Starting phenix.real_space_refine on Tue Feb 13 19:49:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gcm_29935/02_2024/8gcm_29935_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gcm_29935/02_2024/8gcm_29935.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gcm_29935/02_2024/8gcm_29935_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gcm_29935/02_2024/8gcm_29935_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gcm_29935/02_2024/8gcm_29935_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gcm_29935/02_2024/8gcm_29935.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gcm_29935/02_2024/8gcm_29935.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gcm_29935/02_2024/8gcm_29935_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gcm_29935/02_2024/8gcm_29935_neut_updated.pdb" } resolution = 3.5 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= -0.002 sd= 0.060 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: 5 Type Number sf(0) Gaussians S 53 5.16 5 C 4769 2.51 5 N 1295 2.21 5 O 1389 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 15": "NH1" <-> "NH2" Residue "A ARG 21": "NH1" <-> "NH2" Residue "A GLU 207": "OE1" <-> "OE2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 219": "NH1" <-> "NH2" Residue "B ARG 314": "NH1" <-> "NH2" Residue "E ARG 160": "NH1" <-> "NH2" Residue "E GLU 246": "OE1" <-> "OE2" Residue "R ARG 212": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7508 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1430 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'TRANS': 197} Chain breaks: 5 Unresolved non-hydrogen bonds: 187 Unresolved non-hydrogen angles: 224 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'PHE%COO:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 8, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 95 Chain: "B" Number of atoms: 2384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2384 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 279 Unresolved non-hydrogen dihedrals: 171 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 4, 'ASP:plan': 16, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 156 Chain: "C" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 352 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 42 Chain: "E" Number of atoms: 1672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1672 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 10, 'TRANS': 220} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 56 Chain: "R" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1640 Classifications: {'peptide': 254} Incomplete info: {'truncation_to_alanine': 105} Link IDs: {'PTRANS': 10, 'TRANS': 243} Chain breaks: 4 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 389 Unresolved non-hydrogen angles: 497 Unresolved non-hydrogen dihedrals: 321 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'GLN:plan1': 6, 'TYR:plan': 5, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 6, 'GLU:plan': 5, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 193 Chain: "R" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'YX9': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.64, per 1000 atoms: 0.62 Number of scatterers: 7508 At special positions: 0 Unit cell: (89.79, 119.355, 127.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 53 16.00 F 2 9.00 O 1389 8.00 N 1295 7.00 C 4769 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.04 Simple disulfide: pdb=" SG CYS R 92 " - pdb=" SG CYS R 170 " distance=2.04 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: 2.83 Conformation dependent library (CDL) restraints added in 1.6 seconds 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2020 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 14 sheets defined 29.1% alpha, 16.