Starting phenix.real_space_refine on Mon Jun 16 02:48:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tnj_41418/06_2025/8tnj_41418.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tnj_41418/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8tnj_41418/06_2025/8tnj_41418.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tnj_41418/06_2025/8tnj_41418.map" model { file = "/net/cci-nas-00/data/ceres_data/8tnj_41418/06_2025/8tnj_41418.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tnj_41418/06_2025/8tnj_41418.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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, 'TYR:plan': 1, 'ARG:plan': 6, 'ASP:plan': 1, 'GLU: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: 8.58, per 1000 atoms: 0.55 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: 5.05 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.75 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: 9.43 Time building geometry restraints manager: 5.38 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: 84.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.310 Extract box with map and model: 0.600 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 42.440 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 131.510 ------------------------------------------------------------------------------- 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 : 5.67 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (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 TRP 0.007 0.001 TRP F 36 HIS 0.002 0.001 HIS A 404 PHE 0.015 0.001 PHE A 177 TYR 0.016 0.001 TYR C 50 ARG 0.003 0.000 ARG A 121 Details of bonding type rmsd hydrogen bonds : bond 0.24980 ( 300) hydrogen bonds : angle 10.39143 ( 816) SS BOND : bond 0.00283 ( 9) SS BOND : angle 0.51888 ( 18) covalent geometry : bond 0.00312 ( 8284) covalent geometry : angle 0.50989 (11282) *********************** 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 : 1.551 Fit side-chains revert: symmetry clash 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: 0.5804 (p0) outliers start: 4 outliers final: 3 residues processed: 97 average time/residue: 0.4794 time to fit residues: 66.6645 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 : 3.051 ------------------------------------------------------------------------------- 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 86 optimal weight: 1.9990 chunk 77 optimal weight: 0.0980 chunk 42 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 79 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 HIS ** E 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.171418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.137055 restraints weight = 31511.679| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 2.17 r_work: 0.3851 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3724 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.0721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8293 Z= 0.159 Angle : 0.555 4.505 11300 Z= 0.298 Chirality : 0.044 0.190 1222 Planarity : 0.004 0.053 1452 Dihedral : 5.061 54.686 1144 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 1.14 % Allowed : 19.22 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.27), residues: 1022 helix: -0.55 (0.52), residues: 91 sheet: -0.63 (0.26), residues: 411 loop : -0.71 (0.29), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 311 HIS 0.004 0.001 HIS C 191 PHE 0.013 0.001 PHE A 80 TYR 0.018 0.002 TYR C 50 ARG 0.002 0.000 ARG C 144 Details of bonding type rmsd hydrogen bonds : bond 0.05036 ( 300) hydrogen bonds : angle 7.22096 ( 816) SS BOND : bond 0.00345 ( 9) SS BOND : angle 0.56136 ( 18) covalent geometry : bond 0.00357 ( 8284) covalent geometry : angle 0.55459 (11282) *********************** 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 114 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 104 time to evaluate : 1.236 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: C 145 GLU cc_start: 0.7029 (pm20) cc_final: 0.6747 (mp0) REVERT: D 31 ASN cc_start: 0.6724 (t0) cc_final: 0.6498 (p0) REVERT: E 16 GLN cc_start: 0.7171 (mp10) cc_final: 0.6937 (tt0) outliers start: 10 outliers final: 7 residues processed: 112 average time/residue: 0.4102 time to fit residues: 64.8738 Evaluate side-chains 102 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 95 time to evaluate : 1.390 ------------------------------------------------------------------------------- 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 154 ASN Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain E residue 72 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 24 