE C 49 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.10e-01 chirality pdb=" CA ILE F 76 " pdb=" N ILE F 76 " pdb=" C ILE F 76 " pdb=" CB ILE F 76 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.99e-01 chirality pdb=" CA ILE D 206 " pdb=" N ILE D 206 " pdb=" C ILE D 206 " pdb=" CB ILE D 206 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.33e-01 ... (remaining 1219 not shown) Planarity restraints: 2430 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 412 " -0.060 5.00e-02 4.00e+02 8.91e-02 1.27e+01 pdb=" N PRO A 413 " 0.154 5.00e-02 4.00e+02 pdb=" CA PRO A 413 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 413 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR C 96 " -0.022 5.00e-02 4.00e+02 3.26e-02 1.71e+00 pdb=" N PRO C 97 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO C 97 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 97 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL F 59 " -0.019 5.00e-02 4.00e+02 2.92e-02 1.36e+00 pdb=" N PRO F 60 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO F 60 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO F 60 " -0.016 5.00e-02 4.00e+02 ... (remaining 2427 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 697 2.16 - 2.77: 30018 2.77 - 3.38: 43317 3.38 - 3.99: 59045 3.99 - 4.60: 89331 Nonbonded interactions: 222408 Sorted by model distance: nonbonded pdb=" OE1 GLN C 102 " pdb=" H GLN C 102 " model vdw 1.553 2.450 nonbonded pdb="HD22 ASN D 166 " pdb=" O THR D 204 " model vdw 1.554 2.450 nonbonded pdb=" O ARG C 62 " pdb=" H SER C 77 " model vdw 1.576 2.450 nonbonded pdb="HH11 ARG A 255 " pdb=" O GLY A 256 " model vdw 1.584 2.450 nonbonded pdb=" OD1 ASP A 77 " pdb="HH11 ARG A 179 " model vdw 1.589 2.450 ... (remaining 222403 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.100 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.330 Find NCS groups from input model: 0.050 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:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6453 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 : 0.003 0.058 8293 Z= 0.137 Angle : 0.510 4.570 11300 Z= 0.273 Chirality : 0.042 0.156 1222 Planarity : 0.004 0.089 1452 Dihedral : 16.222 88.948 2926 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.46 % Allowed : 18.76 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.98 % 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 aren not related in a simple way. whole: -1.19 (0.27), residues: 1022 helix: -0.60 (0.57), residues: 83 sheet: -0.86 (0.25), residues: 426 loop : -0.61 (0.29), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 121 TYR 0.016 0.001 TYR C 50 PHE 0.015 0.001 PHE A 177 TRP 0.007 0.001 TRP F 36 HIS 0.002 0.001 HIS A 404 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 8284) covalent geometry : angle 0.50989 (11282) SS BOND : bond 0.00283 ( 9) SS BOND : angle 0.51888 ( 18) hydrogen bonds : bond 0.24980 ( 300) hydrogen bonds : angle 10.39143 ( 816) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 43 is missing expected H atoms. Skipping. Residue SER 186 is missing expected H atoms. Skipping. Residue TYR 228 is missing expected H atoms. Skipping. Residue LYS 320 is missing expected H atoms. Skipping. Residue LYS 419 is missing expected H atoms. Skipping. Residue LYS 128 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Evaluate side-chains 98 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 94 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 31 ASN cc_start: 0.6339 (t0) cc_final: 0.5803 (p0) REVERT: D 221 LYS cc_start: 0.4380 (tptt) cc_final: 0.3776 (tmmt) outliers start: 4 outliers final: 3 residues processed: 97 average time/residue: 0.1907 time to fit residues: 26.0176 Evaluate side-chains 96 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 93 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain C residue 98 PHE Chi-restraints excluded: chain E residue 118 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.3980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.2980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 38 optimal weight: 0.0010 chunk 61 optimal weight: 0.