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.66 Creating SS restraints... Processing helix chain 'A' and resid 7 through 29 removed outlier: 4.622A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ASP A 26 " --> pdb=" O ASN A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 52 removed outlier: 3.776A pdb=" N GLN A 52 " --> pdb=" O THR A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 214 removed outlier: 3.802A pdb=" N ILE A 212 " --> pdb=" O ARG A 208 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N HIS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N CYS A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 208 through 214' Processing helix chain 'A' and resid 244 through 253 Processing helix chain 'A' and resid 274 through 278 Processing helix chain 'A' and resid 296 through 310 removed outlier: 3.567A pdb=" N GLU A 308 " --> pdb=" O GLN A 304 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP A 309 " --> pdb=" O CYS A 305 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.674A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR A 340 " --> pdb=" O PHE A 336 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASP A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS A 349 " --> pdb=" O LYS A 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'C' and resid 11 through 22 Processing helix chain 'C' and resid 30 through 41 removed outlier: 4.177A pdb=" N LEU C 37 " --> pdb=" O ALA C 33 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N TYR C 40 " --> pdb=" O ASP C 36 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N CYS C 41 " --> pdb=" O LEU C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 47 No H-bonds generated for 'chain 'C' and resid 45 through 47' Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'R' and resid 25 through 44 removed outlier: 3.790A pdb=" N ILE R 29 " --> pdb=" O ALA R 25 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY R 31 " --> pdb=" O MET R 27 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N VAL R 32 " --> pdb=" O PHE R 28 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL R 33 " --> pdb=" O ILE R 29 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL R 37 " --> pdb=" O VAL R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 47 through 49 No H-bonds generated for 'chain 'R' and resid 47 through 49' Processing helix chain 'R' and resid 55 through 71 removed outlier: 3.601A pdb=" N LEU R 70 " --> pdb=" O LEU R 66 " (cutoff:3.500A) Processing helix chain 'R' and resid 74 through 76 No H-bonds generated for 'chain 'R' and resid 74 through 76' Processing helix chain 'R' and resid 92 through 106 removed outlier: 3.506A pdb=" N LEU R 99 " --> pdb=" O SER R 95 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LEU R 100 " --> pdb=" O THR R 96 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU R 104 " --> pdb=" O LEU R 100 " (cutoff:3.500A) Processing helix chain 'R' and resid 108 through 113 Processing helix chain 'R' and resid 116 through 119 No H-bonds generated for 'chain 'R' and resid 116 through 119' Processing helix chain 'R' and resid 124 through 129 Processing helix chain 'R' and resid 135 through 155 Proline residue: R 154 - end of helix Processing helix chain 'R' and resid 184 through 218 removed outlier: 3.881A pdb=" N CYS R 207 " --> pdb=" O ASN R 203 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU R 211 " --> pdb=" O CYS R 207 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET R 218 " --> pdb=" O HIS R 214 " (cutoff:3.500A) Processing helix chain 'R' and resid 266 through 297 removed outlier: 3.639A pdb=" N VAL R 271 " --> pdb=" O GLU R 267 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ILE R 272 " --> pdb=" O ILE R 268 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LEU R 273 " --> pdb=" O GLN R 269 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER R 285 " --> pdb=" O VAL R 281 " (cutoff:3.500A) Proline residue: R 287 - end of helix removed outlier: 3.567A pdb=" N ASN R 295 " --> pdb=" O ARG R 291 " (cutoff:3.500A) Processing helix chain 'R' and resid 313 through 318 Processing helix chain 'R' and resid 321 through 324 No H-bonds generated for 'chain 'R' and resid 321 through 324' Processing sheet with id= A, first strand: chain 'A' and resid 267 through 269 removed outlier: 3.794A pdb=" N VAL A 225 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN A 269 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N CYS A 224 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE A 199 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASP