Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 02:29:49 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8j_34549/04_2023/8h8j_34549_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8j_34549/04_2023/8h8j_34549.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8j_34549/04_2023/8h8j_34549_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8j_34549/04_2023/8h8j_34549_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8j_34549/04_2023/8h8j_34549_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8j_34549/04_2023/8h8j_34549.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8j_34549/04_2023/8h8j_34549.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8j_34549/04_2023/8h8j_34549_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8j_34549/04_2023/8h8j_34549_neut_updated.pdb" } resolution = 3.2 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= 0.001 sd= 0.025 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: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 S 63 5.16 5 Cl 1 4.86 5 C 5648 2.51 5 N 1511 2.21 5 O 1618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 8842 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1842 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 3, 'TRANS': 221} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 2553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2553 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "C" Number of atoms: 2191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2191 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 271} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "G" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 417 Classifications: {'peptide': 59} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 54} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "H" Number of atoms: 1733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1733 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "C" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 106 Unusual residues: {' CA': 1, 'CLR': 3, 'WYB': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 5.32, per 1000 atoms: 0.60 Number of scatterers: 8842 At special positions: 0 Unit cell: (105.04, 113.36, 127.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 Cl 1 17.00 S 63 16.00 O 1618 8.00 N 1511 7.00 C 5648 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 89 " - pdb=" SG CYS C 162 " distance=2.03 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: 3.71 Conformation dependent library (CDL) restraints added in 1.5 seconds 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2132 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 12 sheets defined 32.2% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 7 through 47 removed outlier: 3.655A pdb=" N THR A 43 " --> pdb=" O SER A 39 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N TYR A 44 " --> pdb=" O ARG A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 72 removed outlier: 3.815A pdb=" N ILE A 70 " --> pdb=" O LYS A 66 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ILE A 71 " --> pdb=" O GLN A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 238 No H-bonds generated for 'chain 'A' and resid 236 through 238' Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 280 through 282 No H-bonds generated for 'chain 'A' and resid 280 through 282' Processing helix chain 'A' and resid 294 through 301 Processing helix chain 'A' and resid 321 through 334 Processing helix chain 'A' and resid 355 through 374 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 30 through 36 removed outlier: 5.217A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 44 removed outlier: 4.136A pdb=" N LEU C 35 " --> pdb=" O LEU C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 78 Proline residue: C 74 - end of helix Processing helix chain 'C' and resid 87 through 118 Processing helix chain 'C' and resid 122 through 124 No H-bonds generated for 'chain 'C' and resid 122 through 124' Processing helix chain 'C' and resid 130 through 157 removed outlier: 3.535A pdb=" N GLN C 157 " --> pdb=" O LEU C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 178 Processing helix chain 'C' and resid 181 through 197 Processing helix chain 'C' and resid 206 through 242 Proline residue: C 232 - end of helix removed outlier: 3.869A pdb=" N LEU C 241 " --> pdb=" O LEU C 237 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ALA C 242 " --> pdb=" O THR C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 271 Processing helix chain 'C' and resid 281 through 287 Processing helix chain 'G' and resid 10 through 23 removed