Starting phenix.real_space_refine on Fri Dec 8 17:31:43 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8j_34549/12_2023/8h8j_34549_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8j_34549/12_2023/8h8j_34549.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8j_34549/12_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_34549/12_2023/8h8j_34549_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8j_34549/12_2023/8h8j_34549_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8j_34549/12_2023/8h8j_34549.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8j_34549/12_2023/8h8j_34549.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8j_34549/12_2023/8h8j_34549_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8j_34549/12_2023/8h8j_34549_neut_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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-1.21rc1-5172/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: 5.26, per 1000 atoms: 0.59 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: 3.81 Conformation dependent library (CDL) restraints added in 1.9 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: 1.76 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: 2.72 Time building geometry restraints manager: 4.06 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: 5216 17.56 - 35.12: 202 35.12 - 52.68: 48 52.68 - 70.25: 15 70.25 - 87.81: 2 Dihedral angle restraints: 5483 sinusoidal: 2182 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 5480 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: 1.570 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: 3.960 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 28.060 Find NCS groups from input model: 0.260 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.970 ------------------------------------------------------------------------------- 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 : 10.393 87.807 3348 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 % Allowed : 4.85 % Favored : 92.56 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.002 0.000 HIS C 168 PHE 0.008 0.001 PHE B 199 TYR 0.006 0.001 TYR C 101 ARG 0.003 0.000 ARG H 72 *********************** 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 : 0.968 Fit side-chains outliers start: 24 outliers final: 11 residues processed: 269 average time/residue: 0.2328 time to fit residues: 83.4428 Evaluate side-chains 229 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 218 time to evaluate : 0.948 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1638 time to fit residues: 3.9196 ------------------------------------------------------------------------------- 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: 0.6983 moved from start: 0.1609 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= 0.214 Angle : 0.519 8.136 12265 Z= 0.268 Chirality : 0.040 0.168 1425 Planarity : 0.004 0.051 1536 Dihedral : 6.238 86.628 1427 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.05 % Allowed : 14.67 % Favored : 83.28 % 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: 0.18 (0.26), residues: 1123 helix: 1.78 (0.27), residues: 390 sheet: -0.24 (0.28), residues: 273 loop : -1.08 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 82 HIS 0.007 0.001 HIS H 167 PHE 0.017 0.002 PHE A 212 TYR 0.012 0.002 TYR H 102 ARG 0.006 0.001 ARG B 49 *********************** 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 228 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 209 time to evaluate : 1.144 Fit side-chains outliers start: 19 outliers final: 7 residues processed: 216 average time/residue: 0.2234 time to fit residues: 65.3435 Evaluate side-chains 206 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 199 time to evaluate : 0.949 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1619 time to fit residues: 3.0012 ------------------------------------------------------------------------------- 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: 1.9990 chunk 31 optimal weight: 0.9980 chunk 83 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 100 optimal weight: 0.0020 chunk 109 optimal weight: 0.5980 chunk 89 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN H 142 GLN H 179 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.2196 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= 0.214 Angle : 0.524 7.399 12265 Z= 0.268 Chirality : 0.040 0.157 1425 Planarity : 0.004 0.054 1536 Dihedral : 5.737 77.451 1427 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.59 % Allowed : 15.43 % Favored : 81.98 % 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: 0.45 (0.26), residues: 1123 helix: 2.03 (0.27), residues: 384 sheet: -0.04 (0.28), residues: 290 loop : -0.98 (0.31), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 82 HIS 0.005 0.001 HIS H 167 PHE 0.033 0.002 PHE C 163 TYR 0.012 0.002 TYR H 59 ARG 0.009 0.001 ARG B 134 *********************** 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 220 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 196 time to evaluate : 0.978 Fit side-chains outliers start: 24 outliers final: 12 residues processed: 210 average time/residue: 0.2239 time to fit residues: 63.8036 Evaluate side-chains 194 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 182 time to evaluate : 0.946 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0892 time to fit residues: 3.2633 ------------------------------------------------------------------------------- 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: 3.9990 chunk 11 optimal weight: 0.7980 chunk 48 optimal weight: 0.0870 chunk 67 optimal weight: 2.9990 chunk 101 optimal weight: 0.0770 chunk 107 