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 21 optimal weight: 0.0270 overall best weight: 0.7844 ------------------------------------------------------------------------------- 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 E 122 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.172271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.137930 restraints weight = 31222.258| |-----------------------------------------------------------------------------| r_work (start): 0.3962 rms_B_bonded: 2.16 r_work: 0.3871 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3739 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8293 Z= 0.132 Angle : 0.519 4.144 11300 Z= 0.275 Chirality : 0.043 0.196 1222 Planarity : 0.004 0.040 1452 Dihedral : 4.813 58.489 1140 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.60 % Allowed : 19.34 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.27), residues: 1022 helix: -0.06 (0.54), residues: 91 sheet: -0.58 (0.25), residues: 414 loop : -0.67 (0.29), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 348 HIS 0.003 0.001 HIS A 404 PHE 0.012 0.001 PHE A 80 TYR 0.016 0.001 TYR C 50 ARG 0.002 0.000 ARG C 144 Details of bonding type rmsd hydrogen bonds : bond 0.04024 ( 300) hydrogen bonds : angle 6.44546 ( 816) SS BOND : bond 0.00292 ( 9) SS BOND : angle 0.49584 ( 18) covalent geometry : bond 0.00300 ( 8284) covalent geometry : angle 0.51917 (11282) *********************** 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 115 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 31 ASN cc_start: 0.6722 (t0) cc_final: 0.6490 (p0) REVERT: E 16 GLN cc_start: 0.7271 (mp10) cc_final: 0.7026 (tt0) outliers start: 14 outliers final: 6 residues processed: 115 average time/residue: 0.3944 time to fit residues: 65.0837 Evaluate side-chains 101 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 95 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 98 PHE Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain D residue 36 SER 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 4 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 85 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 HIS 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 = 0.172645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.138042 restraints weight = 31180.785| |-----------------------------------------------------------------------------| r_work (start): 0.3964 rms_B_bonded: 2.18 r_work: 0.3872 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3740 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8293 Z= 0.131 Angle : 0.519 4.044 11300 Z= 0.273 Chirality : 0.043 0.179 1222 Planarity : 0.004 0.036 1452 Dihedral : 4.785 59.717 1140 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.26 % Allowed : 20.14 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.27), residues: 1022 helix: -0.01 (0.54), residues: 91 sheet: -0.52 (0.25), residues: 414 loop : -0.67 (0.28), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 348 HIS 0.002 0.001 HIS A 404 PHE 0.011 0.001 PHE A 80 TYR 0.016 0.001 TYR C 50 ARG 0.003 0.000 ARG C 144 Details of bonding type rmsd hydrogen bonds : bond 0.03624 ( 300) hydrogen bonds : angle 6.17886 ( 816) SS BOND : bond 0.00286 ( 9) SS BOND : angle 0.55872 ( 18) covalent geometry : bond 0.00300 ( 8284) covalent geometry : angle 0.51869 (11282) *********************** 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 107 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 LYS cc_start: 0.6616 (ptmm) cc_final: 0.6069 (ptmm) REVERT: D 31 ASN cc_start: 0.6607 (t0) cc_final: 0.6348 (p0) REVERT: E 16 GLN cc_start: 0.7274 (mp10) cc_final: 0.7022 (tt0) REVERT: E 113 TYR cc_start: 0.5147 (OUTLIER) cc_final: 0.4675 (m-10) REVERT: F 63 PHE cc_start: 0.7520 (m-80) cc_final: 0.7248 (m-80) outliers start: 11 outliers final: 10 residues processed: 106 average time/residue: 0.4006 time to fit residues: 60.5983 Evaluate side-chains 105 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 154 ASN Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 72 THR 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 113 TYR 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 12 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 74 optimal weight: 6.9990 chunk 0 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.4396 r_free = 0.4396 target = 0.171303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.136833 restraints weight = 31563.440| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 2.18 r_work: 0.3849 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3722 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8293 Z= 0.169 Angle : 