outlier: 4.575A pdb=" N LEU G 15 " --> pdb=" O GLN G 11 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing helix chain 'H' and resid 88 through 90 No H-bonds generated for 'chain 'H' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'A' and resid 343 through 347 removed outlier: 6.701A pdb=" N ILE A 287 " --> pdb=" O TYR A 344 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N HIS A 346 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU A 289 " --> pdb=" O HIS A 346 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.712A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.799A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.637A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 189 through 192 removed outlier: 4.045A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY B 202 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER B 191 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.896A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.619A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.652A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'H' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'H' and resid 115 through 117 removed outlier: 5.782A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'H' and resid 140 through 142 Processing sheet with id= L, first strand: chain 'H' and resid 146 through 148 removed outlier: 6.206A pdb=" N LYS H 244 " --> pdb=" O VAL H 147 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N LEU H 178 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N LEU H 187 " --> pdb=" O LEU H 178 " (cutoff:3.500A) 408 hydrogen bonds defined for protein. 1116 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: 2.81 Time building geometry restraints manager: 3.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 1416 1.27 - 1.41: 2239 1.41 - 1.54: 5262 1.54 - 1.68: 17 1.68 - 1.81: 90 Bond restraints: 9024 Sorted by residual: bond pdb=" CA THR C 166 " pdb=" C THR C 166 " ideal model delta sigma weight residual 1.527 1.489 0.038 1.42e-02 4.96e+03 7.11e+00 bond pdb=" N ASP A 337 " pdb=" CA ASP A 337 " ideal model delta sigma weight residual 1.457 1.491 -0.033 1.29e-02 6.01e+03 6.71e+00 bond pdb=" CA SER C 165 " pdb=" C SER C 165 " ideal model delta sigma weight residual 1.524 1.494 0.029 1.23e-02 6.61e+03 5.72e+00 bond pdb=" N ARG A 336 " pdb=" CA ARG A 336 " ideal model delta sigma weight residual 1.457 1.488 -0.030 1.29e-02 6.01e+03 5.45e+00 bond pdb=" CA SER C 172 " pdb=" C SER C 172 " ideal model delta sigma weight residual 1.524 1.492 0.031 1.37e-02 5.33e+03 5.24e+00 ... (remaining 9019 not shown) Histogram of bond angle deviations from ideal: 98.29 - 114.59: 5665 114.59 - 130.90: 6558 130.90 - 147.21: 41 147.21 - 163.52: 0 163.52 - 179.82: 1 Bond angle restraints: 12265 Sorted by residual: angle pdb=" N HIS C 168 " pdb=" CA HIS C 168 " pdb=" C HIS C 168 " ideal model delta sigma weight residual 108.63 98.29 10.34 1.60e+00 3.91e-01 4.18e+01 angle pdb=" N ASN C 169 " pdb=" CA ASN C 169 " pdb=" C ASN C 169 " ideal model delta sigma weight residual 110.33 118.02 -7.69 1.29e+00 6.01e-01 3.55e+01 angle pdb=" N ASN C 171 " pdb=" CA ASN C 171 " pdb=" C ASN C 171 " ideal model delta sigma weight residual 114.75 108.38 6.37 1.26e+00 6.30e-01 2.56e+01 angle pdb=" N SER C 172 " pdb=" CA SER C 172 " pdb=" C SER C 172 " ideal model delta sigma weight residual 112.45 106.03 6.42 1.39e+00 5.18e-01 2.13e+01 angle pdb=" C THR C 83 " pdb=" N SER C 84 " pdb=" CA SER C 84 " ideal model delta sigma weight residual 121.90 116.43 5.47 1.26e+00 6.30e-01 1.89e+01 ... (remaining 12260 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 5090 17.56 - 35.12: 177 35.12 - 52.68: 33 52.68 - 70.25: 13 70.25 - 87.81: 2 Dihedral angle restraints: 5315 sinusoidal: 2014 harmonic: 3301 Sorted by residual: dihedral pdb=" CB CYS C 89 " pdb=" SG CYS C 89 " pdb=" SG CYS C 162 " pdb=" CB CYS C 162 " ideal model delta sinusoidal sigma weight residual -86.00 -144.27 58.27 1 1.00e+01 1.00e-02 4.55e+01 dihedral pdb=" CA ASP C 82 " pdb=" CB ASP C 82 " pdb=" CG ASP C 82 " pdb=" OD1 ASP C 82 " ideal model delta sinusoidal sigma weight residual -30.00 -85.76 55.76 1 2.00e+01 2.50e-03 1.05e+01 dihedral pdb=" CA MET C 173 " pdb=" CB MET C 173 " pdb=" CG MET C 173 " pdb=" SD MET C 173 " ideal model delta sinusoidal sigma weight residual -180.00 -120.13 -59.87 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 5312 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1172 0.048 - 0.096: 190 0.096 - 0.144: 52 0.144 - 0.192: 5 0.192 - 0.240: 6 Chirality restraints: 1425 Sorted by residual: chirality pdb=" CA ASN C 169 " pdb=" N ASN C 169 " pdb=" C ASN C 169 " pdb=" CB ASN C 169 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" C13 CLR C 404 " pdb=" C12 CLR C 404 " pdb=" C14 CLR C 404 " pdb=" C17 CLR C 404 " both_signs ideal model delta sigma weight residual False -2.93 -2.70 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" C13 CLR C 405 " pdb=" C12 CLR C 405 " pdb=" C14 CLR C 405 " pdb=" C17 CLR C 405 " both_signs ideal model delta sigma weight residual False -2.93 -2.71 -0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 1422 not shown) Planarity restraints: 1536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.033 5.00e-02 4.00e+02 5.02e-02 4.03e+00 pdb=" N PRO B 236 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 335 " 0.009 2.00e-02 2.50e+03 1.86e-02 3.45e+00 pdb=" C ARG A 335 " -0.032 2.00e-02 2.50e+03 pdb=" O ARG A 335 " 0.012 2.00e-02 2.50e+03 pdb=" N ARG A 336 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 217 " -0.027 5.00e-02 4.00e+02 4.12e-02 2.71e+00 pdb=" N PRO A 218 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 218 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 218 " -0.023 5.00e-02 4.00e+02 ... (remaining 1533 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 58 2.53 - 3.12: 6685 3.12 - 3.72: 14033 3.72 - 4.31: 19608 4.31 - 4.90: 32870 Nonbonded interactions: 73254 Sorted by model distance: nonbonded pdb=" O ARG A 332 " pdb=" NE2 GLN A 338 " model vdw 1.939 2.520 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR H 175 " model vdw 2.168 2.440 nonbonded pdb=" OG1 THR B 86 " pdb=" OD1 ASN B 88 " model vdw 2.186 2.440 nonbonded pdb=" O ARG A 335 " pdb=" OE1 GLN A 338 " model vdw 2.200 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.210 2.440 ... (remaining 73249 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 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: 4.410 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 27.220 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 9024 Z= 0.179 Angle : 0.642 10.343 12265 Z= 0.369 Chirality : 0.042 0.240 1425 Planarity : 0.003 0.050 1536 Dihedral : 9.838 87.807 3180 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.32 % Favored : 97.60 % Rotamer Outliers : 2.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.24), residues: 1123 helix: 0.76 (0.25), residues: 393 sheet: -0.54 (0.29), residues: 264 loop : -1.58 (0.28), residues: 466 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 253 time to evaluate : 1.020 Fit side-chains outliers start: 24 outliers final: 11 residues processed: 269 average time/residue: 0.2420 time to fit residues: 86.6049 Evaluate side-chains 229 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 218 time to evaluate : 0.974 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1645 time to fit residues: 3.9567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 46 optimal weight: 0.2980 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 87 optimal weight: 0.3980 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 64 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 GLN A 345 HIS B 176 GLN B 220 GLN B 237 ASN B 295 ASN B 340 ASN C 99 ASN H 142 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 9024 Z= 0.218 Angle : 0.532 8.010 12265 Z= 0.273 Chirality : 0.040 0.162 1425 Planarity : 0.004 0.051 1536 Dihedral : 4.860 89.517 1259 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer Outliers : 2.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.26), residues: 1123 helix: 1.80 (0.27), residues: 389 sheet: -0.27 (0.28), residues: 274 loop : -1.07 (0.30), residues: 460 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 215 time to evaluate : 1.030 Fit side-chains outliers start: 24 outliers final: 8 residues processed: 224 average time/residue: 0.2320 time to fit residues: 70.3568 Evaluate side-chains 211 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 203 time to evaluate : 1.087 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1573 time to fit residues: 3.3495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 0.9980 chunk 31 optimal weight: 0.0970 chunk 83 optimal weight: 0.9980 chunk 68 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 100 optimal weight: 0.0000 chunk 109 optimal weight: 0.3980 chunk 89 optimal weight: 0.4980 chunk 34 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 99 optimal weight: 0.6980 overall best weight: 0.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN B 230 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 9024 Z= 0.160 Angle : 0.501 8.062 12265 Z= 0.256 Chirality : 0.039 0.190 1425 Planarity : 0.004 0.052 1536 Dihedral : 4.640 79.545 1259 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer Outliers : 2.