Starting phenix.real_space_refine on Thu Mar 14 23:57:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmf_13531/03_2024/7pmf_13531_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmf_13531/03_2024/7pmf_13531.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmf_13531/03_2024/7pmf_13531.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmf_13531/03_2024/7pmf_13531.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmf_13531/03_2024/7pmf_13531_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmf_13531/03_2024/7pmf_13531_updated.pdb" } resolution = 3.4 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 6443 2.51 5 N 1719 2.21 5 O 1892 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 123": "OE1" <-> "OE2" Residue "A TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 12": "NH1" <-> "NH2" Residue "A TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 35": "OD1" <-> "OD2" Residue "A ARG 41": "NH1" <-> "NH2" Residue "A ASP 47": "OD1" <-> "OD2" 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 TYR 284": "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 PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 511": "OE1" <-> "OE2" Residue "A GLU 512": "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 ARG 683": "NH1" <-> "NH2" Residue "A PHE 698": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 712": "NH1" <-> "NH2" Residue "A ARG 724": "NH1" <-> "NH2" Residue "A TYR 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 758": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 789": "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 ARG 39": "NH1" <-> "NH2" Residue "C TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 154": "OD1" <-> "OD2" Residue "C PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 241": "OE1" <-> "OE2" Residue "C ARG 254": "NH1" <-> "NH2" Residue "C PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 372": "NH1" <-> "NH2" 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: 10125 Number of models: 1 Model: "" Number of chains: 6 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: 6041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 739, 6041 Classifications: {'peptide': 739} Link IDs: {'PTRANS': 27, 'TRANS': 711} Chain breaks: 6 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: "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: 6.01, per 1000 atoms: 0.59 Number of scatterers: 10125 At special positions: 0 Unit cell: (105.6, 129.8, 150.7, 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 1892 8.00 N 1719 7.00 C 6443 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: 4.48 Conformation dependent library (CDL) restraints added in 1.9 seconds 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 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: 2366 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 60 helices and 12 sheets defined 48.9% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.23 Creating SS restraints... Processing helix chain 'B' and resid 6 through 19 Processing helix chain 'B' and resid 29 through 38 removed outlier: 4.394A pdb=" N GLY B 33 " --> pdb=" O TYR B 29 " (cutoff:3.500A) removed outlier: 4.587A 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: 4.283A 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 helix chain 'A' and resid 82 through 94 Processing helix chain 'A' and resid 117 through 119 No H-bonds generated for 'chain 'A' and resid 117 through 119' Processing helix chain 'A' and resid 121 through 127 Processing helix chain 'A' and resid 139 through 152 Processing helix chain 'A' and resid 169 through 184 Processing helix chain 'A' and resid 192 through 207 removed outlier: 4.007A 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 246 through 249 Processing helix chain 'A' and resid 260 through 270 removed outlier: 3.568A pdb=" N ALA A 269 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ALA A 270 " --> pdb=" O CYS A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 277 removed outlier: 4.101A pdb=" N THR A 276 " --> pdb=" O GLU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 284 No H-bonds generated for 'chain 'A' and resid 282 through 