Starting phenix.real_space_refine on Wed Feb 14 23:09:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d44_27174/02_2024/8d44_27174.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d44_27174/02_2024/8d44_27174.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d44_27174/02_2024/8d44_27174.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d44_27174/02_2024/8d44_27174.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d44_27174/02_2024/8d44_27174.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d44_27174/02_2024/8d44_27174.pdb" } resolution = 2.8 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= 0.055 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 56 5.16 5 C 6568 2.51 5 N 1864 2.21 5 O 1984 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D GLU 82": "OE1" <-> "OE2" Residue "D GLU 100": "OE1" <-> "OE2" Residue "D GLU 326": "OE1" <-> "OE2" Residue "C GLU 200": "OE1" <-> "OE2" Residue "C GLU 322": "OE1" <-> "OE2" Residue "B GLU 15": "OE1" <-> "OE2" Residue "B GLU 61": "OE1" <-> "OE2" Residue "B GLU 100": "OE1" <-> "OE2" Residue "B GLU 200": "OE1" <-> "OE2" Residue "B GLU 277": "OE1" <-> "OE2" Residue "A GLU 53": "OE1" <-> "OE2" Residue "A GLU 100": "OE1" <-> "OE2" Residue "A GLU 200": "OE1" <-> "OE2" Residue "A GLU 277": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10472 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2618 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 329} Chain: "C" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2618 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 329} Chain: "B" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2618 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 329} Chain: "A" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2618 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 329} Time building chain proxies: 5.73, per 1000 atoms: 0.55 Number of scatterers: 10472 At special positions: 0 Unit cell: (105.93, 82.39, 99.51, 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 56 16.00 O 1984 8.00 N 1864 7.00 C 6568 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 4.16 Conformation dependent library (CDL) restraints added in 1.9 seconds 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2528 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 8 sheets defined 52.3% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'D' and resid 9 through 24 removed outlier: 3.783A pdb=" N VAL D 24 " --> pdb=" O ALA D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 46 removed outlier: 4.040A pdb=" N ARG D 46 " --> pdb=" O ASN D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 64 Processing helix chain 'D' and resid 80 through 85 removed outlier: 3.882A pdb=" N TYR D 85 " --> pdb=" O HIS D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 101 Processing helix chain 'D' and resid 130 through 141 removed outlier: 3.793A pdb=" N ARG D 134 " --> pdb=" O GLY D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 182 Processing helix chain 'D' and resid 198 through 220 Processing helix chain 'D' and resid 223 through 227 removed outlier: 3.560A pdb=" N THR D 227 " --> pdb=" O LEU D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 259 Processing helix chain 'D' and resid 276 through 289 Processing helix chain 'D' and resid 308 through 315 Processing helix chain 'D' and resid 320 through 338 removed outlier: 3.686A pdb=" N ARG D 331 " --> pdb=" O ALA D 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 24 removed outlier: 3.786A pdb=" N VAL C 24 " --> pdb=" O ALA C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 45 Processing helix chain 'C' and resid 46 through 48 No H-bonds generated for 'chain 'C' and resid 46 through 48' Processing helix chain 'C' and resid 52 through 65 Processing helix chain 'C' and resid 80 through 85 removed outlier: 4.004A pdb=" N TYR C 85 " --> pdb=" O HIS C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 101 Processing helix chain 'C' and resid 130 through 141 Processing helix chain 'C' and resid 160 through 182 Processing helix chain 'C' and resid 198 through 220 Processing helix chain 'C' and resid 223 through 227 removed outlier: 3.719A pdb=" N THR C 227 " --> pdb=" O LEU C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 261 removed outlier: 3.547A pdb=" N ARG C 259 " --> pdb=" O THR C 255 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR C 260 " --> pdb=" O ALA C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 289 Processing helix chain 'C' and resid 308 through 315 Processing helix chain 'C' and resid 320 through 338 Processing helix chain 'B' and resid 9 through 24 removed outlier: 3.794A pdb=" N VAL B 24 " --> pdb=" O ALA B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 45 Processing helix chain 'B' and resid 46 through 48 No H-bonds generated for 'chain 'B' and resid 46 through 48' Processing helix chain 'B' and resid 52 through 65 Processing helix chain 'B' and resid 67 through 72 removed outlier: 3.712A pdb=" N ASN B 71 " --> pdb=" O SER B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 85 removed outlier: 