Starting phenix.real_space_refine on Sat Dec 28 06:55:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xtb_33445/12_2024/7xtb_33445_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xtb_33445/12_2024/7xtb_33445.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xtb_33445/12_2024/7xtb_33445.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xtb_33445/12_2024/7xtb_33445.map" model { file = "/net/cci-nas-00/data/ceres_data/7xtb_33445/12_2024/7xtb_33445_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xtb_33445/12_2024/7xtb_33445_neut.cif" } resolution = 3.3 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 5135 2.51 5 N 1420 2.21 5 O 1488 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 8101 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1955 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 229} Chain breaks: 2 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 2124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2124 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 260} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "R" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'SRO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.46, per 1000 atoms: 0.67 Number of scatterers: 8101 At special positions: 0 Unit cell: (107.484, 98.358, 110.526, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 58 16.00 O 1488 8.00 N 1420 7.00 C 5135 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 99 " - pdb=" SG CYS R 180 " 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: 2.58 Conformation dependent library (CDL) restraints added in 1.0 seconds 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1946 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 10 sheets defined 43.6% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 9 through 39 removed outlier: 3.679A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 233 through 238 removed outlier: 3.616A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 279 Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 307 through 312 Processing helix chain 'A' and resid 313 through 318 removed outlier: 4.397A pdb=" N ARG A 317 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.651A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.532A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.535A pdb=" N ASN B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 23 Processing helix chain 'G' and resid 29 through 42 Processing helix chain 'G' and resid 44 through 48 removed outlier: 3.790A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.606A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.851A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 27 through 54 removed outlier: 3.530A pdb=" N GLN R 54 " --> pdb=" O LEU R 50 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 79 removed outlier: 4.166A pdb=" N PHE R 64 " --> pdb=" O THR R 60 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU R 65 " --> pdb=" O SER R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 79 through 90 Processing helix chain 'R' and resid 95 through 130 Processing helix chain 'R' and resid 130 through 138 removed outlier: 4.295A pdb=" N LYS R 135 " --> pdb=" O PRO R 131 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N LEU R 136 " --> pdb=" O LEU R 132 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 165 Proline residue: R 161 - end of helix Processing helix chain 'R' and resid 166 through 170 Processing helix chain 'R' and resid 185 through 224 removed outlier: 5.067A pdb=" N LEU R 199 " --> pdb=" O LEU R 195 " (cutoff:3.500A) Proline residue: R 200 - end of helix Processing helix chain 'R' and resid 264 through 293 removed outlier: 3.821A pdb=" N PHE R 277 " --> pdb=" O LEU R 273 " (cutoff:3.500A) Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 298 through 323 removed outlier: 3.571A pdb=" N PHE R 302 " --> pdb=" O SER R 298 " (cutoff:3.500A) Proline residue: R 317 - end of helix removed outlier: 3.813A pdb=" N TYR R 320 " --> pdb=" O ASN R 316 " (cutoff:3.500A) Proline residue: R 321 - end of helix Processing helix chain 'R' and resid 324 through 335 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 5.778A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 9.769A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.579A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR A 360 " --> pdb=" O VAL A 287 