284' Processing helix chain 'A' and resid 286 through 291 removed outlier: 3.882A pdb=" N GLN A 290 " --> pdb=" O HIS A 286 " (cutoff:3.500A) removed outlier: 5.710A 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 315 removed outlier: 3.564A pdb=" N MET A 305 " --> pdb=" O ASP A 301 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN A 307 " --> pdb=" O LYS A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 337 removed outlier: 3.521A pdb=" N MET A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 364 Processing helix chain 'A' and resid 368 through 374 removed outlier: 3.767A pdb=" N HIS A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 423 removed outlier: 4.047A pdb=" N ALA A 422 " --> pdb=" O HIS A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 479 Processing helix chain 'A' and resid 484 through 486 No H-bonds generated for 'chain 'A' and resid 484 through 486' Processing helix chain 'A' and resid 493 through 500 Processing helix chain 'A' and resid 505 through 514 removed outlier: 3.604A 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 567 No H-bonds generated for 'chain 'A' and resid 564 through 567' Processing helix chain 'A' and resid 574 through 581 Processing helix chain 'A' and resid 587 through 593 removed outlier: 4.227A pdb=" N PHE A 593 " --> pdb=" O LEU A 589 " (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 684 removed outlier: 3.848A pdb=" N GLN A 680 " --> pdb=" O LYS A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 696 Processing helix chain 'A' and resid 704 through 714 removed outlier: 6.135A pdb=" N VAL A 713 " --> pdb=" O SER A 709 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N LEU A 714 " --> pdb=" O ARG A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 735 removed outlier: 3.972A 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 Processing helix chain 'C' and resid 55 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 removed outlier: 3.544A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) 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: 3.572A pdb=" N MET C 123 " --> pdb=" O MET C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 removed outlier: 3.544A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.608A 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 182 through 196 removed outlier: 3.689A pdb=" N ASP C 187 " --> pdb=" O ASP C 184 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N MET C 190 " --> pdb=" O ASP C 187 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU C 193 " --> pdb=" O MET C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 removed outlier: 3.591A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 232 Processing helix chain 'C' and resid 253 through 261 Proline residue: C 258 - end of helix removed outlier: 4.611A pdb=" N LEU C 261 " --> pdb=" O CYS C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 284 removed outlier: 3.511A pdb=" N LYS C 284 " --> pdb=" O ASN C 280 " (cutoff:3.500A) 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 335 through 348 removed outlier: 5.115A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY C 342 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA C 347 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 354 removed outlier: 3.543A 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: 3.512A pdb=" N LYS C 373 " --> pdb=" O VAL C 370 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 26 through 28 Processing sheet with id= B, first strand: chain 'A' and resid 11 through 16 removed outlier: 4.085A pdb=" N ALA A 11 " --> pdb=" O LEU A 27 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 48 " --> pdb=" O LEU A 40 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 100 through 103 removed outlier: 3.534A pdb=" N ILE A 662 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N VAL A 659 " --> pdb=" O SER A 158 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ILE A 160 " --> pdb=" O VAL A 659 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N CYS A 661 " --> pdb=" O ILE A 160 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N SER A 162 " --> pdb=" O CYS A 661 