A 200 " --> pdb=" O VAL A 185 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.005A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 103 through 105 removed outlier: 3.687A pdb=" N VAL B 112 " --> pdb=" O TYR B 124 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 178 through 180 removed outlier: 3.660A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 200 through 203 removed outlier: 3.774A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.857A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 276 through 278 removed outlier: 4.050A pdb=" N SER B 277 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA B 287 " --> pdb=" O ASN B 295 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 318 through 320 Processing sheet with id= I, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.646A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 18 through 22 Processing sheet with id= K, first strand: chain 'E' and resid 33 through 35 Processing sheet with id= L, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.820A pdb=" N GLU E 46 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 146 through 148 removed outlier: 7.109A pdb=" N LYS E 244 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 155 through 160 removed outlier: 3.660A pdb=" N ALA E 211 " --> pdb=" O SER E 208 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER E 204 " --> pdb=" O THR E 215 " (cutoff:3.500A) 275 hydrogen bonds defined for protein. 780 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: 2.10 Time building geometry restraints manager: 2.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 1223 1.26 - 1.40: 1952 1.40 - 1.54: 4323 1.54 - 1.68: 73 1.68 - 1.82: 76 Bond restraints: 7647 Sorted by residual: bond pdb=" C14 YX9 R 501 " pdb=" C18 YX9 R 501 " ideal model delta sigma weight residual 1.455 1.305 0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" C17 YX9 R 501 " pdb=" C18 YX9 R 501 " ideal model delta sigma weight residual 1.526 1.665 -0.139 2.00e-02 2.50e+03 4.80e+01 bond pdb=" C ALA B 56 " pdb=" O ALA B 56 " ideal model delta sigma weight residual 1.236 1.192 0.044 7.30e-03 1.88e+04 3.63e+01 bond pdb=" CA ALA A 301 " pdb=" C ALA A 301 " ideal model delta sigma weight residual 1.523 1.445 0.078 1.30e-02 5.92e+03 3.60e+01 bond pdb=" C PHE A 274 " pdb=" O PHE A 274 " ideal model delta sigma weight residual 1.237 1.167 0.070 1.17e-02 7.31e+03 3.58e+01 ... (remaining 7642 not shown) Histogram of bond angle deviations from ideal: 99.02 - 106.49: 191 106.49 - 113.96: 4255 113.96 - 121.43: 4016 121.43 - 128.90: 1918 128.90 - 136.37: 63 Bond angle restraints: 10443 Sorted by residual: angle pdb=" C SER R 73 " pdb=" N PRO R 74 " pdb=" CA PRO R 74 " ideal model delta sigma weight residual 119.19 136.37 -17.18 1.06e+00 8.90e-01 2.63e+02 angle pdb=" N ILE R 29 " pdb=" CA ILE R 29 " pdb=" C ILE R 29 " ideal model delta sigma weight residual 110.72 122.06 -11.34 1.01e+00 9.80e-01 1.26e+02 angle pdb=" N MET R 27 " pdb=" CA MET R 27 " pdb=" C MET R 27 " ideal model delta sigma weight residual 111.03 120.67 -9.64 1.11e+00 8.12e-01 7.54e+01 angle pdb=" C ILE R 23 " pdb=" N PRO R 24 " pdb=" CA PRO R 24 " ideal model delta sigma weight residual 119.84 130.45 -10.61 1.25e+00 6.40e-01 7.20e+01 angle pdb=" N ALA R 25 " pdb=" CA ALA R 25 " pdb=" C ALA R 25 " ideal model delta sigma weight residual 111.28 120.23 -8.95 1.09e+00 8.42e-01 6.74e+01 ... (remaining 10438 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.81: 4192 23.81 - 47.62: 205 47.62 - 71.43: 26 71.43 - 95.25: 4 95.25 - 119.06: 1 Dihedral angle restraints: 4428 sinusoidal: 1310 harmonic: 3118 Sorted by residual: dihedral pdb=" CA PHE R 97 " pdb=" C PHE R 97 " pdb=" N ILE R 98 " pdb=" CA ILE R 98 " ideal model delta harmonic sigma weight residual -180.00 -151.65 -28.35 0 5.00e+00 4.00e-02 3.22e+01 dihedral pdb=" CB CYS R 92 " pdb=" SG CYS R 92 " pdb=" SG CYS R 170 " pdb=" CB CYS R 170 " ideal model delta sinusoidal sigma weight residual 93.00 44.83 48.17 1 1.00e+01 1.00e-02 3.20e+01 dihedral pdb=" C VAL R 306 " pdb=" N VAL R 306 " pdb=" CA VAL R 306 " pdb=" CB VAL R 306 " ideal model delta harmonic sigma weight residual -122.00 -135.79 13.79 0 2.50e+00 1.60e-01 3.04e+01 ... (remaining 4425 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 1107 0.098 - 0.197: 121 0.197 - 0.295: 21 0.295 - 0.393: 3 0.393 - 0.492: 3 Chirality restraints: 1255 Sorted by residual: chirality pdb=" CA VAL R 306 " pdb=" N VAL R 306 " pdb=" C VAL R 306 " pdb=" CB VAL R 306 " both_signs ideal model delta sigma weight residual False 2.44 1.95 0.49 2.00e-01 2.50e+01 6.04e+00 chirality pdb=" CA LYS B 280 " pdb=" N LYS B 280 " pdb=" C LYS B 280 " pdb=" CB LYS B 280 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.45e+00 chirality pdb=" CA MET R 27 " pdb=" N MET R 27 " pdb=" C MET R 27 " pdb=" CB MET R 27 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.29e+00 ... (remaining 1252 not shown) Planarity restraints: 1330 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 276 " -0.020 2.00e-02 2.50e+03 3.99e-02 1.59e+01 pdb=" C VAL B 276 " 0.069 2.00e-02 2.50e+03 pdb=" O VAL B 276 " -0.025 2.00e-02 2.50e+03 pdb=" N SER B 277 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 150 " 0.018 2.00e-02 2.50e+03 3.49e-02 1.22e+01 pdb=" C PHE R 150 " -0.060 2.00e-02 2.50e+03 pdb=" O PHE R 150 " 0.022 2.00e-02 2.50e+03 pdb=" N CYS R 151 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN R 321 " 0.047 5.00e-02 4.00e+02 7.06e-02 7.98e+00 pdb=" N PRO R 322 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO R 322 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO R 322 " 0.038 5.00e-02 4.00e+02 ... (remaining 1327 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1275 2.76 - 3.29: 6758 3.29 - 3.83: 11517 3.83 - 4.36: 12453 4.36 - 4.90: 22560 Nonbonded interactions: 54563 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.223 2.440 nonbonded pdb=" O GLU R 93 " pdb=" OG1 THR R 96 " model vdw 2.284 2.440 nonbonded pdb=" O SER B 67 " pdb=" OG SER B 67 " model vdw 2.304 2.440 nonbonded pdb=" OG SER B 245 " pdb=" N ASP B 246 " model vdw 2.313 2.520 nonbonded pdb=" O SER R 114 " pdb=" OG SER R 114 " model vdw 2.357 2.440 ... (remaining 54558 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 group one per residue 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: 0.790 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: 3.260 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 24.390 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 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 : 0.009 0.150 7647 Z= 0.633 Angle : 1.246 17.178 10443 Z= 0.784 Chirality : 0.071 0.492 1255 Planarity : 0.007 0.071 1330 Dihedral : 14.436 119.057 2402 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.88 % Favored : 91.12 % Rotamer: Outliers : 0.77 % Allowed : 1.85 % Favored : 97.38 % Cbeta Deviations : 0.20 % 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: -3.35 (0.24), residues: 1047 helix: -0.78 (0.29), residues: 312 sheet: -2.82 (0.28), residues: 271 loop : -2.80 (0.25), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP B 339 HIS 0.010 0.001 HIS E 35 PHE 0.026 0.003 PHE B 235 TYR 0.020 0.002 TYR B 85 ARG 0.018 0.001 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 107 time to evaluate : 0.767 Fit side-chains REVERT: B 17 GLN cc_start: 0.8436 (tm-30) cc_final: 0.8119 (tm-30) REVERT: E 246 GLU cc_start: 0.7502 (mm-30) cc_final: 0.7051 (mm-30) REVERT: R 117 ARG cc_start: 0.7936 (mtm110) cc_final: 0.7452 (mtm110) REVERT: R 169 TRP cc_start: 0.6528 (p-90) cc_final: 0.6140 (p-90) REVERT: R 217 PHE cc_start: 0.6523 (OUTLIER) cc_final: 0.5330 (t80) outliers start: 5 outliers final: 3 residues processed: 111 average time/residue: 0.2393 time to fit residues: 35.0449 Evaluate side-chains 89 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 85 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain R residue 23 ILE Chi-restraints excluded: chain R residue 217 PHE Chi-restraints excluded: chain R residue 315 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 chunk 50 optimal weight: 0.0170 chunk 61 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 overall best weight: 0.6020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 313 GLN R 321 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 7647 Z= 0.162 Angle : 