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.865A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.662A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.809A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.534A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.783A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.436A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.237A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 8 removed outlier: 3.596A pdb=" N GLN N 3 " --> pdb=" O SER N 25 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER N 25 " --> pdb=" O GLN N 3 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR N 78 " --> pdb=" O ASP N 73 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12 removed outlier: 5.901A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) 421 hydrogen bonds defined for protein. 1215 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: 2.19 Time building geometry restraints manager: 2.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2664 1.34 - 1.46: 1881 1.46 - 1.58: 3639 1.58 - 1.70: 0 1.70 - 1.81: 80 Bond restraints: 8264 Sorted by residual: bond pdb=" CG SRO R 501 " pdb=" CD2 SRO R 501 " ideal model delta sigma weight residual 1.438 1.361 0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" CD2 SRO R 501 " pdb=" CE2 SRO R 501 " ideal model delta sigma weight residual 1.419 1.364 0.055 2.00e-02 2.50e+03 7.61e+00 bond pdb=" CB SRO R 501 " pdb=" CG SRO R 501 " ideal model delta sigma weight residual 1.498 1.544 -0.046 2.00e-02 2.50e+03 5.36e+00 bond pdb=" N PHE R 188 " pdb=" CA PHE R 188 " ideal model delta sigma weight residual 1.459 1.487 -0.027 1.19e-02 7.06e+03 5.33e+00 bond pdb=" CA SRO R 501 " pdb=" NZ SRO R 501 " ideal model delta sigma weight residual 1.469 1.426 0.043 2.00e-02 2.50e+03 4.63e+00 ... (remaining 8259 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 11140 2.50 - 5.01: 61 5.01 - 7.51: 1 7.51 - 10.02: 0 10.02 - 12.52: 2 Bond angle restraints: 11204 Sorted by residual: angle pdb=" CB SRO R 501 " pdb=" CG SRO R 501 " pdb=" CD1 SRO R 501 " ideal model delta sigma weight residual 128.15 115.63 12.52 3.00e+00 1.11e-01 1.74e+01 angle pdb=" CB SRO R 501 " pdb=" CG SRO R 501 " pdb=" CD2 SRO R 501 " ideal model delta sigma weight residual 125.70 136.10 -10.40 3.00e+00 1.11e-01 1.20e+01 angle pdb=" CG ARG R 333 " pdb=" CD ARG R 333 " pdb=" NE ARG R 333 " ideal model delta sigma weight residual 112.00 117.05 -5.05 2.20e+00 2.07e-01 5.28e+00 angle pdb=" CA PHE R 188 " pdb=" C PHE R 188 " pdb=" O PHE R 188 " ideal model delta sigma weight residual 120.82 118.53 2.29 1.05e+00 9.07e-01 4.75e+00 angle pdb=" CD ARG R 333 " pdb=" NE ARG R 333 " pdb=" CZ ARG R 333 " ideal model delta sigma weight residual 124.40 127.39 -2.99 1.40e+00 5.10e-01 4.57e+00 ... (remaining 11199 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 4523 17.94 - 35.87: 342 35.87 - 53.81: 56 53.81 - 71.74: 14 71.74 - 89.68: 9 Dihedral angle restraints: 4944 sinusoidal: 1940 harmonic: 3004 Sorted by residual: dihedral pdb=" CB CYS R 99 " pdb=" SG CYS R 99 " pdb=" SG CYS R 180 " pdb=" CB CYS R 180 " ideal model delta sinusoidal sigma weight residual 93.00 122.97 -29.97 1 1.00e+01 1.00e-02 1.28e+01 dihedral pdb=" CG ARG R 333 " pdb=" CD ARG R 333 " pdb=" NE ARG R 333 " pdb=" CZ ARG R 333 " ideal model delta sinusoidal sigma weight residual 90.00 41.25 48.75 2 1.50e+01 4.44e-03 1.21e+01 dihedral pdb=" CB GLU B 172 " pdb=" CG GLU B 172 " pdb=" CD GLU B 172 " pdb=" OE1 GLU B 172 " ideal model delta sinusoidal sigma weight residual 0.00 89.68 -89.68 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 4941 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 866 0.028 - 0.056: 268 0.056 - 0.084: 70 0.084 - 0.112: 46 0.112 - 0.140: 25 Chirality restraints: 1275 Sorted by residual: chirality pdb=" CA ILE B 93 " pdb=" N ILE B 93 " pdb=" C ILE B 93 " pdb=" CB ILE B 93 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.87e-01 chirality pdb=" CA ILE A 288 " pdb=" N ILE A 288 " pdb=" C ILE A 288 " pdb=" CB ILE A 288 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.83e-01 chirality pdb=" CA ILE B 229 " pdb=" N ILE B 229 " pdb=" C ILE B 229 " pdb=" CB ILE B 229 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.72e-01 ... (remaining 1272 not shown) Planarity restraints: 1430 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP B 76 " 0.005 2.00e-02 2.50e+03 1.12e-02 1.25e+00 pdb=" CG ASP B 76 " -0.019 2.00e-02 2.50e+03 pdb=" OD1 ASP B 76 " 0.007 2.00e-02 2.50e+03 pdb=" OD2 ASP B 76 