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N LYS A 663 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN A 157 " --> pdb=" O PHE A 432 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLY A 163 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY A 236 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 340 through 342 removed outlier: 3.510A pdb=" N ALA A 341 " --> pdb=" O ALA A 349 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 377 through 382 Processing sheet with id= F, first strand: chain 'A' and resid 547 through 551 Processing sheet with id= G, first strand: chain 'A' and resid 700 through 703 removed outlier: 3.811A pdb=" N SER A 700 " --> pdb=" O PHE A 751 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 8 through 11 Processing sheet with id= I, first strand: chain 'C' and resid 65 through 69 Processing sheet with id= J, first strand: chain 'C' and resid 103 through 107 Processing sheet with id= K, first strand: chain 'C' and resid 297 through 300 removed outlier: 6.548A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 238 through 241 433 hydrogen bonds defined for protein. 1191 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.23 Time building geometry restraints manager: 4.81 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: 1684 1.31 - 1.44: 2738 1.44 - 1.56: 5806 1.56 - 1.69: 8 1.69 - 1.81: 103 Bond restraints: 10339 Sorted by residual: bond pdb=" O3A ANP A1901 " pdb=" PB ANP A1901 " ideal model delta sigma weight residual 1.700 1.546 0.154 2.00e-02 2.50e+03 5.96e+01 bond pdb=" CA EEP H 2 " pdb=" C EEP H 2 " ideal model delta sigma weight residual 1.572 1.446 0.126 2.00e-02 2.50e+03 3.97e+01 bond pdb=" N3B ANP A1901 " pdb=" PG ANP A1901 " ideal model delta sigma weight residual 1.795 1.689 0.106 2.00e-02 2.50e+03 2.80e+01 bond pdb=" O5' ANP A1901 " pdb=" PA ANP A1901 " ideal model delta sigma weight residual 1.655 1.577 0.078 2.00e-02 2.50e+03 1.51e+01 bond pdb=" CA TRP H 1 " pdb=" C TRP H 1 " ideal model delta sigma weight residual 1.525 1.454 0.071 2.10e-02 2.27e+03 1.13e+01 ... (remaining 10334 not shown) Histogram of bond angle deviations from ideal: 99.05 - 106.43: 304 106.43 - 113.81: 5801 113.81 - 121.20: 5370 121.20 - 128.58: 2416 128.58 - 135.97: 77 Bond angle restraints: 13968 Sorted by residual: angle pdb=" PB ANP A1901 " pdb=" N3B ANP A1901 " pdb=" PG ANP A1901 " ideal model delta sigma weight residual 126.95 108.63 18.32 3.00e+00 1.11e-01 3.73e+01 angle pdb=" C HYP H 6 " pdb=" N ALA H 7 " pdb=" CA ALA H 7 " ideal model delta sigma weight residual 121.70 110.98 10.72 1.80e+00 3.09e-01 3.55e+01 angle pdb=" N DTH H 4 " pdb=" CA DTH H 4 " pdb=" CB DTH H 4 " ideal model delta sigma weight residual 111.50 101.72 9.78 1.70e+00 3.46e-01 3.31e+01 angle pdb=" N GLY A 563 " pdb=" CA GLY A 563 " pdb=" C GLY A 563 " ideal model delta sigma weight residual 113.86 122.10 -8.24 1.50e+00 4.44e-01 3.02e+01 angle pdb=" C TRP H 1 " pdb=" CA TRP H 1 " pdb=" CB TRP H 1 " ideal model delta sigma weight residual 110.10 100.45 9.65 1.90e+00 2.77e-01 2.58e+01 ... (remaining 13963 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.14: 6047 28.14 - 56.29: 153 56.29 - 84.43: 41 84.43 - 112.57: 6 112.57 - 140.72: 3 Dihedral angle restraints: 6250 sinusoidal: 2582 harmonic: 3668 Sorted by residual: 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 300.00 159.28 140.72 1 2.00e+01 2.50e-03 4.26e+01 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 300.00 170.09 129.91 1 2.00e+01 2.50e-03 3.94e+01 dihedral pdb=" CA PHE A 593 " pdb=" C PHE A 593 " pdb=" N GLN A 594 " pdb=" CA GLN A 594 " ideal model delta harmonic sigma weight residual -180.00 -151.03 -28.97 0 5.00e+00 4.00e-02 3.36e+01 ... (remaining 6247 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1097 0.060 - 0.120: 356 0.120 - 0.180: 63 0.180 - 0.241: 7 0.241 - 0.301: 1 Chirality restraints: 1524 Sorted by residual: chirality pdb=" C3' ANP A1901 " pdb=" C2' ANP A1901 " pdb=" C4' ANP A1901 " pdb=" O3' ANP A1901 " both_signs ideal model delta sigma weight residual False -2.36 -2.66 0.30 2.00e-01 2.50e+01 2.26e+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 2.27 0.24 2.00e-01 2.50e+01 