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 154 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.172726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.138484 restraints weight = 31208.925| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 2.16 r_work: 0.3874 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3746 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.0782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8293 Z= 0.126 Angle : 0.535 4.233 11300 Z= 0.286 Chirality : 0.044 0.189 1222 Planarity : 0.004 0.052 1452 Dihedral : 4.939 56.041 1144 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.03 % Allowed : 19.22 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.98 % 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 aren not related in a simple way. whole: -0.93 (0.27), residues: 1022 helix: -0.24 (0.54), residues: 91 sheet: -0.56 (0.26), residues: 414 loop : -0.60 (0.29), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 144 TYR 0.016 0.001 TYR C 50 PHE 0.011 0.001 PHE A 177 TRP 0.010 0.001 TRP A 348 HIS 0.003 0.001 HIS A 332 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 8284) covalent geometry : angle 0.53466 (11282) SS BOND : bond 0.00312 ( 9) SS BOND : angle 0.49574 ( 18) hydrogen bonds : bond 0.04718 ( 300) hydrogen bonds : angle 7.07853 ( 816) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 43 is missing expected H atoms. Skipping. Residue SER 186 is missing expected H atoms. Skipping. Residue TYR 228 is missing expected H atoms. Skipping. Residue LYS 320 is missing expected H atoms. Skipping. Residue LYS 419 is missing expected H atoms. Skipping. Residue LYS 128 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Evaluate side-chains 113 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 145 GLU cc_start: 0.6933 (pm20) cc_final: 0.6692 (mp0) REVERT: D 31 ASN cc_start: 0.6712 (t0) cc_final: 0.6482 (p0) REVERT: D 221 LYS cc_start: 0.4738 (tptt) cc_final: 0.4171 (tmmt) REVERT: E 16 GLN cc_start: 0.7154 (mp10) cc_final: 0.6933 (tt0) outliers start: 9 outliers final: 4 residues processed: 111 average time/residue: 0.1578 time to fit residues: 25.5692 Evaluate side-chains 101 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 97 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 98 PHE Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain D residue 200 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 33 optimal weight: 3.9990 chunk 15 optimal weight: 0.1980 chunk 5 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 overall best weight: 1.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 HIS E 122 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.170659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.135993 restraints weight = 31667.363| |-----------------------------------------------------------------------------| r_work (start): 0.3934 rms_B_bonded: 2.18 r_work: 0.3840 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3712 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.0962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8293 Z= 0.198 Angle : 0.561 4.755 11300 Z= 0.299 Chirality : 0.044 0.195 1222 Planarity : 0.004 0.042 1452 Dihedral : 4.987 55.654 1140 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.83 % Allowed : 19.22 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.98 % 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 aren not related in a simple way. whole: -1.12 (0.27), residues: 1022 helix: -0.32 (0.53), residues: 91 sheet: -0.65 (0.25), residues: 414 loop : -0.78 (0.28), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 144 TYR 0.020 0.002 TYR C 50 PHE 0.016 0.002 PHE A 80 TRP 0.008 0.001 TRP D 114 HIS 0.003 0.001 HIS A 404 Details of bonding type rmsd covalent geometry : bond 0.00450 ( 8284) covalent geometry : angle 0.56124 (11282) SS BOND : bond 0.00347 ( 9) SS BOND : angle 0.57674 ( 18) hydrogen bonds : bond 0.04503 ( 300) hydrogen bonds : angle 6.76122 ( 816) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 43 is missing expected H atoms. Skipping. Residue SER 186 is missing expected H atoms. Skipping. Residue TYR 228 is missing expected H atoms. Skipping. Residue LYS 320 is missing expected H atoms. Skipping. Residue LYS 419 is missing expected H atoms. Skipping. Residue LYS 128 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Evaluate side-chains 110 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 145 GLU cc_start: 0.7000 (pm20) cc_final: 0.6767 (mp0) REVERT: C 173 SER cc_start: 0.6964 (OUTLIER) cc_final: 0.6735 (p) REVERT: D 31 ASN cc_start: 0.6759 (t0) cc_final: 0.6526 (p0) REVERT: E 16 GLN cc_start: 0.7244 (mp10) cc_final: 0.6999 (tt0) outliers start: 16 outliers final: 8 residues processed: 108 average time/residue: 0.1737 time to fit residues: 26.9943 Evaluate side-chains 101 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain C residue 98 PHE Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 86 MET Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain E residue 87 ASN Chi-restraints excluded: chain E residue 118 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 43 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 154 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 = 0.4383 r_free = 0.4383 target = 0.170140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.135006 restraints