Starting phenix.real_space_refine (version: 1.21rc1) on Wed Jul 5 20:01:59 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d44_27174/07_2023/8d44_27174.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d44_27174/07_2023/8d44_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_27174/07_2023/8d44_27174.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d44_27174/07_2023/8d44_27174.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d44_27174/07_2023/8d44_27174.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d44_27174/07_2023/8d44_27174.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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-1.21rc1-5013/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: 5.31, per 1000 atoms: 0.51 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: 3.83 Conformation dependent library (CDL) restraints added in 1.5 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: 0.59 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: 3.01 Time building geometry restraints manager: 4.15 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: 1.200 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: 6.710 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 28.110 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: 0.010 Load rotamer database and sin/cos tables:12.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.900 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 1.229 Fit side-chains outliers start: 19 outliers final: 12 residues processed: 138 average time/residue: 1.1711 time to fit residues: 175.1720 Evaluate side-chains 129 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 117 time to evaluate : 1.180 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 9 residues processed: 4 average time/residue: 0.4603 time to fit residues: 3.8091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 0.3980 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: 0.8986 ------------------------------------------------------------------------------- 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 B 258 HIS A 258 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.0687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.027 10648 Z= 0.253 Angle : 0.537 4.929 14396 Z= 0.287 Chirality : 0.042 0.132 1624 Planarity : 0.005 0.054 1888 Dihedral : 4.424 17.055 1460 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer Outliers : 2.45 % 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: 0.73 (0.23), residues: 1364 helix: 2.02 (0.19), residues: 672 sheet: -1.76 (0.29), residues: 248 loop : -0.45 (0.31), residues: 444 *********************** 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 152 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 125 time to evaluate : 1.073 Fit side-chains outliers start: 27 outliers final: 16 residues processed: 147 average time/residue: 1.0989 time to fit residues: 175.4554 Evaluate side-chains 133 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 117 time to evaluate : 1.172 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 14 residues processed: 2 average time/residue: 0.6793 time to fit residues: 3.3022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 102 optimal weight: 0.0870 chunk 84 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 133 optimal weight: 4.9990 chunk 110 optimal weight: 0.4980 chunk 122 optimal weight: 0.5980 chunk 42 optimal weight: 4.9990 chunk 99 optimal weight: 7.9990 overall best weight: 0.8362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 90 GLN D 220 HIS D 258 HIS C 90 GLN 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: 0.7886 moved from start: 0.0884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.025 10648 Z= 0.242 Angle : 0.522 5.209 14396 Z= 0.279 Chirality : 0.041 0.129 1624 Planarity : 0.005 0.047 1888 Dihedral : 4.370 16.970 1460 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer Outliers : 2.55 % 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: 0.89 (0.23), residues: 1364 helix: 2.22 (0.19), residues: 672 sheet: -1.80 (0.29), residues: 248 loop : -0.42 (0.31), residues: 444 *********************** 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 155 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 127 time to evaluate : 1.076 Fit side-chains outliers start: 28 outliers final: 16 residues processed: 151 average time/residue: 1.1721 time to fit residues: 191.8162 Evaluate side-chains 134 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 118 time to evaluate : 1.135 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 15 residues processed: 1 average time/residue: 1.4663 time to fit residues: 3.1765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 0.6980 chunk 93 optimal weight: 0.9980 chunk 64 optimal weight: 0.2980 chunk 13 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 83 optimal weight: 0.4980 chunk 124 optimal weight: 2.9990 chunk 131 optimal weight: 0.9980 chunk 117 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.7870 moved from start: 0.0977 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= 0.206 Angle : 0.496 5.086 14396 Z= 0.266 Chirality : 0.040 0.125 1624 Planarity : 0.004 0.047 1888 Dihedral : 4.233 17.060 1460 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer Outliers : 2.73 % 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: 1.08 (0.23), residues: 1364 helix: 2.42 (0.19), residues: 672 sheet: -1.80 (0.29), residues: 248 loop : -0.34 (0.31), residues: 444 *********************** 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 154 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 124 time to evaluate : 1.249 Fit side-chains outliers start: 30 outliers final: 14 residues processed: 151 average time/residue: 1.1588 time to fit residues: 189.7315 Evaluate side-chains 125 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 111 time to evaluate : 1.120 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 13 residues processed: 1 average time/residue: 1.0776 time to fit residues: 2.7073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 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: 0.2980 chunk 117 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 90 GLN C 220 HIS 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: 0.7911 moved from start: 0.1128 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= 0.291 Angle : 0.552 5.380 14396 Z= 0.294 Chirality : 0.042 0.138 1624 Planarity : 0.005 0.046 1888 Dihedral : 4.450 18.170 1460 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer Outliers : 2.73 % 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: 0.99 (0.23), residues: 1364 helix: 2.30 (0.19), residues: 672 sheet: -1.72 (0.29), residues: 244 loop : -0.41 (0.31), residues: 448 *********************** 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 152 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 122 time to evaluate : 1.188 Fit side-chains outliers start: 30 outliers final: 12 residues processed: 147 average time/residue: 1.1268 time to fit residues: 180.1497 Evaluate side-chains 128 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 116 time to evaluate : 1.186 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 12 residues processed: 0 time to fit residues: 1.5488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 77 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 131 optimal weight: 0.5980 chunk 109 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 126 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.7879 