1.39e+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 2.29 0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 1521 not shown) Planarity restraints: 1781 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 306 " -0.005 2.00e-02 2.50e+03 5.00e-02 5.01e+01 pdb=" CG TYR C 306 " -0.004 2.00e-02 2.50e+03 pdb=" CD1 TYR C 306 " -0.066 2.00e-02 2.50e+03 pdb=" CD2 TYR C 306 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR C 306 " 0.070 2.00e-02 2.50e+03 pdb=" CE2 TYR C 306 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR C 306 " 0.072 2.00e-02 2.50e+03 pdb=" OH TYR C 306 " -0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 206 " 0.163 9.50e-02 1.11e+02 9.40e-02 4.69e+01 pdb=" NE ARG C 206 " -0.048 2.00e-02 2.50e+03 pdb=" CZ ARG C 206 " 0.113 2.00e-02 2.50e+03 pdb=" NH1 ARG C 206 " -0.040 2.00e-02 2.50e+03 pdb=" NH2 ARG C 206 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 183 " 0.141 9.50e-02 1.11e+02 8.12e-02 3.51e+01 pdb=" NE ARG C 183 " -0.042 2.00e-02 2.50e+03 pdb=" CZ ARG C 183 " 0.097 2.00e-02 2.50e+03 pdb=" NH1 ARG C 183 " -0.035 2.00e-02 2.50e+03 pdb=" NH2 ARG C 183 " -0.028 2.00e-02 2.50e+03 ... (remaining 1778 not shown) Histogram of nonbonded interaction distances: 1.31 - 2.03: 4 2.03 - 2.75: 1399 2.75 - 3.47: 14135 3.47 - 4.18: 23501 4.18 - 4.90: 42616 Nonbonded interactions: 81655 Sorted by model distance: nonbonded pdb=" N TRP H 1 " pdb=" C ALA H 7 " model vdw 1.313 3.350 nonbonded pdb=" CD1 TRP H 1 " pdb=" SG CYS H 5 " model vdw 1.731 3.620 nonbonded pdb=" O3B ADP C 401 " pdb="MG MG C 402 " model vdw 1.916 2.170 nonbonded pdb=" O1A ANP A1901 " pdb="MG MG A1903 " model vdw 1.980 2.170 nonbonded pdb=" OH TYR A 456 " pdb=" OE1 GLU A 500 " model vdw 2.039 2.440 ... (remaining 81650 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.810 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 32.530 Find NCS groups from input model: 0.270 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 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 : 0.010 0.154 10339 Z= 0.613 Angle : 0.997 18.321 13968 Z= 0.569 Chirality : 0.059 0.301 1524 Planarity : 0.008 0.094 1781 Dihedral : 15.338 140.715 3884 Min Nonbonded Distance : 1.313 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 0.09 % Allowed : 0.00 % Favored : 99.91 % Cbeta Deviations : 0.08 % 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: -1.44 (0.21), residues: 1225 helix: -1.75 (0.16), residues: 602 sheet: 0.15 (0.38), residues: 159 loop : 0.14 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.005 TRP C 79 HIS 0.014 0.003 HIS A 418 PHE 0.075 0.003 PHE A 564 TYR 0.074 0.007 TYR C 306 ARG 0.114 0.012 ARG C 206 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 92 time to evaluate : 1.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 93 average time/residue: 0.3018 time to fit residues: 37.5032 Evaluate side-chains 59 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 58 time to evaluate : 1.270 ------------------------------------------------------------------------------- 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: 123 random chunks: chunk 103 optimal weight: 0.0980 chunk 93 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 111 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 GLN A 410 ASN A 430 HIS A 455 ASN A 464 GLN A 468 HIS A 474 GLN C 59 GLN C 162 ASN C 280 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10339 Z= 0.188 Angle : 0.612 7.574 13968 Z= 0.318 Chirality : 0.043 0.212 1524 Planarity : 0.004 0.035 1781 Dihedral : 9.732 118.303 1421 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Rotamer: Outliers : 0.37 % Allowed : 2.88 % Favored : 96.75 % 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: 0.66 (0.23), residues: 1225 helix: 0.40 (0.20), residues: 614 sheet: 0.64 (0.39), residues: 163 loop : 0.72 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 1 HIS 0.007 0.001 HIS A 418 PHE 0.033 0.001 PHE B 12 TYR 0.014 0.001 TYR A 102 ARG 0.008 0.001 ARG C 206 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 70 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 MET cc_start: 0.3503 (mtt) cc_final: 0.3163 (mmt) outliers start: 4 outliers final: 2 residues