Starting phenix.real_space_refine on Fri Mar 15 00:54:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmi_13535/03_2024/7pmi_13535_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmi_13535/03_2024/7pmi_13535.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmi_13535/03_2024/7pmi_13535.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmi_13535/03_2024/7pmi_13535.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmi_13535/03_2024/7pmi_13535_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmi_13535/03_2024/7pmi_13535_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 P 5 5.49 5 Mg 3 5.21 5 S 63 5.16 5 C 6482 2.51 5 N 1730 2.21 5 O 1906 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 12": "NH1" <-> "NH2" Residue "A ASP 17": "OD1" <-> "OD2" Residue "A TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 41": "NH1" <-> "NH2" Residue "A TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 213": "NH1" <-> "NH2" Residue "A ARG 219": "NH1" <-> "NH2" Residue "A PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 231": "NH1" <-> "NH2" Residue "A TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 256": "OE1" <-> "OE2" Residue "A PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 343": "NH1" <-> "NH2" Residue "A PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 450": "OE1" <-> "OE2" Residue "A PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 511": "OE1" <-> "OE2" Residue "A GLU 512": "OE1" <-> "OE2" Residue "A GLU 539": "OE1" <-> "OE2" Residue "A PHE 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 673": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 674": "OD1" <-> "OD2" Residue "A PHE 698": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 712": "NH1" <-> "NH2" Residue "A ASP 723": "OD1" <-> "OD2" Residue "A ARG 724": "NH1" <-> "NH2" Residue "A ARG 789": "NH1" <-> "NH2" Residue "A ARG 791": "NH1" <-> "NH2" Residue "A ARG 792": "NH1" <-> "NH2" Residue "C PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 154": "OD1" <-> "OD2" Residue "C ASP 157": "OD1" <-> "OD2" Residue "C TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 241": "OE1" <-> "OE2" Residue "C ARG 254": "NH1" <-> "NH2" Residue "C PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 372": "NH1" <-> "NH2" Residue "B PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 123": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10189 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 6105 Classifications: {'peptide': 747} Link IDs: {'PTRANS': 27, 'TRANS': 719} Chain breaks: 5 Chain: "C" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "B" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1059 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.90, per 1000 atoms: 0.58 Number of scatterers: 10189 At special positions: 0 Unit cell: (108.9, 130.9, 151.8, 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) S 63 16.00 P 5 15.00 Mg 3 11.99 O 1906 8.00 N 1730 7.00 C 6482 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.05 Conformation dependent library (CDL) restraints added in 1.7 seconds 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTH H 4 " Number of C-beta restraints generated: 2382 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 59 helices and 12 sheets defined 48.1% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.02 Creating SS restraints... Processing helix chain 'A' and resid 74 through 76 No H-bonds generated for 'chain 'A' and resid 74 through 76' Processing helix chain 'A' and resid 82 through 94 Processing helix chain 'A' and resid 121 through 127 Processing helix chain 'A' and resid 139 through 152 removed outlier: 3.679A pdb=" N GLU A 145 " --> pdb=" O ALA A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 183 removed outlier: 3.521A pdb=" N ALA A 176 " --> pdb=" O SER A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 207 removed outlier: 3.573A pdb=" N SER A 199 " --> pdb=" O LYS A 195 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASN A 200 " --> pdb=" O VAL A 196 " (cutoff:3.500A) Proline residue: A 201 - end of helix Processing helix chain 'A' and resid 247 through 249 No H-bonds generated for 'chain 'A' and resid 247 through 249' Processing helix chain 'A' and resid 