4.083A pdb=" N TYR B 85 " --> pdb=" O HIS B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 101 Processing helix chain 'B' and resid 130 through 141 Processing helix chain 'B' and resid 160 through 181 Processing helix chain 'B' and resid 198 through 220 Processing helix chain 'B' and resid 223 through 227 removed outlier: 3.723A pdb=" N THR B 227 " --> pdb=" O LEU B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 259 removed outlier: 3.625A pdb=" N ARG B 259 " --> pdb=" O THR B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 289 Processing helix chain 'B' and resid 308 through 315 Processing helix chain 'B' and resid 321 through 340 Processing helix chain 'A' and resid 9 through 24 removed outlier: 3.771A pdb=" N VAL A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 45 Processing helix chain 'A' and resid 46 through 48 No H-bonds generated for 'chain 'A' and resid 46 through 48' Processing helix chain 'A' and resid 52 through 65 Processing helix chain 'A' and resid 67 through 72 removed outlier: 3.676A pdb=" N ASN A 71 " --> pdb=" O SER A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 85 removed outlier: 3.961A pdb=" N TYR A 85 " --> pdb=" O HIS A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 101 Processing helix chain 'A' and resid 130 through 141 Processing helix chain 'A' and resid 160 through 182 Processing helix chain 'A' and resid 198 through 220 Processing helix chain 'A' and resid 223 through 227 removed outlier: 3.720A pdb=" N THR A 227 " --> pdb=" O LEU A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 259 removed outlier: 3.617A pdb=" N ARG A 259 " --> pdb=" O THR A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 289 Processing helix chain 'A' and resid 308 through 315 Processing helix chain 'A' and resid 321 through 338 Processing sheet with id=AA1, first strand: chain 'D' and resid 29 through 32 removed outlier: 6.970A pdb=" N GLY D 29 " --> pdb=" O GLY D 75 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N VAL D 77 " --> pdb=" O GLY D 29 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU D 31 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N LEU D 79 " --> pdb=" O LEU D 31 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N GLY D 75 " --> pdb=" O VAL D 104 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N GLY D 106 " --> pdb=" O GLY D 75 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N VAL D 77 " --> pdb=" O GLY D 106 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N LYS D 108 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N LEU D 79 " --> pdb=" O LYS D 108 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL D 105 " --> pdb=" O PHE D 145 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N LYS D 147 " --> pdb=" O VAL D 105 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE D 107 " --> pdb=" O LYS D 147 " (cutoff:3.500A) removed outlier: 8.552A pdb=" N ARG D 149 " --> pdb=" O ILE D 107 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N LEU D 229 " --> pdb=" O CYS D 269 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ILE D 268 " --> pdb=" O SER D 299 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N SER D 301 " --> pdb=" O ILE D 268 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N PHE D 270 " --> pdb=" O SER D 301 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 112 through 115 Processing sheet with id=AA3, first strand: chain 'C' and resid 29 through 32 removed outlier: 7.067A pdb=" N GLY C 29 " --> pdb=" O GLY C 75 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N VAL C 77 " --> pdb=" O GLY C 29 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU C 31 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N LEU C 79 " --> pdb=" O LEU C 31 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N GLY C 75 " --> pdb=" O VAL C 104 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N GLY C 106 " --> pdb=" O GLY C 75 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N VAL C 77 " --> pdb=" O GLY C 106 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N LYS C 108 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N LEU C 79 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N VAL C 105 " --> pdb=" O PHE C 145 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N LYS C 147 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE C 107 " --> pdb=" O LYS C 147 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N ARG C 149 " --> pdb=" O ILE C 107 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N LEU C 229 " --> pdb=" O CYS C 269 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ILE C 268 " --> pdb=" O SER C 299 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N SER C 301 " --> pdb=" O ILE C 268 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N PHE C 270 " --> pdb=" O SER C 301 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 112 through 115 Processing sheet with id=AA5, first strand: chain 'B' and resid 29 through 32 removed outlier: 7.088A pdb=" N GLY B 29 " --> pdb=" O GLY B 75 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N VAL B 77 