processed: 71 average time/residue: 0.2487 time to fit residues: 25.3616 Evaluate side-chains 60 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 58 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain C residue 257 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 110 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 89 optimal weight: 0.0980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10339 Z= 0.165 Angle : 0.550 8.224 13968 Z= 0.279 Chirality : 0.041 0.177 1524 Planarity : 0.003 0.032 1781 Dihedral : 8.648 118.381 1420 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 0.46 % Allowed : 4.09 % Favored : 95.45 % 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: 1.34 (0.24), residues: 1225 helix: 1.11 (0.21), residues: 609 sheet: 0.74 (0.38), residues: 165 loop : 0.89 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 484 HIS 0.005 0.001 HIS A 418 PHE 0.016 0.001 PHE B 12 TYR 0.010 0.001 TYR A 79 ARG 0.004 0.000 ARG A 343 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 68 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 MET cc_start: 0.3504 (mtt) cc_final: 0.3072 (mmt) REVERT: A 478 MET cc_start: 0.7810 (mmp) cc_final: 0.7143 (mmp) REVERT: A 490 TYR cc_start: 0.6309 (t80) cc_final: 0.5983 (t80) outliers start: 5 outliers final: 2 residues processed: 72 average time/residue: 0.2527 time to fit residues: 26.0525 Evaluate side-chains 62 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 60 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain C residue 257 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 0.5980 chunk 84 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 12 optimal weight: 20.0000 chunk 53 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN C 161 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10339 Z= 0.253 Angle : 0.552 7.762 13968 Z= 0.279 Chirality : 0.041 0.175 1524 Planarity : 0.003 0.033 1781 Dihedral : 8.264 119.853 1420 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 0.46 % Allowed : 4.74 % Favored : 94.80 % 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: 1.58 (0.24), residues: 1225 helix: 1.43 (0.22), residues: 611 sheet: 0.75 (0.38), residues: 169 loop : 0.85 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 484 HIS 0.006 0.001 HIS A 418 PHE 0.012 0.001 PHE B 12 TYR 0.010 0.001 TYR A 490 ARG 0.010 0.000 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 54 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 57 average time/residue: 0.2400 time to fit residues: 20.4116 Evaluate side-chains 55 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 52 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 257 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 136 ASN ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 464 GLN ** A 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 10339 Z= 0.447 Angle : 0.651 7.558 13968 Z= 0.330 Chirality : 0.043 0.177 1524 Planarity : 0.004 0.033 1781 Dihedral : 8.387 126.494 1420 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 0.84 % Allowed : 6.04 % Favored : 93.13 % 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: 1.43 (0.24), residues: 1225 helix: 1.40 (0.22), residues: 603 sheet: 0.61 (0.39), residues: 168 loop : 0.66 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 484 HIS 0.007 0.001 HIS A 418 PHE 0.014 0.002 PHE C 255 TYR 0.015 0.002 TYR A 490 ARG 0.006 0.001 ARG B 37 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 51 time to evaluate : 1.267 Fit side-chains revert: symmetry clash REVERT: B 120 MET cc_start: 0.3529 (mtt) cc_final: 0.3181 (mmt) REVERT: A 478 MET cc_start: 0.8005 (mmp) cc_final: 0.7636 (mmp) outliers start: 9 outliers final: 8 residues processed: 58 average time/residue: 0.2359 time to fit residues: 20.4425 Evaluate side-chains 57 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 49 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 257 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 0.6980 chunk 23 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 119 optimal weight: 0.5980 chunk 98 optimal weight: 0.8980 chunk 55 optimal weight: 0.0980 chunk 9 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 136 ASN ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10339 Z= 0.149 Angle : 0.532 7.006 13968 Z= 0.264 Chirality : 0.040 0.179 1524 Planarity : 0.003 0.032 1781 Dihedral : 7.681 123.196 1420 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 0.56 % Allowed : 6.69 % Favored : 92.