0.571 6.706 10443 Z= 0.304 Chirality : 0.042 0.153 1255 Planarity : 0.004 0.057 1330 Dihedral : 7.343 92.750 1149 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.46 % Allowed : 12.62 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.25), residues: 1047 helix: 0.27 (0.31), residues: 314 sheet: -2.54 (0.28), residues: 277 loop : -2.59 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 82 HIS 0.006 0.001 HIS B 225 PHE 0.016 0.001 PHE R 126 TYR 0.015 0.001 TYR R 184 ARG 0.003 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 94 time to evaluate : 0.857 Fit side-chains revert: symmetry clash REVERT: A 264 ILE cc_start: 0.8641 (mp) cc_final: 0.8419 (mt) REVERT: B 17 GLN cc_start: 0.8285 (tm-30) cc_final: 0.7986 (tm-30) REVERT: B 222 PHE cc_start: 0.8096 (OUTLIER) cc_final: 0.7382 (m-80) REVERT: B 262 MET cc_start: 0.7813 (mmt) cc_final: 0.7544 (mpp) REVERT: E 38 ARG cc_start: 0.8422 (mtm-85) cc_final: 0.8186 (ttm170) REVERT: E 246 GLU cc_start: 0.7332 (mm-30) cc_final: 0.6820 (mm-30) REVERT: R 81 MET cc_start: 0.5950 (mmm) cc_final: 0.5689 (mmm) REVERT: R 111 CYS cc_start: 0.8032 (t) cc_final: 0.7801 (t) outliers start: 3 outliers final: 1 residues processed: 97 average time/residue: 0.2306 time to fit residues: 29.2305 Evaluate side-chains 87 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 85 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 222 PHE Chi-restraints excluded: chain E residue 80 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 52 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 chunk 85 optimal weight: 0.0470 chunk 94 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 overall best weight: 2.5484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 7647 Z= 0.405 Angle : 0.675 6.955 10443 Z= 0.363 Chirality : 0.046 0.209 1255 Planarity : 0.005 0.062 1330 Dihedral : 7.434 83.922 1141 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.74 % Favored : 90.26 % Rotamer: Outliers : 2.15 % Allowed : 17.08 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.25), residues: 1047 helix: 0.45 (0.32), residues: 309 sheet: -2.65 (0.28), residues: 279 loop : -2.69 (0.26), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP B 339 HIS 0.008 0.002 HIS B 225 PHE 0.029 0.003 PHE B 235 TYR 0.014 0.002 TYR E 190 ARG 0.004 0.000 ARG B 283 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 80 time to evaluate : 0.823 Fit side-chains REVERT: B 17 GLN cc_start: 0.8351 (tm-30) cc_final: 0.7994 (tm-30) REVERT: B 222 PHE cc_start: 0.8231 (OUTLIER) cc_final: 0.7519 (m-80) REVERT: E 34 MET cc_start: 0.7468 (tpp) cc_final: 0.7259 (tpp) REVERT: E 246 GLU cc_start: 0.7457 (mm-30) cc_final: 0.6930 (mm-30) REVERT: R 217 PHE cc_start: 0.6443 (OUTLIER) cc_final: 0.4572 (t80) outliers start: 14 outliers final: 8 residues processed: 93 average time/residue: 0.2164 time to fit residues: 26.5777 Evaluate side-chains 89 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 79 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 222 PHE Chi-restraints excluded: chain B residue 298 ASP Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 217 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 94 optimal weight: 0.9980 chunk 71 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 chunk 10 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 101 optimal weight: 0.0670 chunk 50 optimal weight: 0.8980 chunk 90 optimal weight: 10.0000 chunk 27 optimal weight: 0.8980 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 7647 Z= 0.166 Angle : 0.528 6.541 10443 Z= 0.283 Chirality : 0.041 0.132 1255 Planarity : 0.004 0.051 1330 Dihedral : 6.789 89.217 1141 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.15 % Allowed : 19.54 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.26), residues: 1047 helix: 0.80 (0.32), residues: 311 sheet: -2.49 (0.28), residues: 279 loop : -2.42 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP R 169 HIS 0.005 0.001 HIS B 225 PHE 0.009 0.001 PHE A 196 TYR 0.015 0.001 TYR R 184 ARG 0.006 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 84 time to evaluate : 0.797 Fit side-chains REVERT: B 17 GLN cc_start: 0.8326 (tm-30) cc_final: 0.7963 (tm-30) REVERT: B 51 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.8005 (mt) REVERT: E 38 ARG cc_start: 0.8422 (mtm-85) cc_final: 0.8097 (ttp-170) REVERT: E 246 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6855 (mm-30) REVERT: R 117 ARG cc_start: 0.7879 (mtm110) cc_final: 0.7480 (mtm110) outliers start: 14 outliers final: 6 residues processed: 97 average time/residue: 0.2322 time to fit residues: 29.5606 Evaluate side-chains 88 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 81 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 178 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 84 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 75 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 70 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 91 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 7647 Z= 0.348 Angle : 0.637 8.692 10443 Z= 0.337 Chirality : 0.044 0.181 1255 Planarity : 0.004 0.068 1330 Dihedral : 6.813 77.992 1141 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 3.85 % Allowed : 19.85 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.26), residues: 1047 helix: 0.71 (0.32), residues: 309 sheet: -2.65 (0.27), residues: 284 loop : -2.49 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP R 169 HIS 0.007 0.001 HIS B 225 PHE 0.023 0.002 PHE B 235 TYR 0.012 0.002 TYR E 190 ARG 0.005 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 82 time to evaluate : 0.895 Fit side-chains REVERT: A 21 ARG cc_start: 0.7854 (tmm-80) cc_final: 0.7568 (ttp-110) REVERT: B 10 GLU cc_start: 0.6172 (OUTLIER) cc_final: 0.5899 (tp30) REVERT: B 17 GLN cc_start: 0.8396 (tm-30) cc_final: 0.7982 (tm-30) REVERT: B 51 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8289 (mt) REVERT: E 246 GLU cc_start: 0.7302 (mm-30) cc_final: 0.6928 (mm-30) REVERT: R 117 ARG cc_start: 0.8043 (mtm110) cc_final: 0.7562 (mtm110) outliers start: 25 outliers final: 14 residues processed: 104 average time/residue: 0.2176 time to fit residues: 30.0855 Evaluate side-chains 96 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 80 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain E residue 35 HIS Chi-restraints excluded: chain E residue 80 PHE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain R residue 197 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 34 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 84 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 331 ASN ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7647 Z= 0.176 Angle : 0.542 8.138 10443 Z= 0.284 Chirality : 0.041 0.130 1255 Planarity : 0.004 0.054 1330 Dihedral : 6.059 72.469 1141 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.38 % Allowed : 21.23 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.26), residues: 1047 helix: 1.01 (0.32), residues: 308 sheet: -2.36 (0.28), residues: 272 loop : -2.39 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP R 169 HIS 0.005 0.001 HIS B 225 PHE 0.011 0.001 PHE B 235 TYR 0.015 0.001 TYR R 184 ARG 0.006 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 83 time to evaluate : 0.951 Fit side-chains REVERT: A 21 ARG cc_start: 0.7840 (tmm-80) cc_final: 0.7542 (ttp-110) REVERT: B 17 GLN cc_start: 0.8401 (tm-30) cc_final: 0.8081 (tm-30) REVERT: B 51 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.8008 (mt) REVERT: B 301 LYS cc_start: 0.7572 (OUTLIER) cc_final: 0.7355 (mtmm) REVERT: E 231 GLN cc_start: 0.8247 (pp30) cc_final: 0.7899 (pp30) REVERT: E 246 GLU cc_start: 0.7185 (mm-30) cc_final: 0.6844 (mm-30) REVERT: R 117 ARG cc_start: 0.7951 (mtm110) cc_final: 0.7478 (mtm110) outliers start: 22 outliers final: 12 residues processed: 103 average time/residue: 0.2263 time to fit residues: 31.6339 Evaluate side-chains 95 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 81 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 301 LYS Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain R residue 197 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 97 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 85 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 chunk 101 optimal weight: 0.0070 chunk 63 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 