weight = 31636.161| |-----------------------------------------------------------------------------| r_work (start): 0.3923 rms_B_bonded: 2.22 r_work: 0.3829 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3696 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.1106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 8293 Z= 0.209 Angle : 0.576 5.119 11300 Z= 0.307 Chirality : 0.045 0.190 1222 Planarity : 0.004 0.042 1452 Dihedral : 5.134 56.565 1140 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 2.17 % Allowed : 19.57 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.98 % 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 aren not related in a simple way. whole: -1.31 (0.26), residues: 1022 helix: -0.46 (0.52), residues: 91 sheet: -0.75 (0.25), residues: 420 loop : -0.94 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 275 TYR 0.021 0.002 TYR C 50 PHE 0.017 0.002 PHE A 80 TRP 0.008 0.002 TRP A 311 HIS 0.005 0.001 HIS A 404 Details of bonding type rmsd covalent geometry : bond 0.00477 ( 8284) covalent geometry : angle 0.57554 (11282) SS BOND : bond 0.00378 ( 9) SS BOND : angle 0.88578 ( 18) hydrogen bonds : bond 0.04162 ( 300) hydrogen bonds : angle 6.52030 ( 816) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 43 is missing expected H atoms. Skipping. Residue SER 186 is missing expected H atoms. Skipping. Residue TYR 228 is missing expected H atoms. Skipping. Residue LYS 320 is missing expected H atoms. Skipping. Residue LYS 419 is missing expected H atoms. Skipping. Residue LYS 128 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Evaluate side-chains 113 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 145 GLU cc_start: 0.7007 (pm20) cc_final: 0.6777 (mp0) REVERT: C 173 SER cc_start: 0.6969 (OUTLIER) cc_final: 0.6739 (p) REVERT: D 31 ASN cc_start: 0.6721 (t0) cc_final: 0.6482 (p0) REVERT: E 16 GLN cc_start: 0.7300 (mp10) cc_final: 0.7036 (tt0) REVERT: E 113 TYR cc_start: 0.5266 (OUTLIER) cc_final: 0.4850 (m-10) outliers start: 19 outliers final: 13 residues processed: 109 average time/residue: 0.1857 time to fit residues: 28.5677 Evaluate side-chains 104 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain C residue 98 PHE Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 86 MET Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 87 ASN Chi-restraints excluded: chain E residue 113 TYR Chi-restraints excluded: chain E residue 118 ASP Chi-restraints excluded: chain F residue 21 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 HIS C 154 ASN ** D 116 GLN ** 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 = 0.4374 r_free = 0.4374 target = 0.169350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.134265 restraints weight = 31727.574| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 2.19 r_work: 0.3818 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3689 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 8293 Z= 0.236 Angle : 0.599 5.373 11300 Z= 0.320 Chirality : 0.045 0.181 1222 Planarity : 0.005 0.048 1452 Dihedral : 5.336 58.578 1140 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 2.52 % Allowed : 19.91 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.98 % 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 aren not related in a simple way. whole: -1.51 (0.26), residues: 1022 helix: -0.62 (0.51), residues: 91 sheet: -0.82 (0.25), residues: 414 loop : -1.14 (0.28), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 275 TYR 0.024 0.002 TYR C 50 PHE 0.020 0.002 PHE A 80 TRP 0.009 0.002 TRP D 114 HIS 0.005 0.001 HIS A 404 Details of bonding type rmsd covalent geometry : bond 0.00539 ( 8284) covalent geometry : angle 0.59839 (11282) SS BOND : bond 0.00408 ( 9) SS BOND : angle 0.96310 ( 18) hydrogen bonds : bond 0.04185 ( 300) hydrogen bonds : angle 6.42897 ( 816) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 43 is missing expected H atoms. Skipping. Residue SER 186 is missing expected H atoms. Skipping. Residue TYR 228 is missing expected H atoms. Skipping. Residue LYS 320 is missing expected H atoms. Skipping. Residue LYS 419 is missing expected H atoms. Skipping. Residue LYS 128 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Evaluate side-chains 113 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 145 GLU cc_start: 0.7006 (pm20) cc_final: 0.6763 (mp0) REVERT: E 16 GLN cc_start: 0.7296 (mp10) cc_final: 0.7092 (tt0) REVERT: E 113 TYR cc_start: 0.5196 (OUTLIER) cc_final: 0.4833 (m-10) outliers start: 22 outliers final: 18 residues processed: 108 average time/residue: 0.1945 time to fit residues: 29.3783 Evaluate side-chains 109 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 98 PHE Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 86 