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU B 31 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N LEU B 79 " --> pdb=" O LEU B 31 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL B 105 " --> pdb=" O PHE B 145 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N LYS B 147 " --> pdb=" O VAL B 105 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE B 107 " --> pdb=" O LYS B 147 " (cutoff:3.500A) removed outlier: 8.538A pdb=" N ARG B 149 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N LEU B 229 " --> pdb=" O CYS B 269 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ILE B 268 " --> pdb=" O SER B 299 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N SER B 301 " --> pdb=" O ILE B 268 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N PHE B 270 " --> pdb=" O SER B 301 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 112 through 115 Processing sheet with id=AA7, first strand: chain 'A' and resid 29 through 32 removed outlier: 7.059A pdb=" N GLY A 29 " --> pdb=" O GLY A 75 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N VAL A 77 " --> pdb=" O GLY A 29 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU A 31 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N LEU A 79 " --> pdb=" O LEU A 31 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL A 105 " --> pdb=" O PHE A 145 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N LYS A 147 " --> pdb=" O VAL A 105 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE A 107 " --> pdb=" O LYS A 147 " (cutoff:3.500A) removed outlier: 8.529A pdb=" N ARG A 149 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N LEU A 229 " --> pdb=" O CYS A 269 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ILE A 268 " --> pdb=" O SER A 299 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N SER A 301 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N PHE A 270 " --> pdb=" O SER A 301 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 112 through 115 551 hydrogen bonds defined for protein. 1611 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: 2.77 Time building geometry restraints manager: 4.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2220 1.33 - 1.45: 2245 1.45 - 1.57: 6103 1.57 - 1.69: 0 1.69 - 1.81: 80 Bond restraints: 10648 Sorted by residual: bond pdb=" C MET B 251 " pdb=" O MET B 251 " ideal model delta sigma weight residual 1.236 1.206 0.031 1.15e-02 7.56e+03 7.20e+00 bond pdb=" CA ALA B 250 " pdb=" C ALA B 250 " ideal model delta sigma weight residual 1.524 1.495 0.029 1.27e-02 6.20e+03 5.05e+00 bond pdb=" CA MET B 251 " pdb=" C MET B 251 " ideal model delta sigma weight residual 1.524 1.497 0.026 1.27e-02 6.20e+03 4.33e+00 bond pdb=" C THR B 253 " pdb=" O THR B 253 " ideal model delta sigma weight residual 1.236 1.216 0.021 1.15e-02 7.56e+03 3.33e+00 bond pdb=" CA ALA B 250 " pdb=" CB ALA B 250 " ideal model delta sigma weight residual 1.529 1.506 0.023 1.55e-02 4.16e+03 2.25e+00 ... (remaining 10643 not shown) Histogram of bond angle deviations from ideal: 99.89 - 106.70: 258 106.70 - 113.52: 5931 113.52 - 120.33: 3754 120.33 - 127.15: 4358 127.15 - 133.96: 95 Bond angle restraints: 14396 Sorted by residual: angle pdb=" CB MET A 251 " pdb=" CG MET A 251 " pdb=" SD MET A 251 " ideal model delta sigma weight residual 112.70 123.33 -10.63 3.00e+00 1.11e-01 1.26e+01 angle pdb=" CA GLN C 90 " pdb=" CB GLN C 90 " pdb=" CG GLN C 90 " ideal model delta sigma weight residual 114.10 120.93 -6.83 2.00e+00 2.50e-01 1.17e+01 angle pdb=" CB GLN B 58 " pdb=" CG GLN B 58 " pdb=" CD GLN B 58 " ideal model delta sigma weight residual 112.60 117.75 -5.15 1.70e+00 3.46e-01 9.19e+00 angle pdb=" CB GLU D 322 " pdb=" CG GLU D 322 " pdb=" CD GLU D 322 " ideal model delta sigma weight residual 112.60 117.59 -4.99 1.70e+00 3.46e-01 8.62e+00 angle pdb=" CB GLU D 326 " pdb=" CG GLU D 326 " pdb=" CD GLU D 326 " ideal model delta sigma weight residual 112.60 117.53 -4.93 1.70e+00 3.46e-01 8.40e+00 ... (remaining 14391 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 5621 17.79 - 35.59: 623 35.59 - 53.38: 196 53.38 - 71.17: 33 71.17 - 88.97: 15 Dihedral angle restraints: 6488 sinusoidal: 2556 harmonic: 3932 Sorted by residual: dihedral pdb=" CA ALA C 338 " pdb=" C ALA C 338 " pdb=" N ALA C 339 " pdb=" CA ALA C 339 " ideal model delta harmonic sigma weight residual 180.00 162.37 17.63 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA GLN A 111 " pdb=" C GLN A 111 " pdb=" N GLY A 112 " pdb=" CA GLY A 112 " ideal model delta harmonic sigma weight residual 180.00 163.26 16.74 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CA VAL C 24 " pdb=" C VAL C 24 " pdb=" N ALA C 25 " pdb=" CA ALA C 25 " ideal model delta harmonic sigma weight residual -180.00 -163.58 -16.42 0 5.00e+00 4.00e-02 1.08e+01 ... (remaining 6485 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 940 0.027 - 0.055: 387 0.055 - 0.082: 158 0.082 - 0.110: 106 0.110 - 0.137: 33 Chirality restraints: 1624 Sorted by residual: chirality pdb=" CA TYR D 214 " pdb=" N TYR D 214 " pdb=" C TYR D 214 " pdb=" CB TYR D 214 