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR R 320 " 0.018 5.00e-02 4.00e+02 2.75e-02 1.21e+00 pdb=" N PRO R 321 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO R 321 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO R 321 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 76 " 0.005 2.00e-02 2.50e+03 1.07e-02 1.15e+00 pdb=" C ASP B 76 " -0.019 2.00e-02 2.50e+03 pdb=" O ASP B 76 " 0.007 2.00e-02 2.50e+03 pdb=" N GLY B 77 " 0.006 2.00e-02 2.50e+03 ... (remaining 1427 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 69 2.58 - 3.16: 6781 3.16 - 3.74: 12370 3.74 - 4.32: 16556 4.32 - 4.90: 28968 Nonbonded interactions: 64744 Sorted by model distance: nonbonded pdb=" OG SER B 147 " pdb=" O MET B 188 " model vdw 1.996 3.040 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.045 3.040 nonbonded pdb=" O ASP B 333 " pdb=" OG SER B 334 " model vdw 2.118 3.040 nonbonded pdb=" OG1 THR R 280 " pdb=" ND2 ASN R 312 " model vdw 2.124 3.120 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.136 3.040 ... (remaining 64739 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: 0.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.770 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 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 0.077 8264 Z= 0.171 Angle : 0.484 12.523 11204 Z= 0.265 Chirality : 0.037 0.140 1275 Planarity : 0.002 0.027 1430 Dihedral : 13.541 89.676 2989 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.27), residues: 1021 helix: 2.76 (0.26), residues: 409 sheet: 1.45 (0.36), residues: 214 loop : 0.03 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 307 HIS 0.002 0.000 HIS A 357 PHE 0.012 0.001 PHE A 345 TYR 0.009 0.001 TYR A 311 ARG 0.015 0.000 ARG R 333 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.886 Fit side-chains revert: symmetry clash REVERT: G 37 LEU cc_start: 0.7692 (mt) cc_final: 0.7194 (mt) REVERT: G 47 GLU cc_start: 0.7823 (mp0) cc_final: 0.7565 (mp0) REVERT: N 68 PHE cc_start: 0.8319 (m-10) cc_final: 0.7980 (m-10) REVERT: R 316 ASN cc_start: 0.7502 (t0) cc_final: 0.7050 (m-40) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.2165 time to fit residues: 52.3825 Evaluate side-chains 142 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 51 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 58 optimal weight: 9.9990 chunk 90 optimal weight: 6.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 39 GLN R 312 ASN R 316 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8264 Z= 0.238 Angle : 0.563 6.216 11204 Z= 0.300 Chirality : 0.044 0.236 1275 Planarity : 0.004 0.037 1430 Dihedral : 4.452 56.748 1129 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.29 % Allowed : 6.99 % Favored : 90.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.26), residues: 1021 helix: 2.45 (0.26), residues: 415 sheet: 1.38 (0.35), residues: 208 loop : 0.01 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.007 0.001 HIS A 357 PHE 0.020 0.002 PHE A 212 TYR 0.020 0.002 TYR A 311 ARG 0.005 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 147 time to evaluate : 1.018 Fit side-chains REVERT: B 36 ASN cc_start: 0.8173 (m-40) cc_final: 0.7619 (t0) REVERT: B 226 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7758 (mt-10) REVERT: G 42 GLU cc_start: 0.7384 (pm20) cc_final: 0.6853 (pm20) REVERT: N 68 PHE cc_start: 0.8293 (m-10) cc_final: 0.7942 (m-10) outliers start: 20 outliers final: 17 residues processed: 156 average time/residue: 0.2254 time to fit residues: 46.6892 Evaluate side-chains 141 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain R residue 123 ASP Chi-restraints excluded: chain R residue 186 LEU Chi-restraints excluded: chain R residue 297 ILE Chi-restraints excluded: chain R residue 324 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 4.9990 chunk 28 optimal weight: 0.2980 chunk 75 optimal weight: 0.9990 chunk 61 optimal weight: 9.9990 chunk 25 optimal weight: 30.0000 chunk 90 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 31 ASN R 291 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8264 Z= 0.149 Angle : 0.493 6.184 11204 Z= 0.260 Chirality : 0.040 0.160 1275 Planarity : 0.004 0.037 1430 Dihedral : 4.204 44.228 1129 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.63 % Allowed : 8.36 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.26), residues: 1021 helix: 2.48 (0.26), residues: 419 sheet: 1.34 (0.34), residues: 215 loop : -0.02 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 297 HIS 0.004 