260 through 267 Processing helix chain 'A' and resid 273 through 277 removed outlier: 3.560A pdb=" N THR A 276 " --> pdb=" O GLU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 291 removed outlier: 3.869A pdb=" N GLN A 290 " --> pdb=" O HIS A 286 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N GLY A 291 " --> pdb=" O TYR A 287 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 286 through 291' Processing helix chain 'A' and resid 301 through 314 removed outlier: 4.125A pdb=" N VAL A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN A 307 " --> pdb=" O LYS A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 337 removed outlier: 3.756A pdb=" N MET A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY A 324 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 364 Processing helix chain 'A' and resid 368 through 374 Processing helix chain 'A' and resid 393 through 423 Processing helix chain 'A' and resid 449 through 479 Processing helix chain 'A' and resid 493 through 499 Processing helix chain 'A' and resid 505 through 514 removed outlier: 4.009A pdb=" N LYS A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 531 Processing helix chain 'A' and resid 564 through 568 Processing helix chain 'A' and resid 574 through 582 Processing helix chain 'A' and resid 587 through 594 removed outlier: 4.150A pdb=" N PHE A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 633 No H-bonds generated for 'chain 'A' and resid 631 through 633' Processing helix chain 'A' and resid 636 through 652 Processing helix chain 'A' and resid 675 through 685 removed outlier: 3.861A pdb=" N GLN A 680 " --> pdb=" O LYS A 676 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG A 683 " --> pdb=" O VAL A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 695 Processing helix chain 'A' and resid 704 through 714 removed outlier: 5.686A pdb=" N VAL A 713 " --> pdb=" O SER A 709 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N LEU A 714 " --> pdb=" O ARG A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 735 removed outlier: 3.662A pdb=" N GLU A 733 " --> pdb=" O LYS A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 741 No H-bonds generated for 'chain 'A' and resid 739 through 741' Processing helix chain 'A' and resid 755 through 791 removed outlier: 3.750A pdb=" N THR A 777 " --> pdb=" O ARG A 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 79 through 91 Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 113 through 125 removed outlier: 3.721A pdb=" N MET C 123 " --> pdb=" O MET C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 removed outlier: 3.758A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 183 through 196 removed outlier: 3.849A pdb=" N TYR C 188 " --> pdb=" O ASP C 184 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LYS C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 removed outlier: 3.783A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 231 Processing helix chain 'C' and resid 252 through 261 Proline residue: C 258 - end of helix removed outlier: 4.616A pdb=" N LEU C 261 " --> pdb=" O CYS C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 266 No H-bonds generated for 'chain 'C' and resid 264 through 266' Processing helix chain 'C' and resid 274 through 283 Processing helix chain 'C' and resid 290 through 294 Processing helix chain 'C' and resid 302 through 305 Processing helix chain 'C' and resid 309 through 320 Processing helix chain 'C' and resid 333 through 348 removed outlier: 4.602A pdb=" N LYS C 336 " --> pdb=" O PRO C 333 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY C 342 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA C 347 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 354 removed outlier: 4.006A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 351 through 354' Processing helix chain 'C' and resid 359 through 365 Processing helix chain 'C' and resid 367 through 373 removed outlier: 3.522A pdb=" N VAL C 370 " --> pdb=" O PRO C 367 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS C 373 " --> pdb=" O VAL C 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 19 Processing helix chain 'B' and resid 29 through 39 removed outlier: 4.239A pdb=" N GLY B 33 " --> pdb=" O TYR B 29 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ASP B 34 " --> pdb=" O SER B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 52 Processing helix chain 'B' and resid 57 through 62 Processing helix chain 'B' and resid 67 through 78 Proline residue: B 72 - end of helix Processing helix chain 'B' and resid 87 through 96 removed outlier: 4.160A pdb=" N PHE B 96 " --> pdb=" O GLY B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 115 Processing helix chain 'B' and resid 122 through 129 Processing helix chain 'B' and resid 141 through 149 Processing sheet with id= A, first strand: chain 'A' and resid 12 through 16 removed outlier: 7.302A pdb=" N GLN A 39 " --> pdb=" O LEU A 28 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 100 through 103 removed outlier: 4.024A pdb=" N GLY A 236 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 340 through 342 Processing sheet with id= D, first strand: chain 'A' and resid 377 through 381 Processing sheet with id= E, first strand: chain 'A' and resid 547 through 551 Processing sheet with id= F, first strand: chain 'A' and resid 700 through 703 removed outlier: 3.594A pdb=" N SER A 700 " --> pdb=" O PHE A 751 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 8 through 11 Processing sheet with id= H, first strand: chain 'C' and resid 34 through 38 Processing sheet with id= I, first strand: chain 'C' and resid 103 through 107 Processing sheet with id= J, first strand: chain 'C' and resid 297 through 300 removed outlier: 6.359A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 238 through 241 Processing sheet with id= L, first strand: chain 'B' and resid 26 through 28 428 hydrogen bonds defined for protein. 1218 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: 2.85 Time building geometry restraints manager: 5.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1714 1.31 - 1.44: 2744 1.44 - 1.56: 5835 1.56 - 1.69: 9 1.69 - 1.81: 102 Bond restraints: 10404 Sorted by residual: bond pdb=" O3A ANP A1901 " pdb=" PB ANP A1901 " ideal model delta sigma weight residual 1.700 1.539 0.161 2.00e-02 2.50e+03 6.48e+01 bond pdb=" CA EEP H 2 " pdb=" C EEP H 2 " ideal model delta sigma weight residual 1.572 1.436 0.136 2.00e-02 2.50e+03 4.62e+01 bond pdb=" N3B ANP A1901 " pdb=" PG ANP A1901 " ideal model delta sigma weight residual 1.795 1.686 0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" C EEP H 2 " pdb=" O EEP H 2 " ideal model delta sigma weight residual 1.263 1.192 0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" O5' ANP A1901 " pdb=" PA ANP A1901 " ideal model delta sigma weight residual 1.655 1.585 0.070 2.00e-02 2.50e+03 1.24e+01 ... (remaining 10399 not shown) Histogram of bond angle deviations from ideal: 96.55 - 104.33: 184 104.33 - 112.11: 4993 112.11 - 119.89: 4340 119.89 - 127.67: 4438 127.67 - 135.45: 101 Bond angle restraints: 14056 Sorted by residual: angle pdb=" PB ANP A1901 " pdb=" N3B ANP A1901 " pdb=" PG ANP A1901 " ideal model delta sigma weight residual 126.95 105.87 21.08 3.00e+00 1.11e-01 4.94e+01 angle pdb=" N CYS H 5 " pdb=" CA CYS H 5 " pdb=" CB CYS H 5 " ideal model delta sigma weight residual 110.50 100.16 10.34 1.70e+00 3.46e-01 3.70e+01 angle pdb=" C HYP H 6 " pdb=" N ALA H 7 " pdb=" CA ALA H 7 " ideal model delta sigma weight residual 121.70 111.89 9.81 1.80e+00 3.09e-01 2.97e+01 angle pdb=" N DTH H 4 " pdb=" CA DTH H 4 " pdb=" CB DTH H 4 " ideal model delta sigma weight residual 111.50 103.03 8.47 1.70e+00 3.46e-01 2.48e+01 angle pdb=" N GLY A 563 " pdb=" CA GLY A 563 " pdb=" C GLY A 563 " ideal model delta sigma weight residual 113.86 121.03 -7.17 1.50e+00 4.44e-01 2.29e+01 ... (remaining 14051 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.26: 6036 27.26 - 54.52: 196 54.52 - 81.78: 49 81.78 - 109.04: 8 109.04 - 136.30: 5 Dihedral angle restraints: 6294 sinusoidal: 2601 harmonic: 3693 Sorted by residual: dihedral pdb=" C5' ADP C 401 " pdb=" O5' ADP C 401 " pdb=" PA ADP C 401 " pdb=" O2A ADP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 171.94 128.06 1 2.00e+01 2.50e-03 3.88e+01 dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 61.86 -121.86 1 2.00e+01 2.50e-03 3.67e+01 dihedral pdb=" O2A ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PA