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.72e-01 chirality pdb=" CA VAL C 187 " pdb=" N VAL C 187 " pdb=" C VAL C 187 " pdb=" CB VAL C 187 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 chirality pdb=" CA VAL A 187 " pdb=" N VAL A 187 " pdb=" C VAL A 187 " pdb=" CB VAL A 187 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.34e-01 ... (remaining 1621 not shown) Planarity restraints: 1888 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 114 " -0.047 5.00e-02 4.00e+02 7.14e-02 8.15e+00 pdb=" N PRO B 115 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO B 115 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 115 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 114 " -0.045 5.00e-02 4.00e+02 6.84e-02 7.49e+00 pdb=" N PRO C 115 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO C 115 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 115 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 114 " 0.042 5.00e-02 4.00e+02 6.47e-02 6.69e+00 pdb=" N PRO A 115 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 115 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 115 " 0.035 5.00e-02 4.00e+02 ... (remaining 1885 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1770 2.77 - 3.30: 9787 3.30 - 3.83: 18980 3.83 - 4.37: 22189 4.37 - 4.90: 37800 Nonbonded interactions: 90526 Sorted by model distance: nonbonded pdb=" O GLU D 61 " pdb=" OG SER D 65 " model vdw 2.232 2.440 nonbonded pdb=" O LEU A 116 " pdb=" OG1 THR A 119 " model vdw 2.244 2.440 nonbonded pdb=" O LEU B 116 " pdb=" OG1 THR B 119 " model vdw 2.250 2.440 nonbonded pdb=" NH1 ARG B 149 " pdb=" OE1 GLU B 190 " model vdw 2.254 2.520 nonbonded pdb=" O LEU D 116 " pdb=" OG1 THR D 119 " model vdw 2.272 2.440 ... (remaining 90521 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.740 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: 6.360 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 30.420 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.050 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:10.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10648 Z= 0.251 Angle : 0.628 10.635 14396 Z= 0.353 Chirality : 0.043 0.137 1624 Planarity : 0.006 0.071 1888 Dihedral : 16.987 88.965 3960 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 1.73 % Allowed : 15.82 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.38 (0.23), residues: 1364 helix: 1.65 (0.19), residues: 668 sheet: -1.68 (0.29), residues: 248 loop : -0.60 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 148 HIS 0.006 0.001 HIS C 197 PHE 0.012 0.002 PHE C 145 TYR 0.019 0.002 TYR B 174 ARG 0.003 0.000 ARG B 57 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 124 time to evaluate : 1.242 Fit side-chains REVERT: D 110 ASP cc_start: 0.8200 (p0) cc_final: 0.7981 (p0) REVERT: C 296 TRP cc_start: 0.8654 (OUTLIER) cc_final: 0.8367 (m-90) REVERT: B 110 ASP cc_start: 0.8277 (p0) cc_final: 0.7942 (p0) REVERT: A 110 ASP cc_start: 0.8345 (p0) cc_final: 0.8119 (p0) outliers start: 19 outliers final: 12 residues processed: 138 average time/residue: 1.1952 time to fit residues: 178.5751 Evaluate side-chains 129 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 116 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 82 GLU Chi-restraints excluded: chain D residue 129 ASP Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 296 TRP Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 202 CYS Chi-restraints excluded: chain C residue 251 MET Chi-restraints excluded: chain C residue 296 TRP Chi-restraints excluded: chain B residue 296 TRP Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 202 CYS Chi-restraints excluded: chain A residue 296 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 106 optimal weight: 7.9990 chunk 41 optimal weight: 0.9990 chunk 64 optimal weight: 0.0980 chunk 79 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 GLN C 258 HIS ** C 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 HIS A 258 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 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 0.030 10648 Z= 0.276 Angle : 0.551 4.906 14396 Z= 0.295 Chirality : 0.042 0.136 1624 Planarity : 0.005 0.053 1888 Dihedral : 5.558 53.346 1486 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.27 % Allowed : 14.82 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.68 (0.23), residues: 1364 helix: 1.98 (0.19), residues: 672 sheet: -1.77 (0.29), residues: 248 loop : -0.47 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 148 HIS 0.005 0.001 HIS C 197 PHE 0.013 0.002 PHE B 145 TYR 0.017 0.002 TYR C 214 ARG 0.002 0.000 ARG A 173 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 125 time to evaluate : 1.193 Fit side-chains REVERT: D 110 ASP cc_start: 0.8141 (p0) cc_final: 0.7918 (p0) REVERT: C 80 PHE cc_start: 0.7300 (t80) cc_final: 0.6984 (t80) REVERT: C 174 TYR cc_start: 0.8801 (OUTLIER) cc_final: 0.8123 (t80) REVERT: C 251 MET cc_start: 0.7572 (tpp) cc_final: 0.7074 (tpp) REVERT: B 110 ASP cc_start: 0.8278 (p0) cc_final: 0.8057 (p0) REVERT: B 174 TYR cc_start: 0.8749 (OUTLIER) cc_final: 0.8079 (t80) REVERT: A 174 TYR cc_start: 0.8793 (OUTLIER) cc_final: 0.8117 (t80) outliers start: 25 outliers final: 11 residues processed: 144 average time/residue: 1.1231 time to fit residues: 175.5087 Evaluate side-chains 130 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 116 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 296 TRP Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 275 MET Chi-restraints excluded: chain C residue 296 TRP Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 174 TYR Chi-restraints excluded: chain B residue 296 TRP Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 174 TYR Chi-restraints excluded: chain A residue 296 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 0.0000 chunk 38 optimal weight: 0.9980 chunk 102 optimal weight: 0.0870 chunk 84 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 133 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 overall best weight: 0.5562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 90 GLN D 258 HIS C 90 GLN C 258 HIS B 258 HIS A 258 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.0809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10648 Z= 0.190 Angle : 0.485 5.070 14396 Z= 0.260 Chirality : 0.040 0.122 1624 Planarity : 0.005 0.048 1888 Dihedral : 4.856 45.294 1470 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 1.82 % Allowed : 16.09 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.98 (0.23), residues: 1364 helix: 2.30 (0.19), residues: 672 sheet: -1.78 (0.29), residues: 248 loop : -0.38 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 148 HIS 0.004 0.001 HIS C 197 PHE 0.013 0.001 PHE B 145 TYR 0.012 0.001 TYR C 214 ARG 0.003 0.000 ARG D 57 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 125 time to evaluate : 1.257 Fit side-chains REVERT: D 174 TYR cc_start: 0.8647 (OUTLIER) cc_final: 0.8001 (t80) REVERT: C 80 PHE cc_start: 0.7296 (t80) cc_final: 0.7039 (t80) REVERT: C 174 TYR cc_start: 0.8651 (OUTLIER) cc_final: 0.8004 (t80) REVERT: C 248 GLN cc_start: 0.8003 (mt0) cc_final: 0.7718 (mt0) REVERT: C 251 MET cc_start: 0.7599 (tpp) cc_final: 0.7048 (tpp) REVERT: B 110 ASP cc_start: 0.8188 (p0) cc_final: 0.7891 (p0) REVERT: B 174 TYR cc_start: 0.8615 (OUTLIER) cc_final: 0.7992 (t80) REVERT: A 174 TYR cc_start: 0.8672 (OUTLIER) cc_final: 0.8018 (t80) REVERT: A 251 MET cc_start: 0.7535 (tpp) cc_final: 0.7298 (tpp) outliers start: 20 outliers final: 7 residues processed: 142 average time/residue: 1.2687 time to fit residues: 195.2495 Evaluate side-chains 125 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 114 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 296 TRP Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 275 MET Chi-restraints excluded: chain C residue 296 TRP Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 174 TYR Chi-restraints excluded: chain B residue 296 TRP Chi-restraints excluded: chain A residue 174 TYR Chi-restraints excluded: chain A residue 296 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 64 optimal weight: 0.0270 chunk 13 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 83 optimal weight: 0.4980 chunk 124 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 overall best weight: 0.6640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 90 GLN C 258 HIS B 258 HIS A 258 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.0932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10648 Z= 0.210 Angle : 0.495 5.000 14396 Z= 0.265 Chirality : 0.040 0.126 1624 Planarity : 0.004 0.048 1888 Dihedral : 4.832 46.440 1468 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 2.18 % Allowed : 16.36 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.10 (0.23), residues: 1364 helix: 2.42 (0.19), residues: 672 sheet: -1.65 (0.32), residues: 212 loop : -0.54 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 148 HIS 0.008 0.001 HIS D 258 PHE 0.013 0.002 PHE B 59 TYR 0.014 0.002 TYR B 214 ARG 0.003 0.000 ARG D 57 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 122 time to evaluate : 1.803 Fit side-chains REVERT: D 174 TYR cc_start: 0.8680 (OUTLIER) cc_final: 0.7974 (t80) REVERT: C 174 TYR cc_start: 0.8693 (OUTLIER) cc_final: 0.8092 (t80) REVERT: C 251 MET cc_start: 0.7598 (tpp) cc_final: 0.7035 (tpp) REVERT: B 110 ASP cc_start: 0.8085 (p0) cc_final: 0.7812 (p0) REVERT: B 174 TYR cc_start: 0.8645 (OUTLIER) cc_final: 0.8057 (t80) REVERT: B 251 MET cc_start: 0.7177 (tpp) cc_final: 0.6633 (tpp) REVERT: A 140 LYS cc_start: 0.8010 (OUTLIER) cc_final: 0.7789 (mtpt) REVERT: A 174 TYR cc_start: 0.8721 (OUTLIER) cc_final: 0.8047 (t80) REVERT: A 251 MET cc_start: 0.7603 (tpp) cc_final: 0.7326 (tpp) outliers start: 24 outliers final: 8 residues processed: 143 average time/residue: 1.1815 time to fit residues: 184.2837 Evaluate side-chains 127 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 114 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 126 GLN Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 296 TRP Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 296 TRP Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 