0.000 HIS A 357 PHE 0.015 0.001 PHE A 212 TYR 0.023 0.001 TYR A 311 ARG 0.008 0.000 ARG R 329 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 145 time to evaluate : 0.950 Fit side-chains revert: symmetry clash REVERT: B 226 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7737 (mt-10) REVERT: N 68 PHE cc_start: 0.8391 (m-10) cc_final: 0.8077 (m-10) outliers start: 23 outliers final: 11 residues processed: 154 average time/residue: 0.2256 time to fit residues: 46.8682 Evaluate side-chains 140 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain R residue 123 ASP Chi-restraints excluded: chain R residue 186 LEU Chi-restraints excluded: chain R residue 268 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 91 optimal weight: 0.9980 chunk 96 optimal weight: 6.9990 chunk 86 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 80 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN B 340 ASN R 116 ASN R 312 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8264 Z= 0.286 Angle : 0.579 6.525 11204 Z= 0.307 Chirality : 0.044 0.209 1275 Planarity : 0.004 0.040 1430 Dihedral : 4.282 23.986 1129 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 4.12 % Allowed : 9.39 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.26), residues: 1021 helix: 2.28 (0.26), residues: 414 sheet: 0.92 (0.32), residues: 225 loop : -0.19 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 234 HIS 0.005 0.001 HIS A 357 PHE 0.019 0.002 PHE A 212 TYR 0.031 0.002 TYR A 311 ARG 0.005 0.000 ARG R 210 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 135 time to evaluate : 0.874 Fit side-chains revert: symmetry clash REVERT: B 226 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7922 (mt-10) REVERT: B 264 TYR cc_start: 0.8825 (m-80) cc_final: 0.8624 (m-10) REVERT: G 42 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7364 (pm20) REVERT: N 68 PHE cc_start: 0.8538 (m-10) cc_final: 0.8269 (m-10) REVERT: N 117 TYR cc_start: 0.8736 (m-80) cc_final: 0.8349 (m-80) REVERT: R 216 ARG cc_start: 0.7411 (mmp-170) cc_final: 0.7046 (mmp-170) REVERT: R 269 THR cc_start: 0.7855 (OUTLIER) cc_final: 0.7577 (m) REVERT: R 316 ASN cc_start: 0.7615 (t0) cc_final: 0.7124 (t0) outliers start: 36 outliers final: 21 residues processed: 152 average time/residue: 0.1972 time to fit residues: 41.3031 Evaluate side-chains 149 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain R residue 123 ASP Chi-restraints excluded: chain R residue 186 LEU Chi-restraints excluded: chain R residue 269 THR Chi-restraints excluded: chain R residue 297 ILE Chi-restraints excluded: chain R residue 324 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 4.9990 chunk 71 optimal weight: 0.4980 chunk 39 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 66 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 49 optimal weight: 0.2980 chunk 86 optimal weight: 0.7980 chunk 24 optimal weight: 10.0000 chunk 32 optimal weight: 0.0670 chunk 87 optimal weight: 8.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN N 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8264 Z= 0.147 Angle : 0.510 6.355 11204 Z= 0.269 Chirality : 0.040 0.154 1275 Planarity : 0.004 0.037 1430 Dihedral : 4.002 21.356 1129 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.86 % Allowed : 12.26 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.26), residues: 1021 helix: 2.40 (0.26), residues: 410 sheet: 1.00 (0.32), residues: 225 loop : -0.20 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 297 HIS 0.003 0.000 HIS A 357 PHE 0.014 0.001 PHE A 212 TYR 0.025 0.001 TYR A 311 ARG 0.004 0.000 ARG R 329 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 0.864 Fit side-chains revert: symmetry clash REVERT: B 275 SER cc_start: 0.8503 (m) cc_final: 0.8166 (m) REVERT: G 42 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7503 (pm20) REVERT: R 216 ARG cc_start: 0.7187 (mmp-170) cc_final: 0.6807 (mmp-170) outliers start: 25 outliers final: 16 residues processed: 148 average time/residue: 0.2118 time to fit residues: 43.0755 Evaluate side-chains 144 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain R residue 123 ASP Chi-restraints excluded: chain R residue 186 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 23 optimal weight: 20.0000 chunk 96 optimal weight: 6.9990 chunk 80 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 93 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN B 36 ASN B 88 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 