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.25), residues: 1225 helix: 1.60 (0.22), residues: 604 sheet: 0.72 (0.39), residues: 165 loop : 0.84 (0.31), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 484 HIS 0.004 0.001 HIS A 418 PHE 0.012 0.001 PHE C 223 TYR 0.011 0.001 TYR A 490 ARG 0.012 0.000 ARG A 41 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 52 time to evaluate : 1.322 Fit side-chains REVERT: B 120 MET cc_start: 0.3511 (mtt) cc_final: 0.3159 (mmt) REVERT: A 503 MET cc_start: 0.7860 (mmm) cc_final: 0.7625 (mmp) outliers start: 6 outliers final: 3 residues processed: 57 average time/residue: 0.2117 time to fit residues: 18.8919 Evaluate side-chains 50 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 47 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain C residue 17 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 66 optimal weight: 0.2980 chunk 118 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 136 ASN ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10339 Z= 0.194 Angle : 0.542 10.375 13968 Z= 0.265 Chirality : 0.040 0.174 1524 Planarity : 0.003 0.032 1781 Dihedral : 7.273 123.950 1420 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 0.84 % Allowed : 7.34 % Favored : 91.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.25), residues: 1225 helix: 1.67 (0.22), residues: 606 sheet: 0.75 (0.38), residues: 168 loop : 0.80 (0.31), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 484 HIS 0.004 0.001 HIS A 418 PHE 0.009 0.001 PHE C 223 TYR 0.009 0.001 TYR A 490 ARG 0.007 0.000 ARG A 41 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 48 time to evaluate : 1.426 Fit side-chains REVERT: B 120 MET cc_start: 0.3579 (mtt) cc_final: 0.3247 (mmt) REVERT: A 486 LEU cc_start: 0.8021 (mp) cc_final: 0.7806 (pp) outliers start: 9 outliers final: 9 residues processed: 56 average time/residue: 0.2063 time to fit residues: 18.1743 Evaluate side-chains 56 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 47 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 ASN Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 257 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 75 optimal weight: 0.0060 chunk 80 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 chunk 11 optimal weight: 10.0000 chunk 93 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 113 optimal weight: 0.8980 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 136 ASN ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 10339 Z= 0.157 Angle : 0.544 12.128 13968 Z= 0.262 Chirality : 0.040 0.177 1524 Planarity : 0.003 0.030 1781 Dihedral : 7.040 123.126 1420 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 0.74 % Allowed : 7.52 % Favored : 91.74 % 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: 1.82 (0.25), residues: 1225 helix: 1.75 (0.22), residues: 600 sheet: 0.75 (0.39), residues: 165 loop : 0.84 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 484 HIS 0.004 0.001 HIS A 418 PHE 0.007 0.001 PHE C 255 TYR 0.009 0.001 TYR A 79 ARG 0.007 0.000 ARG A 231 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 51 time to evaluate : 1.263 Fit side-chains REVERT: B 36 MET cc_start: 0.8841 (mmm) cc_final: 0.8258 (mmm) REVERT: B 73 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.8438 (mpp) REVERT: B 120 MET cc_start: 0.3591 (mtt) cc_final: 0.3303 (mmt) REVERT: A 478 MET cc_start: 0.7907 (mmm) cc_final: 0.6565 (mmp) REVERT: A 486 LEU cc_start: 0.7989 (mp) cc_final: 0.7758 (pp) outliers start: 8 outliers final: 5 residues processed: 58 average time/residue: 0.2001 time to fit residues: 18.2314 Evaluate side-chains 55 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 49 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 257 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.0010 chunk 110 optimal weight: 0.7980 chunk 113 