ADP C 401 " pdb=" PB ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 57.07 -117.07 1 2.00e+01 2.50e-03 3.49e+01 ... (remaining 6291 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1158 0.076 - 0.152: 334 0.152 - 0.228: 35 0.228 - 0.304: 5 0.304 - 0.380: 2 Chirality restraints: 1534 Sorted by residual: chirality pdb=" CA MET A 478 " pdb=" N MET A 478 " pdb=" C MET A 478 " pdb=" CB MET A 478 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.61e+00 chirality pdb=" CA GLU C 316 " pdb=" N GLU C 316 " pdb=" C GLU C 316 " pdb=" CB GLU C 316 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" CA PHE A 564 " pdb=" N PHE A 564 " pdb=" C PHE A 564 " pdb=" CB PHE A 564 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.96e+00 ... (remaining 1531 not shown) Planarity restraints: 1793 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 784 " -0.284 9.50e-02 1.11e+02 1.55e-01 1.08e+02 pdb=" NE ARG A 784 " 0.077 2.00e-02 2.50e+03 pdb=" CZ ARG A 784 " -0.168 2.00e-02 2.50e+03 pdb=" NH1 ARG A 784 " 0.059 2.00e-02 2.50e+03 pdb=" NH2 ARG A 784 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 564 " -0.044 2.00e-02 2.50e+03 4.36e-02 3.32e+01 pdb=" CG PHE A 564 " 0.101 2.00e-02 2.50e+03 pdb=" CD1 PHE A 564 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 PHE A 564 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE A 564 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 564 " -0.012 2.00e-02 2.50e+03 pdb=" CZ PHE A 564 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 116 " -0.105 9.50e-02 1.11e+02 6.15e-02 2.08e+01 pdb=" NE ARG C 116 " 0.032 2.00e-02 2.50e+03 pdb=" CZ ARG C 116 " -0.075 2.00e-02 2.50e+03 pdb=" NH1 ARG C 116 " 0.027 2.00e-02 2.50e+03 pdb=" NH2 ARG C 116 " 0.022 2.00e-02 2.50e+03 ... (remaining 1790 not shown) Histogram of nonbonded interaction distances: 1.31 - 2.02: 4 2.02 - 2.74: 1491 2.74 - 3.46: 14295 3.46 - 4.18: 23695 4.18 - 4.90: 42969 Nonbonded interactions: 82454 Sorted by model distance: nonbonded pdb=" N TRP H 1 " pdb=" C ALA H 7 " model vdw 1.306 3.350 nonbonded pdb=" CD1 TRP H 1 " pdb=" SG CYS H 5 " model vdw 1.733 3.620 nonbonded pdb=" O3B ADP C 401 " pdb="MG MG C 402 " model vdw 1.928 2.170 nonbonded pdb=" O2G ANP A1901 " pdb="MG MG A1902 " model vdw 1.940 2.170 nonbonded pdb=" NH1 ARG A 784 " pdb=" O ARG B 37 " model vdw 2.086 2.520 ... (remaining 82449 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: 2.140 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: 7.040 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 30.890 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 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 : 0.014 0.161 10404 Z= 0.902 Angle : 1.173 21.081 14056 Z= 0.659 Chirality : 0.069 0.380 1534 Planarity : 0.010 0.155 1793 Dihedral : 15.800 136.295 3912 Min Nonbonded Distance : 1.306 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 0.09 % Allowed : 0.28 % Favored : 99.63 % Cbeta Deviations : 0.17 % 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: -1.50 (0.21), residues: 1235 helix: -1.73 (0.16), residues: 627 sheet: 0.33 (0.37), residues: 167 loop : 0.02 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.006 TRP A 484 HIS 0.014 0.003 HIS A 418 PHE 0.101 0.004 PHE A 564 TYR 0.039 0.007 TYR A 477 ARG 0.171 0.015 ARG A 784 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 84 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 ASP cc_start: 0.9297 (p0) cc_final: 0.8919 (p0) outliers start: 1 outliers final: 1 residues processed: 85 average time/residue: 0.3304 time to fit residues: 37.5891 Evaluate side-chains 59 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 58 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.5980 chunk 93 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 37 optimal weight: 0.0970 chunk 59 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 GLN A 398 ASN A 455 ASN C 162 ASN C 280 ASN C 296 ASN B 75 GLN B 140 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10404 Z= 0.200 Angle : 0.640 8.194 14056 Z= 0.333 Chirality : 0.043 0.203 1534 Planarity : 0.004 0.041 1793 Dihedral : 10.758 149.058 1430 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 0.37 % Allowed : 3.96 % Favored : 95.67 % 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: 0.57 (0.23), residues: 1235 helix: 0.36 (0.20), residues: 628 sheet: 1.02 (0.40), residues: 153 loop : 0.44 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 484 HIS 0.006 0.001 HIS C 275 PHE 0.015 0.001 PHE B 93 TYR 0.012 0.001 TYR A 787 ARG 0.007 0.001 ARG A 683 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 66 time to evaluate : 1.