moved from start: 0.1136 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= 0.205 Angle : 0.500 5.020 14396 Z= 0.268 Chirality : 0.040 0.125 1624 Planarity : 0.004 0.046 1888 Dihedral : 4.238 16.590 1460 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer Outliers : 2.82 % 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: 1.16 (0.23), residues: 1364 helix: 2.50 (0.19), residues: 672 sheet: -1.72 (0.29), residues: 244 loop : -0.39 (0.31), residues: 448 *********************** 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 152 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 121 time to evaluate : 1.194 Fit side-chains outliers start: 31 outliers final: 14 residues processed: 148 average time/residue: 1.1369 time to fit residues: 183.2964 Evaluate side-chains 128 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 114 time to evaluate : 1.077 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 14 residues processed: 0 time to fit residues: 1.4793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 110 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 131 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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: 0.7892 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.028 10648 Z= 0.245 Angle : 0.524 5.852 14396 Z= 0.279 Chirality : 0.041 0.129 1624 Planarity : 0.004 0.047 1888 Dihedral : 4.322 17.309 1460 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer Outliers : 2.00 % 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: 1.14 (0.23), residues: 1364 helix: 2.46 (0.19), residues: 672 sheet: -1.66 (0.32), residues: 212 loop : -0.53 (0.29), residues: 480 *********************** 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 144 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 122 time to evaluate : 1.215 Fit side-chains outliers start: 22 outliers final: 15 residues processed: 143 average time/residue: 1.1134 time to fit residues: 173.5655 Evaluate side-chains 134 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 119 time to evaluate : 1.135 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 15 residues processed: 0 time to fit residues: 1.7216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 chunk 64 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 125 optimal weight: 5.9990 chunk 114 optimal weight: 0.4980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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: 0.7892 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.028 10648 Z= 0.239 Angle : 0.525 6.614 14396 Z= 0.279 Chirality : 0.041 0.129 1624 Planarity : 0.004 0.046 1888 Dihedral : 4.287 16.823 1460 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer Outliers : 2.00 % 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: 1.15 (0.23), residues: 1364 helix: 2.49 (0.19), residues: 672 sheet: -1.67 (0.32), residues: 212 loop : -0.54 (0.30), residues: 480 *********************** 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 146 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 124 time to evaluate : 1.175 Fit side-chains outliers start: 22 outliers final: 16 residues processed: 145 average time/residue: 1.1623 time to fit residues: 182.7071 Evaluate side-chains 130 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 114 time to evaluate : 1.116 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 16 residues processed: 0 time to fit residues: 1.7902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 1.9990 chunk 125 optimal weight: 0.7980 chunk 73 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 95 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 110 optimal weight: 4.9990 chunk 115 optimal weight: 0.6980 chunk 121 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 129 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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: 0.7913 moved from start: 0.1280 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= 0.288 Angle : 0.562 7.987 14396 Z= 0.297 Chirality : 0.042 0.136 1624 Planarity : 0.005 0.046 1888 Dihedral : 4.423 18.336 1460 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer Outliers : 2.45 % 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: 1.07 (0.23), residues: 1364 helix: 2.40 (0.19), residues: 672 sheet: -1.71 (0.30), residues: 244 loop : -0.42 (0.31), residues: 448 *********************** 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 145 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 118 time to evaluate : 1.194 Fit side-chains outliers start: 27 outliers final: 18 residues processed: 142 average time/residue: 1.1393 time to fit residues: 175.9688 Evaluate side-chains 132 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 114 time to evaluate : 1.094 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 16 residues processed: 2 average time/residue: 0.9053 time to fit residues: 3.5018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0570 chunk 89 optimal weight: 0.8980 chunk 135 optimal weight: 5.9990 chunk 124 optimal weight: 0.3980 chunk 107 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 85 optimal weight: 0.9990 chunk 114 optimal weight: 0.9980 overall best weight: 0.6700 ------------------------------------------------------------------------------- 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: 0.7884 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 10648 Z= 0.218 Angle : 0.519 7.558 14396 Z= 0.276 Chirality : 0.041 0.127 1624 Planarity : 0.004 0.046 1888 Dihedral : 4.251 16.717 1460 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer Outliers : 1.91 % 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: 1.18 (0.23), residues: 1364 helix: 2.54 (0.19), residues: 672 sheet: -1.70 (0.32), residues: 212 loop : -0.54 (0.29), residues: 480 ********************** 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 139 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 118 time to evaluate : 1.279 Fit side-chains outliers start: 21 outliers final: 14 residues processed: 138 average time/residue: 1.1414 time to fit residues: 171.4883 Evaluate side-chains 129 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 115 time to evaluate : 1.200 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 14 residues processed: 0 time to fit residues: 1.6049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 15 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 108 optimal weight: 3.9990 chunk 45 optimal weight: 0.4980 chunk 110 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 94 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.175915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.132903 restraints weight = 9903.019| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.70 r_work: 0.3369 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.1278 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= 0.224 Angle : 0.522 7.703 14396 Z= 0.277 Chirality : 0.041 0.127 1624 Planarity : 0.004 0.046 1888 Dihedral : 4.250 17.002 1460 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer Outliers : 1.91 % 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: 1.22 (0.23), residues: 1364 helix: 2.58 (0.19), residues: 672 sheet: -1.67 (0.32), residues: 212 loop : -0.54 (0.30), residues: 480 =============================================================================== Job complete usr+sys time: 3513.99 seconds wall clock time: 63 minutes 28.76 seconds (3808.76 seconds total)