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 48 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 104 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 136 ASN ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 10339 Z= 0.142 Angle : 0.545 11.017 13968 Z= 0.260 Chirality : 0.040 0.176 1524 Planarity : 0.003 0.031 1781 Dihedral : 6.910 122.331 1420 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 0.74 % Allowed : 7.52 % Favored : 91.74 % 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 (0.25), residues: 1225 helix: 1.72 (0.22), residues: 599 sheet: 0.78 (0.39), residues: 165 loop : 0.79 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP A 484 HIS 0.004 0.001 HIS A 418 PHE 0.008 0.001 PHE C 223 TYR 0.009 0.001 TYR A 79 ARG 0.006 0.000 ARG A 41 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 50 time to evaluate : 1.292 Fit side-chains REVERT: B 36 MET cc_start: 0.8784 (mmm) cc_final: 0.8183 (mmm) REVERT: B 73 MET cc_start: 0.8701 (OUTLIER) cc_final: 0.8437 (mpp) REVERT: B 120 MET cc_start: 0.3468 (mtt) cc_final: 0.3122 (mmt) outliers start: 8 outliers final: 5 residues processed: 56 average time/residue: 0.2090 time to fit residues: 18.4290 Evaluate side-chains 55 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 49 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 136 ASN Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain C residue 257 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 122 optimal weight: 0.1980 chunk 112 optimal weight: 0.2980 chunk 97 optimal weight: 0.7980 chunk 10 optimal weight: 7.9990 chunk 75 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 136 ASN ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 10339 Z= 0.147 Angle : 0.551 10.683 13968 Z= 0.263 Chirality : 0.040 0.177 1524 Planarity : 0.003 0.035 1781 Dihedral : 6.859 122.212 1420 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.56 % Allowed : 7.61 % Favored : 91.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.25), residues: 1225 helix: 1.72 (0.22), residues: 600 sheet: 0.78 (0.39), residues: 165 loop : 0.77 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP A 484 HIS 0.004 0.001 HIS A 418 PHE 0.008 0.001 PHE C 223 TYR 0.009 0.001 TYR A 79 ARG 0.006 0.000 ARG A 231 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 50 time to evaluate : 1.495 Fit side-chains REVERT: B 36 MET cc_start: 0.8787 (mmm) cc_final: 0.8179 (mmm) REVERT: B 73 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.8451 (mpp) REVERT: B 120 MET cc_start: 0.3509 (mtt) cc_final: 0.3150 (mmt) REVERT: A 478 MET cc_start: 0.7752 (mmp) cc_final: 0.7463 (mmp) outliers start: 6 outliers final: 5 residues processed: 54 average time/residue: 0.2015 time to fit residues: 17.0931 Evaluate side-chains 55 residues out of total 1088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 49 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 136 ASN Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain C residue 257 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 97 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 12 optimal weight: 8.9990 chunk 18 optimal weight: 0.6980 chunk 85 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.046833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.033564 restraints weight = 57960.988| |-----------------------------------------------------------------------------| r_work (start): 0.2753 rms_B_bonded: 4.04 r_work: 0.2589 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10339 Z= 0.222 Angle : 0.571 13.315 13968 Z= 0.274 Chirality : 0.040 0.180 1524 Planarity : 0.003 0.036 1781 Dihedral : 6.875 123.364 1420 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.65 % Allowed : 7.89 % Favored : 91.46 % 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 (0.25), residues: 1225 helix: 1.80 (0.22), residues: 599 sheet: 0.69 (0.39), residues: 166 loop : 0.72 (0.31), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A 484 HIS 0.004 0.001 HIS A 418 PHE 0.016 0.001 PHE A 220 TYR 0.010 0.001 TYR A 79 ARG 0.006 0.000 ARG A 231 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2148.12 seconds wall clock time: 39 minutes 34.95 seconds (2374.95 seconds total)