0.539 4.441 11300 Z= 0.285 Chirality : 0.044 0.179 1222 Planarity : 0.004 0.041 1452 Dihedral : 4.935 59.809 1140 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 1.95 % Allowed : 19.79 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.26), residues: 1022 helix: -0.16 (0.53), residues: 91 sheet: -0.58 (0.25), residues: 414 loop : -0.78 (0.28), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 348 HIS 0.002 0.001 HIS A 332 PHE 0.014 0.002 PHE A 80 TYR 0.019 0.002 TYR C 50 ARG 0.002 0.000 ARG A 275 Details of bonding type rmsd hydrogen bonds : bond 0.03721 ( 300) hydrogen bonds : angle 6.06724 ( 816) SS BOND : bond 0.00328 ( 9) SS BOND : angle 0.76189 ( 18) covalent geometry : bond 0.00386 ( 8284) covalent geometry : angle 0.53840 (11282) *********************** 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 111 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 31 ASN cc_start: 0.6604 (t0) cc_final: 0.6331 (p0) REVERT: D 221 LYS cc_start: 0.4705 (tptt) cc_final: 0.4124 (tmmt) REVERT: E 16 GLN cc_start: 0.7291 (mp10) cc_final: 0.7041 (tt0) REVERT: E 113 TYR cc_start: 0.5219 (OUTLIER) cc_final: 0.4779 (m-10) outliers start: 17 outliers final: 12 residues processed: 108 average time/residue: 0.3990 time to fit residues: 61.0356 Evaluate side-chains 104 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 1.316 ------------------------------------------------------------------------------- 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 36 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 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 54 optimal weight: 6.9990 chunk 88 optimal weight: 5.9990 chunk 68 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 19 optimal weight: 0.1980 chunk 2 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 72 optimal weight: 6.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.4405 r_free = 0.4405 target = 0.172101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.137425 restraints weight = 31524.193| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 2.20 r_work: 0.3861 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3731 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.1368 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= 0.143 Angle : 0.520 3.950 11300 Z= 0.275 Chirality : 0.043 0.185 1222 Planarity : 0.004 0.042 1452 Dihedral : 4.843 57.881 1140 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.06 % Allowed : 19.68 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.26), residues: 1022 helix: -0.06 (0.53), residues: 91 sheet: -0.56 (0.25), residues: 414 loop : -0.74 (0.28), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 348 HIS 0.002 0.001 HIS D 38 PHE 0.012 0.001 PHE A 80 TYR 0.017 0.001 TYR C 50 ARG 0.002 0.000 ARG C 144 Details of bonding type rmsd hydrogen bonds : bond 0.03504 ( 300) hydrogen bonds : angle 5.88492 ( 816) SS BOND : bond 0.00253 ( 9) SS BOND : angle 0.60780 ( 18) covalent geometry : bond 0.00328 ( 8284) covalent geometry : angle 0.52021 (11282) *********************** 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 113 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 31 ASN cc_start: 0.6581 (t0) cc_final: 0.6309 (p0) REVERT: D 221 LYS cc_start: 0.4740 (tptt) cc_final: 0.4202 (tmmt) REVERT: E 16 GLN cc_start: 0.7292 (mp10) cc_final: 0.7034 (tt0) REVERT: E 113 TYR cc_start: 0.5198 (OUTLIER) cc_final: 0.4760 (m-10) outliers start: 18 outliers final: 12 residues processed: 109 average time/residue: 0.3753 time to fit residues: 58.2484 Evaluate side-chains 105 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 1.295 ------------------------------------------------------------------------------- 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 36 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 F residue 21 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 3 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 = 0.4389 r_free = 0.4389 target = 0.170750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.135727 restraints weight = 31860.781| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 2.21 r_work: 0.3840 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3708 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 8293 Z= 0.199 Angle : 0.559 4.536 11300 Z= 0.297 Chirality : 0.044 0.181 1222 Planarity : 0.004 0.046 1452 Dihedral : 5.042 58.062 1140 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 2.52 % Allowed : 19.