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 ASP cc_start: 0.9321 (p0) cc_final: 0.8986 (t70) REVERT: B 120 MET cc_start: 0.7337 (mtm) cc_final: 0.6904 (ptm) outliers start: 4 outliers final: 0 residues processed: 69 average time/residue: 0.2618 time to fit residues: 26.0931 Evaluate side-chains 58 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 76 optimal weight: 0.1980 chunk 31 optimal weight: 0.9990 chunk 112 optimal weight: 8.9990 chunk 121 optimal weight: 9.9990 chunk 100 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 455 ASN B 140 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10404 Z= 0.280 Angle : 0.590 8.328 14056 Z= 0.304 Chirality : 0.042 0.166 1534 Planarity : 0.004 0.046 1793 Dihedral : 9.927 147.735 1429 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 0.46 % Allowed : 4.42 % Favored : 95.12 % 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: 1.16 (0.24), residues: 1235 helix: 1.07 (0.21), residues: 611 sheet: 0.73 (0.38), residues: 166 loop : 0.61 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 781 HIS 0.006 0.001 HIS A 418 PHE 0.016 0.001 PHE A 564 TYR 0.011 0.001 TYR A 10 ARG 0.007 0.000 ARG B 37 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 57 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 ASP cc_start: 0.9286 (p0) cc_final: 0.8912 (t0) REVERT: B 120 MET cc_start: 0.7347 (mtm) cc_final: 0.6904 (ptm) outliers start: 5 outliers final: 2 residues processed: 59 average time/residue: 0.2462 time to fit residues: 21.3580 Evaluate side-chains 58 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 56 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 384 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 12 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 113 optimal weight: 0.4980 chunk 119 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 455 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10404 Z= 0.209 Angle : 0.541 7.217 14056 Z= 0.274 Chirality : 0.040 0.170 1534 Planarity : 0.003 0.036 1793 Dihedral : 9.489 149.002 1429 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 0.74 % Allowed : 5.53 % Favored : 93.73 % 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: 1.33 (0.24), residues: 1235 helix: 1.34 (0.22), residues: 609 sheet: 0.70 (0.38), residues: 166 loop : 0.51 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 781 HIS 0.005 0.001 HIS A 418 PHE 0.012 0.001 PHE B 93 TYR 0.010 0.001 TYR A 10 ARG 0.002 0.000 ARG B 64 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 59 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 715 MET cc_start: 0.5592 (mmm) cc_final: 0.5374 (mmp) REVERT: B 66 ASP cc_start: 0.9267 (p0) cc_final: 0.8842 (t70) REVERT: B 120 MET cc_start: 0.7102 (mtm) cc_final: 0.6615 (ptm) outliers start: 8 outliers final: 2 residues processed: 64 average time/residue: 0.2515 time to fit residues: 23.3591 Evaluate side-chains 62 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 60 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain B residue 36 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 chunk 49 optimal weight: 0.0270 chunk 102 optimal weight: 0.0870 chunk 82 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 30 optimal weight: 0.0470 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10404 Z= 0.142 Angle : 0.515 8.095 14056 Z= 0.258 Chirality : 0.039 0.170 1534 Planarity : 0.003 0.038 1793 Dihedral : 9.116 151.181 1429 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.46 % Allowed : 6.27 % Favored : 93.27 % 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: 1.42 (0.24), residues: 1235 helix: 1.51 (0.22), residues: 609 sheet: 0.73 (0.38), residues: 167 loop : 0.41 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 484 HIS 0.003 0.001 HIS A 418 PHE 0.012 0.001 PHE B 93 TYR 0.009 0.001 TYR A 102 ARG 