62 optimal weight: 0.4980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 331 ASN ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 7647 Z= 0.150 Angle : 0.525 8.244 10443 Z= 0.272 Chirality : 0.041 0.142 1255 Planarity : 0.004 0.063 1330 Dihedral : 5.665 67.171 1141 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.08 % Allowed : 22.00 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.26), residues: 1047 helix: 1.30 (0.32), residues: 309 sheet: -2.24 (0.28), residues: 281 loop : -2.27 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.004 0.001 HIS B 225 PHE 0.009 0.001 PHE B 235 TYR 0.016 0.001 TYR R 184 ARG 0.003 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 89 time to evaluate : 0.852 Fit side-chains REVERT: A 21 ARG cc_start: 0.7765 (tmm-80) cc_final: 0.7514 (ttp-110) REVERT: B 17 GLN cc_start: 0.8445 (tm-30) cc_final: 0.8106 (tm-30) REVERT: B 51 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.8027 (mt) REVERT: B 262 MET cc_start: 0.7637 (mmt) cc_final: 0.7400 (tpp) REVERT: E 38 ARG cc_start: 0.8287 (mtm-85) cc_final: 0.7984 (ttp-170) REVERT: E 246 GLU cc_start: 0.7080 (mm-30) cc_final: 0.6810 (mm-30) REVERT: R 117 ARG cc_start: 0.7905 (mtm110) cc_final: 0.7451 (mtm110) outliers start: 20 outliers final: 14 residues processed: 107 average time/residue: 0.2261 time to fit residues: 31.6060 Evaluate side-chains 96 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 81 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain R residue 197 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 40 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 19 optimal weight: 10.0000 chunk 64 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 50 optimal weight: 0.1980 chunk 9 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 92 optimal weight: 20.0000 chunk 96 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 331 ASN ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7647 Z= 0.212 Angle : 0.569 7.912 10443 Z= 0.297 Chirality : 0.042 0.144 1255 Planarity : 0.004 0.058 1330 Dihedral : 5.726 64.714 1141 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.54 % Allowed : 22.31 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.26), residues: 1047 helix: 1.30 (0.32), residues: 311 sheet: -2.26 (0.28), residues: 276 loop : -2.21 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 82 HIS 0.005 0.001 HIS B 225 PHE 0.013 0.001 PHE B 235 TYR 0.014 0.001 TYR R 184 ARG 0.006 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 81 time to evaluate : 0.837 Fit side-chains REVERT: A 21 ARG cc_start: 0.7800 (tmm-80) cc_final: 0.7516 (ttp-110) REVERT: B 17 GLN cc_start: 0.8460 (tm-30) cc_final: 0.8141 (tm-30) REVERT: B 51 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8080 (mt) REVERT: B 262 MET cc_start: 0.7685 (mmt) cc_final: 0.7458 (tpp) REVERT: E 38 ARG cc_start: 0.8351 (mtm-85) cc_final: 0.8017 (ttp-170) REVERT: E 246 GLU cc_start: 0.7098 (mm-30) cc_final: 0.6837 (mm-30) REVERT: R 117 ARG cc_start: 0.7929 (mtm110) cc_final: 0.7451 (mtm110) outliers start: 23 outliers final: 19 residues processed: 102 average time/residue: 0.2095 time to fit residues: 28.4812 Evaluate side-chains 98 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 78 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain E residue 35 HIS Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain R residue 197 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 3.9990 chunk 94 optimal weight: 9.9990 chunk 96 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 331 ASN ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 GLN ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 7647 Z= 0.322 Angle : 0.627 8.254 10443 Z= 0.331 Chirality : 0.044 0.173 1255 Planarity : 0.004 0.059 1330 Dihedral : 6.078 62.095 1141 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 4.46 % Allowed : 21.54 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.26), residues: 1047 helix: 1.17 (0.32), residues: 309 sheet: -2.36 (0.28), residues: 277 loop : -2.28 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 82 HIS 0.006 0.001 HIS B 225 PHE 0.020 0.002 PHE B 235 TYR 0.014 0.002 