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.26), residues: 1022 helix: -0.27 (0.52), residues: 91 sheet: -0.64 (0.25), residues: 420 loop : -0.88 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 114 HIS 0.004 0.001 HIS A 404 PHE 0.016 0.002 PHE A 80 TYR 0.021 0.002 TYR C 50 ARG 0.003 0.000 ARG C 144 Details of bonding type rmsd hydrogen bonds : bond 0.03787 ( 300) hydrogen bonds : angle 5.97339 ( 816) SS BOND : bond 0.00340 ( 9) SS BOND : angle 1.02077 ( 18) covalent geometry : bond 0.00455 ( 8284) covalent geometry : angle 0.55836 (11282) *********************** 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 112 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 31 ASN cc_start: 0.6697 (t0) cc_final: 0.6334 (p0) REVERT: E 16 GLN cc_start: 0.7296 (mp10) cc_final: 0.7040 (tt0) REVERT: E 113 TYR cc_start: 0.5245 (OUTLIER) cc_final: 0.4813 (m-10) outliers start: 22 outliers final: 17 residues processed: 106 average time/residue: 0.3946 time to fit residues: 59.6298 Evaluate side-chains 107 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 1.356 ------------------------------------------------------------------------------- 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 A residue 335 HIS Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain C residue 98 PHE Chi-restraints excluded: chain C residue 213 ARG Chi-restraints excluded: chain D residue 36 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 9 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 52 optimal weight: 0.2980 chunk 34 optimal weight: 0.0670 chunk 85 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 74 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.5718 ------------------------------------------------------------------------------- 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 = 0.4415 r_free = 0.4415 target = 0.172964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.138814 restraints weight = 31247.728| |-----------------------------------------------------------------------------| r_work (start): 0.3971 rms_B_bonded: 2.17 r_work: 0.3876 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3749 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8293 Z= 0.111 Angle : 0.505 4.106 11300 Z= 0.266 Chirality : 0.043 0.186 1222 Planarity : 0.004 0.045 1452 Dihedral : 4.722 54.194 1140 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.83 % Allowed : 19.79 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.27), residues: 1022 helix: 0.11 (0.54), residues: 91 sheet: -0.53 (0.26), residues: 415 loop : -0.74 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 348 HIS 0.002 0.001 HIS D 38 PHE 0.011 0.001 PHE A 80 TYR 0.014 0.001 TYR C 50 ARG 0.002 0.000 ARG A 2 Details of bonding type rmsd hydrogen bonds : bond 0.03276 ( 300) hydrogen bonds : angle 5.69542 ( 816) SS BOND : bond 0.00333 ( 9) SS BOND : angle 0.68076 ( 18) covalent geometry : bond 0.00254 ( 8284) covalent geometry : angle 0.50480 (11282) *********************** 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 108 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 31 ASN cc_start: 0.6659 (t0) cc_final: 0.6303 (p0) REVERT: E 16 GLN cc_start: 0.7279 (mp10) cc_final: 0.7048 (tt0) REVERT: E 113 TYR cc_start: 0.5158 (OUTLIER) cc_final: 0.4683 (m-10) outliers start: 16 outliers final: 13 residues processed: 105 average time/residue: 0.3774 time to fit residues: 56.5270 Evaluate side-chains 104 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 213 ARG Chi-restraints excluded: chain D residue 36 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 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 56 optimal weight: 9.9990 chunk 60 optimal weight: 0.0270 chunk 54 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 101 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 overall best weight: 0.7438 ------------------------------------------------------------------------------- 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 = 0.4414 r_free = 0.4414 target = 0.172861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.138291 restraints weight = 31394.692| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 2.21 r_work: 0.3874 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3742 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8293 Z= 0.126 Angle : 0.508 4.274 11300 Z= 0.268 Chirality : 0.043 0.178 1222 Planarity : 0.004 0.045 1452 Dihedral : 4.676 53.445 1140 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.72 % Allowed : 20.