0.003 0.000 ARG A 692 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 67 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 299 MET cc_start: 0.7870 (mtp) cc_final: 0.7527 (mtp) REVERT: B 120 MET cc_start: 0.7132 (mtm) cc_final: 0.6687 (ptm) outliers start: 5 outliers final: 1 residues processed: 71 average time/residue: 0.2461 time to fit residues: 25.4186 Evaluate side-chains 53 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 52 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 119 optimal weight: 9.9990 chunk 99 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 ASN A 455 ASN A 638 HIS ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 10404 Z= 0.320 Angle : 0.603 11.773 14056 Z= 0.299 Chirality : 0.041 0.165 1534 Planarity : 0.003 0.038 1793 Dihedral : 9.110 150.834 1429 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.11 % Allowed : 6.54 % Favored : 92.35 % 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: 1.41 (0.24), residues: 1235 helix: 1.52 (0.22), residues: 618 sheet: 0.56 (0.37), residues: 168 loop : 0.43 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 781 HIS 0.005 0.001 HIS A 418 PHE 0.014 0.001 PHE A 564 TYR 0.010 0.001 TYR A 10 ARG 0.006 0.000 ARG B 64 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 52 time to evaluate : 1.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 299 MET cc_start: 0.7953 (mtp) cc_final: 0.7516 (mtp) REVERT: B 120 MET cc_start: 0.7038 (mtm) cc_final: 0.6610 (ptm) outliers start: 12 outliers final: 4 residues processed: 60 average time/residue: 0.2157 time to fit residues: 19.9418 Evaluate side-chains 54 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 50 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain B residue 73 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 0.1980 chunk 13 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 67 optimal weight: 10.0000 chunk 100 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 119 optimal weight: 8.9990 chunk 74 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 455 ASN ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10404 Z= 0.250 Angle : 0.577 12.771 14056 Z= 0.283 Chirality : 0.041 0.171 1534 Planarity : 0.003 0.042 1793 Dihedral : 8.997 152.135 1429 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.74 % Allowed : 7.47 % Favored : 91.80 % 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: 1.42 (0.24), residues: 1235 helix: 1.59 (0.22), residues: 607 sheet: 0.49 (0.37), residues: 167 loop : 0.39 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 781 HIS 0.006 0.001 HIS A 418 PHE 0.009 0.001 PHE C 255 TYR 0.010 0.001 TYR A 787 ARG 0.004 0.000 ARG B 64 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 54 time to evaluate : 1.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 MET cc_start: 0.7059 (mtm) cc_final: 0.6628 (ptm) outliers start: 8 outliers final: 4 residues processed: 59 average time/residue: 0.2295 time to fit residues: 20.7554 Evaluate side-chains 54 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 50 time to evaluate : 1.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 73 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 455 ASN ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 10404 Z= 0.434 Angle : 0.680 13.997 14056 Z= 0.335 Chirality : 0.043 0.173 1534 Planarity : 0.004 0.043 1793 Dihedral : 9.078 150.699 1429 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.20 % Allowed : 7.74 % Favored : 91.06 % 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: 1.27 (0.24), residues: 1235 helix: 1.48 (0.22), residues: 612 sheet: 0.31 (0.37), residues: 167 loop : 0.34 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 781 HIS 0.008 0.001 HIS A 418 PHE 0.020 0.001 PHE A 564 TYR 0.012 0.001 TYR A 10 ARG 0.004 0.000 ARG A 784 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 52 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 MET cc_start: 0.7138 (mtm) cc_final: 0.6626 (ptm) outliers start: 13 outliers final: 8 residues processed: 58 average time/residue: 0.1986 time to fit residues: 18.1381 Evaluate side-chains 58 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 50 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 790 