MET Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 87 ASN Chi-restraints excluded: chain E residue 113 TYR Chi-restraints excluded: chain E residue 118 ASP Chi-restraints excluded: chain F residue 21 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 88 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 81 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.170486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.135549 restraints weight = 31632.603| |-----------------------------------------------------------------------------| r_work (start): 0.3929 rms_B_bonded: 2.21 r_work: 0.3832 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3704 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8293 Z= 0.169 Angle : 0.559 6.111 11300 Z= 0.298 Chirality : 0.044 0.180 1222 Planarity : 0.004 0.047 1452 Dihedral : 5.186 58.919 1140 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.17 % Allowed : 20.14 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.98 % 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 aren not related in a simple way. whole: -1.41 (0.26), residues: 1022 helix: -0.46 (0.52), residues: 91 sheet: -0.83 (0.25), residues: 420 loop : -1.01 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 144 TYR 0.020 0.002 TYR C 50 PHE 0.016 0.001 PHE A 80 TRP 0.008 0.001 TRP A 348 HIS 0.003 0.001 HIS D 38 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 8284) covalent geometry : angle 0.55916 (11282) SS BOND : bond 0.00266 ( 9) SS BOND : angle 0.72089 ( 18) hydrogen bonds : bond 0.03779 ( 300) hydrogen bonds : angle 6.22006 ( 816) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 43 is missing expected H atoms. Skipping. Residue SER 186 is missing expected H atoms. Skipping. Residue TYR 228 is missing expected H atoms. Skipping. Residue LYS 320 is missing expected H atoms. Skipping. Residue LYS 419 is missing expected H atoms. Skipping. Residue LYS 128 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Evaluate side-chains 110 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 145 GLU cc_start: 0.7041 (pm20) cc_final: 0.6826 (mp0) REVERT: E 16 GLN cc_start: 0.7293 (mp10) cc_final: 0.7036 (tt0) REVERT: E 113 TYR cc_start: 0.5227 (OUTLIER) cc_final: 0.4822 (m-10) outliers start: 19 outliers final: 11 residues processed: 107 average time/residue: 0.2151 time to fit residues: 32.0607 Evaluate side-chains 99 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain C residue 98 PHE Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 86 MET Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 87 ASN Chi-restraints excluded: chain E residue 113 TYR Chi-restraints excluded: chain F residue 21 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 41 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 75 optimal weight: 0.0970 chunk 60 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 50 optimal weight: 0.7980 chunk 42 optimal weight: 0.0870 chunk 62 optimal weight: 0.8980 overall best weight: 0.5556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 154 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 = 0.4411 r_free = 0.4411 target = 0.172765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.138275 restraints weight = 31440.755| |-----------------------------------------------------------------------------| r_work (start): 0.3966 rms_B_bonded: 2.19 r_work: 0.3871 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3741 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8293 Z= 0.111 Angle : 0.511 4.137 11300 Z= 0.269 Chirality : 0.043 0.196 1222 Planarity : 0.004 0.041 1452 Dihedral : 4.767 54.657 1140 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.60 % Allowed : 20.59 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.98 % 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 aren not related in a simple way. whole: -1.10 (0.26), residues: 1022 helix: -0.07 (0.54), residues: 91 sheet: -0.69 (0.25), residues: 416 loop : -0.76 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 2 TYR 0.013 0.001 TYR C 50 PHE 0.011 0.001 PHE A 177 TRP 0.014 0.001 TRP A 348 HIS 0.003 0.001 HIS D 38 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 8284) covalent geometry : angle 0.51083 (11282) SS BOND : bond 0.00226 ( 9) SS BOND : angle 0.56329 ( 18) hydrogen bonds : bond 0.03318 ( 300) hydrogen bonds : angle 5.83424 ( 816) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 43 is missing expected H atoms. Skipping. Residue SER 186 is missing expected H atoms. Skipping. Residue TYR 228 is missing expected H atoms. Skipping. Residue LYS 320 is missing expected H atoms. Skipping. Residue LYS 419 is missing expected H atoms. Skipping. Residue LYS 128 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Evaluate side-chains 108 