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.26), residues: 1022 helix: 0.12 (0.54), residues: 91 sheet: -0.54 (0.25), residues: 415 loop : -0.75 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 348 HIS 0.002 0.001 HIS A 332 PHE 0.020 0.001 PHE C 118 TYR 0.016 0.001 TYR C 50 ARG 0.002 0.000 ARG C 144 Details of bonding type rmsd hydrogen bonds : bond 0.03290 ( 300) hydrogen bonds : angle 5.61982 ( 816) SS BOND : bond 0.00417 ( 9) SS BOND : angle 0.68540 ( 18) covalent geometry : bond 0.00290 ( 8284) covalent geometry : angle 0.50805 (11282) *********************** 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 109 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 31 ASN cc_start: 0.6661 (t0) cc_final: 0.6300 (p0) REVERT: E 16 GLN cc_start: 0.7278 (mp10) cc_final: 0.7038 (tt0) REVERT: E 113 TYR cc_start: 0.5166 (OUTLIER) cc_final: 0.4683 (m-10) REVERT: F 63 PHE cc_start: 0.7532 (m-80) cc_final: 0.7188 (m-80) outliers start: 15 outliers final: 14 residues processed: 106 average time/residue: 0.3833 time to fit residues: 57.8009 Evaluate side-chains 107 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 213 ARG Chi-restraints excluded: chain D residue 36 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 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 60 optimal weight: 1.9990 chunk 72 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 79 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 53 optimal weight: 0.3980 chunk 62 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.4400 r_free = 0.4400 target = 0.171584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.136893 restraints weight = 31517.446| |-----------------------------------------------------------------------------| r_work (start): 0.3948 rms_B_bonded: 2.18 r_work: 0.3854 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3724 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8293 Z= 0.166 Angle : 0.534 4.306 11300 Z= 0.283 Chirality : 0.044 0.185 1222 Planarity : 0.004 0.046 1452 Dihedral : 4.819 53.067 1140 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.17 % Allowed : 20.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.26), residues: 1022 helix: -0.04 (0.53), residues: 91 sheet: -0.63 (0.25), residues: 416 loop : -0.86 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 114 HIS 0.003 0.001 HIS A 332 PHE 0.013 0.002 PHE A 80 TYR 0.020 0.002 TYR C 50 ARG 0.003 0.000 ARG C 144 Details of bonding type rmsd hydrogen bonds : bond 0.03497 ( 300) hydrogen bonds : angle 5.68672 ( 816) SS BOND : bond 0.00378 ( 9) SS BOND : angle 0.73437 ( 18) covalent geometry : bond 0.00382 ( 8284) covalent geometry : angle 0.53410 (11282) ********************** 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 107 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 1.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 31 ASN cc_start: 0.6671 (t0) cc_final: 0.6327 (p0) REVERT: E 16 GLN cc_start: 0.7291 (mp10) cc_final: 0.7043 (tt0) REVERT: E 113 TYR cc_start: 0.5124 (OUTLIER) cc_final: 0.4658 (m-10) REVERT: F 63 PHE cc_start: 0.7602 (m-80) cc_final: 0.7369 (m-80) outliers start: 19 outliers final: 17 residues processed: 102 average time/residue: 0.3916 time to fit residues: 56.8279 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 : 1.275 ------------------------------------------------------------------------------- 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 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 36 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 D residue 206 ILE 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 45 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 HIS ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 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 = 0.4384 r_free = 0.4384 target = 0.170201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.134729 restraints weight = 31798.166| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 2.28 r_work: 0.3822 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3688 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 8293 Z= 0.212 Angle : 0.571 4.766 11300 Z= 0.304 Chirality : 0.045 0.192 1222 Planarity : 0.004 0.050 1452 Dihedral : 5.051 51.485 1140 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 2.40 % Allowed : 19.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.26), residues: 1022 helix: -0.31 (0.52), residues: 91 sheet: -0.71 (0.25), residues: 416 loop : -1.02 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 114 HIS 0.003 0.001 HIS A 237 PHE 0.017 0.002 PHE A 80 TYR 0.023 0.002 TYR C 50 ARG 0.003 0.001 ARG C 144 Details of bonding type rmsd hydrogen bonds : bond 0.03753 ( 300) hydrogen bonds : angle 5.84496 ( 816) SS BOND : bond 0.00395 ( 9) SS BOND : angle 0.82359 ( 18) covalent geometry : bond 0.00484 ( 8284) covalent geometry : angle 0.57095 (11282) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9535.68 seconds wall clock time: 164 minutes 4.33 seconds (9844.33 seconds total)