MET Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 194 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 chunk 67 optimal weight: 8.9990 chunk 48 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 chunk 110 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 455 ASN A 474 GLN ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10404 Z= 0.214 Angle : 0.607 12.572 14056 Z= 0.298 Chirality : 0.041 0.219 1534 Planarity : 0.003 0.043 1793 Dihedral : 8.931 152.394 1429 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.65 % Allowed : 8.29 % Favored : 91.06 % 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: 1.32 (0.24), residues: 1235 helix: 1.56 (0.22), residues: 608 sheet: 0.28 (0.37), residues: 170 loop : 0.34 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 781 HIS 0.004 0.001 HIS A 418 PHE 0.008 0.001 PHE B 93 TYR 0.010 0.001 TYR A 10 ARG 0.003 0.000 ARG B 64 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 53 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 MET cc_start: 0.7038 (mtm) cc_final: 0.6569 (ptm) outliers start: 7 outliers final: 6 residues processed: 57 average time/residue: 0.2142 time to fit residues: 18.7799 Evaluate side-chains 59 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 53 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 790 MET Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 184 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 0.7980 chunk 71 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 123 optimal weight: 8.9990 chunk 113 optimal weight: 6.9990 chunk 98 optimal weight: 0.9980 chunk 10 optimal weight: 0.0980 chunk 75 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 78 optimal weight: 0.5980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 455 ASN A 463 GLN ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10404 Z= 0.227 Angle : 0.606 12.301 14056 Z= 0.297 Chirality : 0.041 0.197 1534 Planarity : 0.003 0.043 1793 Dihedral : 8.797 152.455 1429 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.55 % Allowed : 8.02 % Favored : 91.43 % 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: 1.33 (0.24), residues: 1235 helix: 1.60 (0.22), residues: 609 sheet: 0.27 (0.37), residues: 170 loop : 0.31 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 781 HIS 0.005 0.001 HIS A 418 PHE 0.009 0.001 PHE A 432 TYR 0.010 0.001 TYR A 10 ARG 0.003 0.000 ARG B 64 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 54 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 MET cc_start: 0.7305 (mtm) cc_final: 0.6768 (ptm) outliers start: 6 outliers final: 6 residues processed: 57 average time/residue: 0.2220 time to fit residues: 19.4574 Evaluate side-chains 59 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 53 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 790 MET Chi-restraints excluded: chain C residue 17 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.9990 chunk 30 optimal weight: 0.0010 chunk 90 optimal weight: 0.0170 chunk 14 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 chunk 101 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 overall best weight: 0.5626 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 455 ASN ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.049988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.035740 restraints weight = 54414.823| |-----------------------------------------------------------------------------| r_work (start): 0.2788 rms_B_bonded: 3.96 r_work: 0.2622 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 10404 Z= 0.164 Angle : 0.588 12.163 14056 Z= 0.287 Chirality : 0.041 0.195 1534 Planarity : 0.003 0.043 1793 Dihedral : 8.641 153.227 1429 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.46 % Allowed : 8.48 % Favored : 91.06 % 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: 1.35 (0.24), residues: 1235 helix: 1.60 (0.22), residues: 607 sheet: 0.30 (0.38), residues: 168 loop : 0.33 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 781 HIS 0.004 0.000 HIS A 418 PHE 0.009 0.001 PHE B 93 TYR 0.009 0.001 TYR A 102 ARG 0.004 0.000 ARG A 309 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2046.40 seconds wall clock time: 37 minutes 49.27 seconds (2269.27 seconds total)