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.26), residues: 1123 helix: 1.96 (0.27), residues: 391 sheet: -0.04 (0.29), residues: 276 loop : -0.87 (0.31), residues: 456 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 196 time to evaluate : 1.054 Fit side-chains outliers start: 22 outliers final: 10 residues processed: 207 average time/residue: 0.2206 time to fit residues: 62.1070 Evaluate side-chains 203 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 193 time to evaluate : 1.078 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0958 time to fit residues: 3.1547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 1.9990 chunk 52 optimal weight: 0.1980 chunk 11 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 101 optimal weight: 0.0570 chunk 107 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 60 optimal weight: 0.5980 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN H 142 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 9024 Z= 0.183 Angle : 0.520 11.637 12265 Z= 0.264 Chirality : 0.039 0.153 1425 Planarity : 0.004 0.049 1536 Dihedral : 4.802 89.540 1259 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer Outliers : 0.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.26), residues: 1123 helix: 2.00 (0.27), residues: 391 sheet: 0.09 (0.29), residues: 289 loop : -0.85 (0.32), residues: 443 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 209 time to evaluate : 0.984 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 212 average time/residue: 0.2233 time to fit residues: 64.4155 Evaluate side-chains 202 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 198 time to evaluate : 1.086 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1799 time to fit residues: 2.4308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.9990 chunk 79 optimal weight: 0.0470 chunk 44 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 36 optimal weight: 0.0170 chunk 21 optimal weight: 0.5980 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN H 142 GLN H 179 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 9024 Z= 0.193 Angle : 0.524 12.644 12265 Z= 0.265 Chirality : 0.039 0.140 1425 Planarity : 0.004 0.048 1536 Dihedral : 4.787 85.579 1259 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer Outliers : 1.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.26), residues: 1123 helix: 2.00 (0.27), residues: 392 sheet: 0.19 (0.29), residues: 286 loop : -0.64 (0.32), residues: 445 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 207 time to evaluate : 1.111 Fit side-chains outliers start: 15 outliers final: 6 residues processed: 213 average time/residue: 0.2231 time to fit residues: 64.7943 Evaluate side-chains 207 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 201 time to evaluate : 0.997 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0909 time to fit residues: 2.3344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 8 optimal weight: 0.0670 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 12 optimal weight: 0.0980 chunk 61 optimal weight: 1.9990 overall best weight: 0.5520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN C 200 GLN H 142 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 9024 Z= 0.214 Angle : 0.533 13.087 12265 Z= 0.270 Chirality : 0.040 0.140 1425 Planarity : 0.004 0.047 1536 Dihedral : 4.777 82.049 1259 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer Outliers : 2.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.26), residues: 1123 helix: 2.08 (0.28), residues: 386 sheet: 0.13 (0.28), residues: 292 loop : -0.64 (0.32), residues: 445 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 209 time to evaluate : 1.069 Fit side-chains outliers start: 20 outliers final: 9 residues processed: 217 average time/residue: 0.2437 time to fit residues: 71.2607 Evaluate side-chains 218 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 209 time to evaluate : 1.104 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1055 time to fit residues: 3.1697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.0050 chunk 60 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 106 optimal weight: 0.1980 chunk 66 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 9024 Z= 0.201 Angle : 0.540 12.082 12265 Z= 0.271 Chirality : 0.040 0.147 1425 Planarity : 0.004 0.047 1536 Dihedral : 4.880 85.514 1259 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer Outliers : 1.