TYR R 184 ARG 0.003 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 78 time to evaluate : 0.918 Fit side-chains REVERT: A 21 ARG cc_start: 0.7798 (tmm-80) cc_final: 0.7512 (ttp-110) REVERT: A 333 GLN cc_start: 0.7883 (tm-30) cc_final: 0.7633 (tm-30) REVERT: B 17 GLN cc_start: 0.8477 (tm-30) cc_final: 0.8125 (tm-30) REVERT: B 51 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8212 (mt) REVERT: E 246 GLU cc_start: 0.7217 (mm-30) cc_final: 0.6907 (mm-30) REVERT: R 117 ARG cc_start: 0.8021 (mtm110) cc_final: 0.7527 (mtm110) REVERT: R 217 PHE cc_start: 0.6424 (OUTLIER) cc_final: 0.4522 (t80) outliers start: 29 outliers final: 19 residues processed: 104 average time/residue: 0.2047 time to fit residues: 28.9925 Evaluate side-chains 99 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 78 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 298 ASP Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain E residue 35 HIS Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 217 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 99 optimal weight: 9.9990 chunk 60 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 69 optimal weight: 4.9990 chunk 104 optimal weight: 0.7980 chunk 96 optimal weight: 0.9990 chunk 83 optimal weight: 7.9990 chunk 8 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 66 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 331 ASN ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 231 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7647 Z= 0.180 Angle : 0.567 8.964 10443 Z= 0.297 Chirality : 0.041 0.143 1255 Planarity : 0.004 0.059 1330 Dihedral : 5.667 59.635 1141 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 3.08 % Allowed : 23.23 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.27), residues: 1047 helix: 1.34 (0.32), residues: 310 sheet: -2.24 (0.28), residues: 277 loop : -2.18 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 82 HIS 0.005 0.001 HIS B 225 PHE 0.010 0.001 PHE B 234 TYR 0.017 0.001 TYR R 184 ARG 0.006 0.000 ARG E 160 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 80 time to evaluate : 0.838 Fit side-chains REVERT: A 21 ARG cc_start: 0.7710 (tmm-80) cc_final: 0.7508 (ttp-110) REVERT: B 17 GLN cc_start: 0.8451 (tm-30) cc_final: 0.8119 (tm-30) REVERT: B 51 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7904 (mp) REVERT: E 38 ARG cc_start: 0.8401 (mtm-85) cc_final: 0.8095 (ttp-170) REVERT: E 246 GLU cc_start: 0.7082 (mm-30) cc_final: 0.6824 (mm-30) REVERT: R 117 ARG cc_start: 0.7942 (mtm110) cc_final: 0.7444 (mtm110) outliers start: 20 outliers final: 17 residues processed: 99 average time/residue: 0.2157 time to fit residues: 28.6168 Evaluate side-chains 97 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 79 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain E residue 35 HIS Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain R residue 197 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 85 optimal weight: 0.5980 chunk 10 optimal weight: 10.0000 chunk 15 optimal weight: 0.8980 chunk 73 optimal weight: 0.2980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 231 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.136012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.104520 restraints weight = 12438.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.103866 restraints weight = 8373.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.105385 restraints weight = 7181.773| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7647 Z= 0.171 Angle : 0.557 9.480 10443 Z= 0.291 Chirality : 0.041 0.140 1255 Planarity : 0.004 0.059 1330 Dihedral : 5.433 58.123 1141 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 3.38 % Allowed : 22.92 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.27), residues: 1047 helix: 1.47 (0.32), residues: 311 sheet: -2.11 (0.28), residues: 282 loop : -2.15 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 82 HIS 0.005 0.001 HIS B 225 PHE 0.010 0.001 PHE B 234 TYR 0.017 0.001 TYR R 184 ARG 0.003 0.000 ARG E 160 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1662.29 seconds wall clock time: 31 minutes 6.17 seconds (1866.17 seconds total)