174 TYR Chi-restraints excluded: chain B residue 296 TRP Chi-restraints excluded: chain A residue 140 LYS Chi-restraints excluded: chain A residue 174 TYR Chi-restraints excluded: chain A residue 296 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 220 HIS C 90 GLN C 220 HIS C 258 HIS ** C 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 GLN B 258 HIS A 258 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 10648 Z= 0.447 Angle : 0.646 6.358 14396 Z= 0.343 Chirality : 0.047 0.157 1624 Planarity : 0.005 0.048 1888 Dihedral : 5.398 48.740 1468 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 3.18 % Allowed : 16.00 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.66 (0.23), residues: 1364 helix: 1.97 (0.19), residues: 676 sheet: -1.78 (0.29), residues: 244 loop : -0.53 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP C 148 HIS 0.011 0.002 HIS D 258 PHE 0.017 0.003 PHE B 145 TYR 0.021 0.002 TYR D 214 ARG 0.003 0.001 ARG B 43 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 113 time to evaluate : 1.066 Fit side-chains REVERT: D 174 TYR cc_start: 0.8885 (OUTLIER) cc_final: 0.8138 (t80) REVERT: C 174 TYR cc_start: 0.8893 (OUTLIER) cc_final: 0.8179 (t80) REVERT: C 251 MET cc_start: 0.7625 (tpp) cc_final: 0.7131 (tpp) REVERT: B 18 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7782 (mt-10) REVERT: B 174 TYR cc_start: 0.8846 (OUTLIER) cc_final: 0.8166 (t80) REVERT: B 190 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7683 (tt0) REVERT: A 174 TYR cc_start: 0.8870 (OUTLIER) cc_final: 0.8152 (t80) REVERT: A 200 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7583 (mp0) REVERT: A 251 MET cc_start: 0.7731 (tpp) cc_final: 0.7393 (tpp) outliers start: 35 outliers final: 13 residues processed: 137 average time/residue: 1.2649 time to fit residues: 186.4513 Evaluate side-chains 122 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 103 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 275 MET Chi-restraints excluded: chain D residue 296 TRP Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 296 TRP Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 174 TYR Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 296 TRP Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 174 TYR Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 296 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 109 optimal weight: 0.3980 chunk 60 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 chunk 126 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 90 GLN D 258 HIS C 90 GLN C 221 HIS C 258 HIS B 258 HIS A 258 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10648 Z= 0.201 Angle : 0.500 5.017 14396 Z= 0.270 Chirality : 0.040 0.126 1624 Planarity : 0.005 0.047 1888 Dihedral : 4.996 49.375 1468 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.09 % Allowed : 17.36 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.11 (0.23), residues: 1364 helix: 2.41 (0.19), residues: 672 sheet: -1.70 (0.29), residues: 244 loop : -0.34 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 148 HIS 0.005 0.001 HIS D 258 PHE 0.014 0.002 PHE B 145 TYR 0.014 0.001 TYR A 214 ARG 0.002 0.000 ARG D 57 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 119 time to evaluate : 1.146 Fit side-chains REVERT: D 174 TYR cc_start: 0.8668 (OUTLIER) cc_final: 0.7986 (t80) REVERT: C 174 TYR cc_start: 0.8697 (OUTLIER) cc_final: 0.8030 (t80) REVERT: C 251 MET cc_start: 0.7625 (tpp) cc_final: 0.7153 (tpp) REVERT: B 174 TYR cc_start: 0.8644 (OUTLIER) cc_final: 0.7989 (t80) REVERT: B 190 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7637 (tt0) REVERT: B 251 MET cc_start: 0.7138 (tpp) cc_final: 0.6638 (tpp) REVERT: A 174 TYR cc_start: 0.8709 (OUTLIER) cc_final: 0.8038 (t80) REVERT: A 251 MET cc_start: 0.7726 (tpp) cc_final: 0.7369 (tpp) outliers start: 23 outliers final: 9 residues processed: 139 average time/residue: 1.1718 time to fit residues: 176.4083 Evaluate side-chains 124 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 110 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 296 TRP Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 275 MET Chi-restraints excluded: chain C residue 296 TRP Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 174 TYR Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 296 TRP Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 174 TYR Chi-restraints excluded: chain A residue 296 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 0.5980 chunk 74 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 131 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 81 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 258 HIS C 90 GLN C 258 HIS B 258 HIS A 258 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10648 Z= 0.232 Angle : 0.514 4.989 14396 Z= 0.276 Chirality : 0.041 0.129 1624 Planarity : 0.005 0.047 1888 Dihedral : 5.017 49.508 1468 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.09 % Allowed : 17.64 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.15 (0.23), residues: 1364 helix: 2.45 (0.19), residues: 672 sheet: -1.65 (0.29), residues: 244 loop : -0.35 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 148 HIS 0.004 0.001 HIS D 258 PHE 0.013 0.002 PHE B 145 TYR 0.015 0.002 TYR D 214 ARG 0.003 0.000 ARG D 57 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 114 time to evaluate : 1.098 Fit side-chains REVERT: D 174 TYR cc_start: 0.8704 (OUTLIER) cc_final: 0.8012 (t80) REVERT: C 174 TYR cc_start: 0.8730 (OUTLIER) cc_final: 0.8111 (t80) REVERT: C 251 MET cc_start: 0.7596 (tpp) cc_final: 0.7126 (tpp) REVERT: B 174 TYR cc_start: 0.8706 (OUTLIER) cc_final: 0.8114 (t80) REVERT: B 190 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7644 (tt0) REVERT: B 251 MET cc_start: 0.7135 (tpp) cc_final: 0.6640 (tpp) REVERT: A 126 GLN cc_start: 0.8951 (OUTLIER) cc_final: 0.8710 (mt0) REVERT: A 174 TYR cc_start: 0.8744 (OUTLIER) cc_final: 0.8067 (t80) REVERT: A 251 MET cc_start: 0.7707 (tpp) cc_final: 0.7416 (tpp) outliers start: 23 outliers final: 10 residues processed: 134 average time/residue: 1.1678 time to fit residues: 169.5824 Evaluate side-chains 125 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 109 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 296 TRP Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 275 MET Chi-restraints excluded: chain C residue 296 TRP Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 174 TYR Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 296 TRP Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 126 GLN Chi-restraints excluded: chain A residue 174 TYR Chi-restraints excluded: chain A residue 296 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 83 optimal weight: 0.6980 chunk 89 optimal weight: 0.5980 chunk 64 optimal weight: 0.0010 chunk 12 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 125 optimal weight: 4.9990 chunk 114 optimal weight: 0.6980 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 258 HIS C 90 GLN C 258 HIS B 258 HIS A 258 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10648 Z= 0.191 Angle : 0.483 5.070 14396 Z= 0.260 Chirality : 0.040 0.123 1624 Planarity : 0.004 0.047 1888 Dihedral : 4.857 49.609 1468 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.00 % Allowed : 17.64 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.29 (0.23), residues: 1364 helix: 2.60 (0.19), residues: 672 sheet: -1.55 (0.32), residues: 212 loop : -0.50 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 148 HIS 0.004 0.001 HIS D 258 PHE 0.013 0.001 PHE B 145 TYR 0.012 0.001 TYR D 214 ARG 0.004 0.000 ARG D 57 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 118 time to evaluate : 1.142 Fit side-chains REVERT: D 110 ASP cc_start: 0.8096 (p0) cc_final: 0.7887 (p0) REVERT: D 174 TYR cc_start: 0.8614 (OUTLIER) cc_final: 0.7932 (t80) REVERT: C 174 TYR cc_start: 0.8638 (OUTLIER) cc_final: 0.8040 (t80) REVERT: C 251 MET cc_start: 0.7596 (tpp) cc_final: 0.7147 (tpp) REVERT: B 174 TYR cc_start: 0.8612 (OUTLIER) cc_final: 0.8019 (t80) REVERT: B 190 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7629 (tt0) REVERT: B 251 MET cc_start: 0.7240 (tpp) cc_final: 0.6749 (tpp) REVERT: A 126 GLN cc_start: 0.8940 (OUTLIER) cc_final: 0.8684 (mt0) REVERT: A 174 TYR cc_start: 0.8654 (OUTLIER) cc_final: 0.7986 (t80) REVERT: A 251 MET cc_start: 0.7718 (tpp) cc_final: 0.7421 (tpp) outliers start: 22 outliers final: 8 residues processed: 138 average time/residue: 1.2345 time to fit residues: 183.7512 Evaluate side-chains 124 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 110 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 296 TRP Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 296 TRP Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 174 TYR Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 296 TRP Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 126 GLN Chi-restraints excluded: chain A residue 174 TYR Chi-restraints excluded: chain A residue 296 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 0.9980 chunk 125 optimal weight: 0.0980 chunk 73 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 chunk 110 optimal weight: 0.0060 chunk 115 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 129 optimal weight: 0.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 258 HIS C 90 GLN C 258 HIS B 258 HIS A 258 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10648 Z= 0.203 Angle : 0.493 5.023 14396 Z= 0.265 Chirality : 0.040 0.124 1624 Planarity : 0.004 0.047 1888 Dihedral : 4.854 49.718 1468 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 1.73 % Allowed : 18.09 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 (0.23), residues: 1364 helix: 2.63 (0.19), residues: 672 sheet: -1.54 (0.32), residues: 212 loop : -0.50 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 148 HIS 0.004 0.001 HIS C 197 PHE 0.013 0.001 PHE B 145 TYR 0.013 0.001 TYR A 214 ARG 0.003 0.000 ARG D 57 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 113 time to evaluate : 1.111 Fit side-chains REVERT: D 110 ASP cc_start: 0.8122 (p0) cc_final: 0.7879 (p0) REVERT: D 174 TYR cc_start: 0.8657 (OUTLIER) cc_final: 0.7976 (t80) REVERT: C 