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.26), residues: 1123 helix: 2.11 (0.28), residues: 388 sheet: 0.13 (0.28), residues: 292 loop : -0.61 (0.32), residues: 443 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 226 time to evaluate : 1.087 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 230 average time/residue: 0.2504 time to fit residues: 77.0688 Evaluate side-chains 223 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 218 time to evaluate : 1.067 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0903 time to fit residues: 2.3051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 52 optimal weight: 0.0000 chunk 9 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 93 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN B 340 ASN G 59 ASN H 142 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 9024 Z= 0.250 Angle : 0.573 11.514 12265 Z= 0.289 Chirality : 0.041 0.181 1425 Planarity : 0.004 0.052 1536 Dihedral : 4.971 84.482 1259 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer Outliers : 1.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.26), residues: 1123 helix: 1.99 (0.27), residues: 391 sheet: 0.09 (0.28), residues: 298 loop : -0.58 (0.32), residues: 434 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 213 time to evaluate : 1.197 Fit side-chains outliers start: 11 outliers final: 6 residues processed: 215 average time/residue: 0.2489 time to fit residues: 71.3151 Evaluate side-chains 213 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 207 time to evaluate : 1.035 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1916 time to fit residues: 2.9080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 78 optimal weight: 0.0070 chunk 30 optimal weight: 0.4980 chunk 90 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 105 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 59 ASN H 142 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 9024 Z= 0.237 Angle : 0.585 11.478 12265 Z= 0.293 Chirality : 0.041 0.205 1425 Planarity : 0.004 0.056 1536 Dihedral : 5.032 86.469 1259 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer Outliers : 0.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.26), residues: 1123 helix: 1.93 (0.27), residues: 392 sheet: 0.00 (0.28), residues: 297 loop : -0.48 (0.32), residues: 434 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 210 time to evaluate : 0.989 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 210 average time/residue: 0.2434 time to fit residues: 68.1126 Evaluate side-chains 211 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 208 time to evaluate : 1.041 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1097 time to fit residues: 2.0181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.5980 chunk 73 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 9 optimal weight: 0.0870 chunk 68 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 9024 Z= 0.259 Angle : 0.608 12.314 12265 Z= 0.303 Chirality : 0.041 0.154 1425 Planarity : 0.004 0.058 1536 Dihedral : 5.092 86.252 1259 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer Outliers : 0.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.26), residues: 1123 helix: 1.88 (0.27), residues: 392 sheet: 0.01 (0.28), residues: 295 loop : -0.54 (0.32), residues: 436 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 218 time to evaluate : 1.081 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 219 average time/residue: 0.2417 time to fit residues: 70.5864 Evaluate side-chains 212 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 209 time to evaluate : 0.975 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1020 time to fit residues: 1.8597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 2.9990 chunk 13 optimal weight: 0.0870 chunk 24 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN G 59 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.135691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.121355 restraints weight = 12083.701| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 1.88 r_work: 0.3468 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 9024 Z= 0.291 Angle : 0.628 12.403 12265 Z= 0.313 Chirality : 0.042 0.155 1425 Planarity : 0.004 0.059 1536 Dihedral : 5.187 87.013 1259 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer Outliers : 0.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.26), residues: 1123 helix: 1.87 (0.27), residues: 391 sheet: -0.01 (0.28), residues: 295 loop : -0.55 (0.32), residues: 437 =============================================================================== Job complete usr+sys time: 2448.96 seconds wall clock time: 45 minutes 4.14 seconds (2704.14 seconds total)