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 221 LYS cc_start: 0.4823 (tptt) cc_final: 0.4082 (tmmt) REVERT: E 16 GLN cc_start: 0.7223 (mp10) cc_final: 0.6982 (tt0) REVERT: E 113 TYR cc_start: 0.5101 (OUTLIER) cc_final: 0.4680 (m-10) REVERT: F 63 PHE cc_start: 0.7309 (m-80) cc_final: 0.7061 (m-80) outliers start: 14 outliers final: 10 residues processed: 104 average time/residue: 0.1879 time to fit residues: 27.7125 Evaluate side-chains 100 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 98 PHE Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 87 ASN Chi-restraints excluded: chain E residue 113 TYR Chi-restraints excluded: chain F residue 21 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 10 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 74 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 154 ASN ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.170773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.135854 restraints weight = 31690.946| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 2.20 r_work: 0.3841 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3711 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8293 Z= 0.182 Angle : 0.553 4.287 11300 Z= 0.293 Chirality : 0.044 0.186 1222 Planarity : 0.004 0.046 1452 Dihedral : 4.984 55.763 1140 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.06 % Allowed : 19.79 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.98 % 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 aren not related in a simple way. whole: -1.24 (0.26), residues: 1022 helix: -0.27 (0.52), residues: 91 sheet: -0.68 (0.25), residues: 414 loop : -0.95 (0.28), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 144 TYR 0.020 0.002 TYR C 50 PHE 0.015 0.002 PHE A 80 TRP 0.010 0.001 TRP A 348 HIS 0.004 0.001 HIS A 404 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 8284) covalent geometry : angle 0.55212 (11282) SS BOND : bond 0.00436 ( 9) SS BOND : angle 0.93089 ( 18) hydrogen bonds : bond 0.03655 ( 300) hydrogen bonds : angle 5.90682 ( 816) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 43 is missing expected H atoms. Skipping. Residue SER 186 is missing expected H atoms. Skipping. Residue TYR 228 is missing expected H atoms. Skipping. Residue LYS 320 is missing expected H atoms. Skipping. Residue LYS 419 is missing expected H atoms. Skipping. Residue LYS 128 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Evaluate side-chains 106 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 221 LYS cc_start: 0.4718 (tptt) cc_final: 0.4150 (tmmt) REVERT: E 16 GLN cc_start: 0.7304 (mp10) cc_final: 0.7033 (tt0) REVERT: E 113 TYR cc_start: 0.5241 (OUTLIER) cc_final: 0.4808 (m-10) outliers start: 18 outliers final: 15 residues processed: 103 average time/residue: 0.1859 time to fit residues: 27.0975 Evaluate side-chains 102 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 98 PHE Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 86 MET Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 87 ASN Chi-restraints excluded: chain E residue 113 TYR Chi-restraints excluded: chain F residue 21 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 28 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 34 optimal weight: 0.4980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.171781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.137119 restraints weight = 31600.592| |-----------------------------------------------------------------------------| r_work (start): 0.3949 rms_B_bonded: 2.20 r_work: 0.3850 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3723 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8293 Z= 0.138 Angle : 0.532 4.382 11300 Z= 0.281 Chirality : 0.043 0.184 1222 Planarity : 0.004 0.045 1452 Dihedral : 4.907 53.748 1140 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.83 % Allowed : 20.02 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.98 % 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 aren not related in a simple way. whole: -1.13 (0.26), residues: 1022 helix: -0.13 (0.53), residues: 91 sheet: -0.65 (0.26), residues: 414 loop : -0.84 (0.28), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 144 TYR 0.017 0.001 TYR C 50 PHE 0.013 0.001 PHE A 80 TRP 0.012 0.001 TRP A 348 HIS 0.003 0.001 HIS D 38 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 8284) covalent geometry : angle 0.53109 (11282) SS BOND : bond 0.00331 ( 9) SS BOND : angle 0.84008 ( 18) hydrogen bonds : bond 0.03442 ( 300) hydrogen bonds : angle 5.79139 ( 816) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 43 is missing expected H atoms. Skipping. Residue SER 186 is missing expected H atoms. Skipping. Residue TYR 228 is missing expected H atoms. Skipping. Residue LYS 320 is missing expected