8264 Z= 0.419 Angle : 0.657 8.728 11204 Z= 0.347 Chirality : 0.047 0.318 1275 Planarity : 0.005 0.041 1430 Dihedral : 4.539 26.464 1129 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.67 % Allowed : 12.14 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.26), residues: 1021 helix: 1.93 (0.26), residues: 410 sheet: 0.69 (0.32), residues: 232 loop : -0.34 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 234 HIS 0.006 0.001 HIS A 357 PHE 0.031 0.003 PHE N 68 TYR 0.031 0.002 TYR B 85 ARG 0.004 0.000 ARG R 210 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 139 time to evaluate : 0.897 Fit side-chains revert: symmetry clash REVERT: G 42 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7426 (pm20) REVERT: N 34 MET cc_start: 0.8635 (mmm) cc_final: 0.8383 (mmt) REVERT: R 269 THR cc_start: 0.8279 (OUTLIER) cc_final: 0.8008 (m) outliers start: 32 outliers final: 25 residues processed: 157 average time/residue: 0.2076 time to fit residues: 44.3276 Evaluate side-chains 153 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 126 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 29 VAL Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain R residue 123 ASP Chi-restraints excluded: chain R residue 186 LEU Chi-restraints excluded: chain R residue 269 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 96 optimal weight: 8.9990 chunk 60 optimal weight: 0.0770 chunk 58 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 overall best weight: 1.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8264 Z= 0.223 Angle : 0.561 7.653 11204 Z= 0.296 Chirality : 0.043 0.312 1275 Planarity : 0.004 0.037 1430 Dihedral : 4.325 24.484 1129 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.44 % Allowed : 13.97 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.27 (0.26), residues: 1021 helix: 2.06 (0.26), residues: 409 sheet: 0.61 (0.32), residues: 234 loop : -0.32 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 297 HIS 0.004 0.001 HIS A 357 PHE 0.016 0.002 PHE A 212 TYR 0.022 0.001 TYR A 311 ARG 0.012 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 132 time to evaluate : 0.891 Fit side-chains REVERT: G 38 MET cc_start: 0.7828 (mtm) cc_final: 0.7340 (mtm) REVERT: G 42 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7473 (pm20) REVERT: N 108 PHE cc_start: 0.8458 (OUTLIER) cc_final: 0.7751 (m-80) REVERT: R 269 THR cc_start: 0.8232 (OUTLIER) cc_final: 0.7945 (m) REVERT: R 316 ASN cc_start: 0.7572 (t0) cc_final: 0.6961 (t0) outliers start: 30 outliers final: 23 residues processed: 147 average time/residue: 0.2101 time to fit residues: 42.2318 Evaluate side-chains 151 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 29 VAL Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain R residue 123 ASP Chi-restraints excluded: chain R residue 186 LEU Chi-restraints excluded: chain R residue 207 THR Chi-restraints excluded: chain R residue 269 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 61 optimal weight: 0.0000 chunk 65 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 89 optimal weight: 0.8980 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8264 Z= 0.165 Angle : 0.534 8.072 11204 Z= 0.281 Chirality : 0.042 0.285 1275 Planarity : 0.004 0.042 1430 Dihedral : 4.105 24.086 1129 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.86 % Allowed : 14.43 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.26), residues: 1021 helix: 2.17 (0.26), residues: 410 sheet: 0.72 (0.33), residues: 223 loop : -0.32 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 297 HIS 0.003 0.000 HIS A 357 PHE 0.013 0.001 PHE A 212 TYR 0.020 0.001 TYR A 311 ARG 0.013 0.000 ARG R 329 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 129 time to evaluate : 0.965 Fit side-chains REVERT: A 392 GLU cc_start: 0.7985 (tp30) cc_final: 0.7729 (tp30) REVERT: B 275 SER cc_start: 0.8518 (m) cc_final: 0.8196 (m) REVERT: G 38 MET cc_start: 0.7782 (mtm) cc_final: 0.7309 (mtm) REVERT: G 42 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7460 (pm20) REVERT: R 269 THR cc_start: 0.8126 (OUTLIER) cc_final: 0.7794 (m) REVERT: R 316 ASN cc_start: 0.7539 (t0) cc_final: 0.6965 (t0) outliers start: 25 outliers final: 19 residues processed: 145 average time/residue: 0.2037 time to fit residues: 40.2463 Evaluate side-chains 142 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain R residue 186 LEU Chi-restraints excluded: chain R residue 207 THR Chi-restraints excluded: chain R residue 269 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 58 optimal weight: 0.3980 chunk 94 optimal weight: 0.8980 chunk 57 optimal weight: 10.0000 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN N 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8264 Z= 0.168 Angle : 0.552 11.219 11204 Z= 0.284 Chirality : 0.041 0.273 1275 Planarity : 0.004 0.036 1430 Dihedral : 4.056 24.177 1129 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.63 % Allowed : 15.12 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.26), residues: 1021 helix: 2.22 (0.26), residues: 410 sheet: 0.74 (0.33), residues: 223 loop : -0.32 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 297 HIS 0.003 0.001 HIS A 357 PHE 0.013 0.001 PHE A 212 TYR 0.019 0.001 TYR A 311 ARG 0.009 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 0.873 Fit side-chains REVERT: A 392 GLU cc_start: 0.8016 (tp30) cc_final: 0.7775 (tp30) REVERT: B 275 SER cc_start: 0.8499 (m) cc_final: 0.8182 (m) REVERT: G 38 MET cc_start: 0.7769 (mtm) cc_final: 0.7264 (mtm) REVERT: G 42 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7423 (pm20) REVERT: N 108 PHE cc_start: 0.8365 (OUTLIER) cc_final: 0.7323 (m-80) REVERT: R 269 THR cc_start: 0.8100 (OUTLIER) cc_final: 0.7758 (m) REVERT: R 316 ASN cc_start: 0.7534 (t0) cc_final: 0.6969 (t0) outliers start: 23 outliers final: 18 residues processed: 138 average time/residue: 0.2051 time to fit residues: 38.7829 Evaluate side-chains 143 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain R residue 186 LEU Chi-restraints excluded: chain R residue 207 THR Chi-restraints excluded: chain R residue 269 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 7.9990 chunk 66 optimal weight: 0.0030 chunk 99 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 chunk 79 optimal weight: 6.9990 chunk 8 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 overall best weight: 0.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8264 Z= 0.162 Angle : 0.546 9.851 11204 Z= 0.282 Chirality : 0.041 0.256 1275 Planarity : 0.004 0.036 1430 Dihedral : 3.998 24.120 1129 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.75 % Allowed : 15.35 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.43 (0.26), residues: 1021 helix: 2.25 (0.26), residues: 410 sheet: 0.78 (0.33), residues: 223 loop : -0.34 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 297 HIS 0.003 0.000 HIS A 357 PHE 0.012 0.001 PHE A 212 TYR 0.019 0.001 TYR A 311 ARG 0.009 0.000 ARG B 219 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 0.892 Fit side-chains REVERT: A 392 GLU cc_start: 0.7974 (tp30) cc_final: 0.7760 (tp30) REVERT: B 275 SER cc_start: 0.8514 (m) cc_final: 0.8197 (m) REVERT: G 38 MET cc_start: 0.7743 (mtm) cc_final: 0.7203 (mtm) REVERT: G 42 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7424 (pm20) REVERT: N 108 PHE cc_start: 0.8355 (OUTLIER) cc_final: 0.7329 (m-80) REVERT: R 269 THR cc_start: 0.7976 (OUTLIER) cc_final: 0.7640 (m) REVERT: R 316 ASN cc_start: 0.7560 (t0) cc_final: 0.7021 (t0) outliers start: 24 outliers final: 20 residues processed: 145 average time/residue: 0.2056 time to fit residues: 40.7817 Evaluate side-chains 147 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain R residue 186 LEU Chi-restraints excluded: chain R residue 207 THR Chi-restraints excluded: chain R residue 269 THR Chi-restraints excluded: chain R residue 297 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 57 optimal weight: 9.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 291 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.158935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.121855 restraints weight = 10710.956| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.56 r_work: 0.3286 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8264 Z= 0.165 Angle : 0.545 9.711 11204 Z= 0.281 Chirality : 0.041 0.247 1275 Planarity : 0.004 0.036 1430 Dihedral : 3.973 24.303 1129 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.52 % Allowed : 15.81 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.26), residues: 1021 helix: 2.27 (0.26), residues: 411 sheet: 0.85 (0.33), residues: 221 loop : -0.35 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 297 HIS 0.002 0.000 HIS A 357 PHE 0.012 0.001 PHE A 212 TYR 0.019 0.001 TYR A 311 ARG 0.009 0.000 ARG B 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1899.96 seconds wall clock time: 35 minutes 28.58 seconds (2128.58 seconds total)