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN H 142 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9024 Z= 0.221 Angle : 0.525 10.060 12265 Z= 0.269 Chirality : 0.040 0.151 1425 Planarity : 0.004 0.051 1536 Dihedral : 5.612 86.003 1427 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.94 % Allowed : 16.94 % Favored : 81.12 % 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: 0.60 (0.26), residues: 1123 helix: 1.97 (0.27), residues: 393 sheet: 0.01 (0.28), residues: 298 loop : -0.75 (0.32), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 82 HIS 0.006 0.001 HIS C 234 PHE 0.018 0.002 PHE H 29 TYR 0.018 0.002 TYR B 145 ARG 0.008 0.000 ARG B 134 *********************** 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 227 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 209 time to evaluate : 0.916 Fit side-chains outliers start: 18 outliers final: 9 residues processed: 213 average time/residue: 0.2131 time to fit residues: 62.2266 Evaluate side-chains 212 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 203 time to evaluate : 0.882 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1144 time to fit residues: 2.9926 ------------------------------------------------------------------------------- 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: 0.9980 chunk 79 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 74 optimal weight: 0.0070 chunk 0 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 0.0970 chunk 21 optimal weight: 0.6980 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN H 142 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9024 Z= 0.188 Angle : 0.528 12.702 12265 Z= 0.266 Chirality : 0.040 0.179 1425 Planarity : 0.004 0.049 1536 Dihedral : 5.534 85.823 1427 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.51 % Allowed : 18.66 % Favored : 79.83 % 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: 2.03 (0.28), residues: 387 sheet: 0.13 (0.28), residues: 297 loop : -0.60 (0.32), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 82 HIS 0.005 0.001 HIS C 234 PHE 0.019 0.002 PHE H 212 TYR 0.013 0.001 TYR B 145 ARG 0.010 0.000 ARG B 134 *********************** 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 230 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 216 time to evaluate : 1.068 Fit side-chains outliers start: 14 outliers final: 6 residues processed: 222 average time/residue: 0.2213 time to fit residues: 67.4041 Evaluate side-chains 220 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 214 time to evaluate : 0.936 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0969 time to fit residues: 2.3578 ------------------------------------------------------------------------------- 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: 0.0870 chunk 26 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 8 optimal weight: 0.2980 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 103 optimal weight: 0.0670 chunk 12 optimal weight: 0.0980 chunk 61 optimal weight: 1.9990 overall best weight: 0.2696 ------------------------------------------------------------------------------- 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: 0.7017 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9024 Z= 0.156 Angle : 0.524 12.529 12265 Z= 0.262 Chirality : 0.039 0.129 1425 Planarity : 0.004 0.047 1536 Dihedral : 5.456 89.905 1427 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.51 % Allowed : 20.06 % Favored : 78.43 % 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: 0.81 (0.26), residues: 1123 helix: 2.00 (0.28), residues: 394 sheet: 0.22 (0.28), residues: 299 loop : -0.55 (0.33), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 82 HIS 0.006 0.001 HIS C 234 PHE 0.023 0.001 PHE H 29 TYR 0.011 0.001 TYR C 101 ARG 0.012 0.001 ARG B 134 *********************** 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 223 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 209 time to evaluate : 1.042 Fit side-chains outliers start: 14 outliers final: 6 residues processed: 215 average time/residue: 0.2648 time to fit residues: 78.0306 Evaluate side-chains 210 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 204 time to evaluate : 1.029 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1566 time to fit residues: 2.8456 ------------------------------------------------------------------------------- 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: 0.5980 chunk 60 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 59 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN B 340 ASN H 142 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9024 Z= 0.268 Angle : 0.558 11.202 12265 Z= 0.284 Chirality : 0.041 0.147 1425 Planarity : 0.004 0.047 1536 Dihedral : 5.568 88.797 1427 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.97 % Allowed : 20.50 % Favored : 78.53 % 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: 0.75 (0.26), residues: 1123 helix: 2.06 (0.28), residues: 387 sheet: 0.15 (0.28), residues: 298 loop : -0.64 (0.32), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 82 HIS 0.006 0.001 HIS C 234 PHE 0.022 0.002 PHE B 234 TYR 0.015 0.002 TYR H 59 ARG 0.013 0.001 ARG B 134 *********************** 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 233 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 224 time to evaluate : 1.075 Fit side-chains outliers start: 9 outliers final: 3 residues processed: 226 average time/residue: 0.2470 time to fit residues: 75.4560 Evaluate side-chains 225 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 222 time to evaluate : 1.033 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0841 time to fit residues: 1.8925 ------------------------------------------------------------------------------- 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: 0.5980 chunk 20 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 72 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 84 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 99 optimal weight: 0.1980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 230 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 142 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 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 0.037 9024 Z= 0.232 Angle : 0.559 11.212 12265 Z= 0.286 Chirality : 0.040 0.164 1425 Planarity : 0.004 0.053 1536 Dihedral : 5.593 89.177 1427 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.76 % Allowed : 21.47 % Favored : 77.78 % 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: 1.96 (0.27), residues: 390 sheet: 0.18 (0.28), residues: 297 loop : -0.60 (0.32), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 82 HIS 0.005 0.001 HIS C 234 PHE 0.021 0.002 PHE H 29 TYR 0.015 0.002 TYR H 190 ARG 0.013 0.001 ARG B 134 *********************** 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 228 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 221 time to evaluate : 0.996 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 223 average time/residue: 0.2364 time to fit residues: 70.6400 Evaluate side-chains 219 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 215 time to evaluate : 0.966 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1018 time to fit residues: 2.0541 ------------------------------------------------------------------------------- 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: 3.9990 chunk 60 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 90 optimal weight: 0.6980 chunk 94 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 105 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** H 142 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9024 Z= 0.267 Angle : 0.589 11.006 12265 Z= 0.299 Chirality : 0.041 0.185 1425 Planarity : 0.004 0.054 1536 Dihedral : 5.608 86.699 1427 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.43 % Allowed : 22.01 % Favored : 77.56 % 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: 1.88 (0.27), residues: 390 sheet: 0.03 (0.28), residues: 299 loop : -0.59 (0.32), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP B 82 HIS 0.005 0.001 HIS C 234 PHE 0.021 0.002 PHE H 29 TYR 0.017 0.002 TYR H 59 ARG 0.014 0.001 ARG B 134 *********************** 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 225 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 221 time to evaluate : 1.031 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 222 average time/residue: 0.2422 time to fit residues: 71.9142 Evaluate side-chains 218 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 216 time to evaluate : 1.007 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2810 time to fit residues: 2.0913 ------------------------------------------------------------------------------- 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: 0.9980 chunk 73 optimal weight: 0.9980 chunk 110 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 142 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9024 Z= 0.332 Angle : 0.630 11.060 12265 Z= 0.321 Chirality : 0.043 0.179 1425 Planarity : 0.004 0.057 1536 Dihedral : 5.769 89.338 1427 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.43 % Allowed : 22.87 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.26), residues: 1123 helix: 1.84 (0.27), residues: 389 sheet: -0.06 (0.28), residues: 296 loop : -0.62 (0.32), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP B 82 HIS 0.005 0.001 HIS B 91 PHE 0.023 0.002 PHE B 234 TYR 0.021 0.002 TYR H 59 ARG 0.014 0.001 ARG B 134 ********************** 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 218 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 214 time to evaluate : 0.973 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 214 average time/residue: 0.2457 time to fit residues: 69.9628 Evaluate side-chains 213 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 211 time to evaluate : 0.889 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1168 time to fit residues: 1.5966 ------------------------------------------------------------------------------- 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: 0.5980 chunk 13 optimal weight: 0.9980 chunk 24 optimal weight: 0.4980 chunk 88 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 0.4980 chunk 77 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 63 optimal weight: 0.0570 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 GLN H 142 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.137184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.122801 restraints weight = 12048.407| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 1.89 r_work: 0.3491 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9024 Z= 0.211 Angle : 0.596 11.029 12265 Z= 0.298 Chirality : 0.041 0.161 1425 Planarity : 0.004 0.058 1536 Dihedral : 5.601 89.237 1427 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.76 % Allowed : 22.33 % Favored : 76.91 % 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: 0.62 (0.26), residues: 1123 helix: 1.94 (0.27), residues: 389 sheet: -0.09 (0.28), residues: 296 loop : -0.56 (0.32), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 82 HIS 0.005 0.001 HIS C 234 PHE 0.020 0.002 PHE H 29 TYR 0.018 0.002 TYR H 190 ARG 0.014 0.001 ARG B 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2434.08 seconds wall clock time: 44 minutes 51.33 seconds (2691.33 seconds total)