H atoms. Skipping. Residue LYS 419 is missing expected H atoms. Skipping. Residue LYS 128 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Evaluate side-chains 107 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 16 GLN cc_start: 0.7285 (mp10) cc_final: 0.7038 (tt0) REVERT: E 113 TYR cc_start: 0.5211 (OUTLIER) cc_final: 0.4785 (m-10) outliers start: 16 outliers final: 14 residues processed: 104 average time/residue: 0.1875 time to fit residues: 27.6923 Evaluate side-chains 104 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 98 PHE Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 86 MET Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 87 ASN Chi-restraints excluded: chain E residue 113 TYR Chi-restraints excluded: chain F residue 21 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 25 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 27 optimal weight: 0.4980 chunk 31 optimal weight: 3.9990 chunk 15 optimal weight: 0.3980 chunk 2 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 101 optimal weight: 0.4980 chunk 76 optimal weight: 4.9990 chunk 46 optimal weight: 0.2980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 154 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.173460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.138875 restraints weight = 31347.399| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 2.20 r_work: 0.3880 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3750 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8293 Z= 0.106 Angle : 0.505 4.678 11300 Z= 0.266 Chirality : 0.043 0.173 1222 Planarity : 0.004 0.049 1452 Dihedral : 4.630 50.653 1140 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.26 % Allowed : 20.71 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.98 % 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 aren not related in a simple way. whole: -0.94 (0.27), residues: 1022 helix: 0.13 (0.54), residues: 91 sheet: -0.54 (0.25), residues: 417 loop : -0.73 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 101 TYR 0.013 0.001 TYR C 50 PHE 0.011 0.001 PHE A 177 TRP 0.017 0.001 TRP A 348 HIS 0.002 0.001 HIS D 38 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 8284) covalent geometry : angle 0.50440 (11282) SS BOND : bond 0.00355 ( 9) SS BOND : angle 0.68727 ( 18) hydrogen bonds : bond 0.03153 ( 300) hydrogen bonds : angle 5.56301 ( 816) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 43 is missing expected H atoms. Skipping. Residue SER 186 is missing expected H atoms. Skipping. Residue TYR 228 is missing expected H atoms. Skipping. Residue LYS 320 is missing expected H atoms. Skipping. Residue LYS 419 is missing expected H atoms. Skipping. Residue LYS 128 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Evaluate side-chains 101 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 221 LYS cc_start: 0.4669 (tptt) cc_final: 0.4062 (tmmt) REVERT: E 16 GLN cc_start: 0.7198 (mp10) cc_final: 0.6967 (tt0) REVERT: E 113 TYR cc_start: 0.5095 (OUTLIER) cc_final: 0.4598 (m-10) outliers start: 11 outliers final: 9 residues processed: 99 average time/residue: 0.1944 time to fit residues: 27.1955 Evaluate side-chains 99 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 113 TYR Chi-restraints excluded: chain F residue 21 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 78 optimal weight: 6.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.172708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.138093 restraints weight = 31298.111| |-----------------------------------------------------------------------------| r_work (start): 0.3962 rms_B_bonded: 2.19 r_work: 0.3866 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3738 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8293 Z= 0.138 Angle : 0.520 4.661 11300 Z= 0.274 Chirality : 0.043 0.175 1222 Planarity : 0.004 0.049 1452 Dihedral : 4.433 18.205 1138 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.37 % Allowed : 20.48 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.98 % 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 aren not related in a simple way. whole: -0.97 (0.27), residues: 1022 helix: 0.07 (0.54), residues: 91 sheet: -0.55 (0.25), residues: 417 loop : -0.75 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 2 TYR 0.015 0.001 TYR C 50 PHE 0.012 0.001 PHE A 80 TRP 0.013 0.001 TRP A 348 HIS 0.002 0.001 HIS D 38 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 8284) covalent geometry : angle 0.52000 (11282) SS BOND : bond 0.00312 ( 9) SS BOND : angle 0.74401 ( 18) hydrogen bonds : bond 0.03251 ( 300) hydrogen bonds : angle 5.57489 ( 816) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4924.94 seconds wall clock time: 84 minutes 8.08 seconds (5048.08 seconds total)