174 TYR cc_start: 0.8674 (OUTLIER) cc_final: 0.8072 (t80) REVERT: C 251 MET cc_start: 0.7592 (tpp) cc_final: 0.7145 (tpp) REVERT: B 111 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.6707 (mp10) REVERT: B 174 TYR cc_start: 0.8628 (OUTLIER) cc_final: 0.8027 (t80) REVERT: B 190 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7601 (tt0) REVERT: B 251 MET cc_start: 0.7231 (tpp) cc_final: 0.6745 (tpp) REVERT: A 110 ASP cc_start: 0.8164 (p0) cc_final: 0.7963 (p0) REVERT: A 126 GLN cc_start: 0.8941 (OUTLIER) cc_final: 0.8681 (mt0) REVERT: A 174 TYR cc_start: 0.8665 (OUTLIER) cc_final: 0.7993 (t80) REVERT: A 251 MET cc_start: 0.7717 (tpp) cc_final: 0.7423 (tpp) outliers start: 19 outliers final: 8 residues processed: 132 average time/residue: 1.1911 time to fit residues: 169.9299 Evaluate side-chains 124 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 109 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 296 TRP Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 296 TRP Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 174 TYR Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 296 TRP Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 126 GLN Chi-restraints excluded: chain A residue 174 TYR Chi-restraints excluded: chain A residue 296 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 89 optimal weight: 0.6980 chunk 135 optimal weight: 4.9990 chunk 124 optimal weight: 0.5980 chunk 107 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 114 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 90 GLN D 258 HIS C 90 GLN C 258 HIS B 86 GLN B 258 HIS A 258 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10648 Z= 0.230 Angle : 0.510 4.898 14396 Z= 0.274 Chirality : 0.041 0.127 1624 Planarity : 0.004 0.047 1888 Dihedral : 4.925 50.304 1468 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.18 % Allowed : 17.73 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.26 (0.23), residues: 1364 helix: 2.59 (0.19), residues: 672 sheet: -1.56 (0.32), residues: 212 loop : -0.53 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 148 HIS 0.004 0.001 HIS C 197 PHE 0.013 0.002 PHE B 145 TYR 0.013 0.001 TYR D 214 ARG 0.003 0.000 ARG D 57 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 112 time to evaluate : 1.181 Fit side-chains REVERT: D 90 GLN cc_start: 0.6734 (OUTLIER) cc_final: 0.6504 (mt0) REVERT: D 110 ASP cc_start: 0.8123 (p0) cc_final: 0.7880 (p0) REVERT: D 174 TYR cc_start: 0.8698 (OUTLIER) cc_final: 0.8010 (t80) REVERT: C 110 ASP cc_start: 0.8190 (p0) cc_final: 0.7968 (p0) REVERT: C 174 TYR cc_start: 0.8718 (OUTLIER) cc_final: 0.8105 (t80) REVERT: C 251 MET cc_start: 0.7592 (tpp) cc_final: 0.7139 (tpp) REVERT: B 111 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.6698 (mp10) REVERT: B 174 TYR cc_start: 0.8697 (OUTLIER) cc_final: 0.8113 (t80) REVERT: B 190 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7613 (tt0) REVERT: B 251 MET cc_start: 0.7133 (tpp) cc_final: 0.6652 (tpp) REVERT: A 110 ASP cc_start: 0.8145 (p0) cc_final: 0.7934 (p0) REVERT: A 126 GLN cc_start: 0.8945 (OUTLIER) cc_final: 0.8691 (mt0) REVERT: A 174 TYR cc_start: 0.8738 (OUTLIER) cc_final: 0.8064 (t80) REVERT: A 251 MET cc_start: 0.7714 (tpp) cc_final: 0.7434 (tpp) outliers start: 24 outliers final: 10 residues processed: 133 average time/residue: 1.1422 time to fit residues: 164.6484 Evaluate side-chains 129 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 111 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 296 TRP Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 275 MET Chi-restraints excluded: chain C residue 296 TRP Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 174 TYR Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 296 TRP Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 126 GLN Chi-restraints excluded: chain A residue 174 TYR Chi-restraints excluded: chain A residue 296 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 110 optimal weight: 0.2980 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 0.2980 chunk 94 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 90 GLN D 258 HIS C 90 GLN C 258 HIS B 258 HIS A 258 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.176291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.132944 restraints weight = 9916.662| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 1.83 r_work: 0.3379 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10648 Z= 0.206 Angle : 0.496 5.376 14396 Z= 0.266 Chirality : 0.040 0.124 1624 Planarity : 0.004 0.047 1888 Dihedral : 4.868 50.109 1468 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.00 % Allowed : 18.00 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 (0.23), residues: 1364 helix: 2.65 (0.19), residues: 672 sheet: -1.58 (0.32), residues: 212 loop : -0.52 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 148 HIS 0.004 0.001 HIS C 197 PHE 0.013 0.001 PHE B 145 TYR 0.012 0.001 TYR B 214 ARG 0.003 0.000 ARG D 57 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3677.01 seconds wall clock time: 66 minutes 35.16 seconds (3995.16 seconds total)