Starting phenix.real_space_refine on Fri Mar 15 00:13:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm7_13523/03_2024/7pm7_13523_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm7_13523/03_2024/7pm7_13523.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm7_13523/03_2024/7pm7_13523.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm7_13523/03_2024/7pm7_13523.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm7_13523/03_2024/7pm7_13523_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm7_13523/03_2024/7pm7_13523_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 4 5.49 5 Mg 2 5.21 5 S 63 5.16 5 C 6462 2.51 5 N 1724 2.21 5 O 1894 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 ASP 17": "OD1" <-> "OD2" Residue "A ASP 136": "OD1" <-> "OD2" Residue "A GLU 145": "OE1" <-> "OE2" Residue "A GLU 164": "OE1" <-> "OE2" 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 ARG 233": "NH1" <-> "NH2" Residue "A PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 343": "NH1" <-> "NH2" Residue "A PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 362": "OD1" <-> "OD2" Residue "A TYR 368": "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 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 539": "OE1" <-> "OE2" Residue "A PHE 586": "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 701": "NH1" <-> "NH2" Residue "A PHE 708": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 712": "NH1" <-> "NH2" Residue "A PHE 751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 758": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 768": "NH1" <-> "NH2" Residue "A ARG 789": "NH1" <-> "NH2" Residue "A ARG 791": "NH1" <-> "NH2" Residue "A ARG 792": "NH1" <-> "NH2" Residue "C ASP 25": "OD1" <-> "OD2" Residue "C PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 154": "OD1" <-> "OD2" Residue "C ASP 184": "OD1" <-> "OD2" Residue "C GLU 195": "OE1" <-> "OE2" Residue "C PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 254": "NH1" <-> "NH2" Residue "C PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10149 Number of models: 1 Model: "" Number of chains: 6 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: 6070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 6070 Classifications: {'peptide': 743} Link IDs: {'PTRANS': 27, 'TRANS': 715} 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: "A" 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} 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: 5.94, per 1000 atoms: 0.59 Number of scatterers: 10149 At special positions: 0 Unit cell: (107.06, 139.92, 147.34, 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 4 15.00 Mg 2 11.99 O 1894 8.00 N 1724 7.00 C 6462 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: 4.52 Conformation dependent library (CDL) restraints added in 2.1 seconds 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 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: 2374 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 61 helices and 12 sheets defined 49.2% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.30 Creating SS restraints... Processing helix chain 'B' and resid 6 through 19 Processing helix chain 'B' and resid 29 through 38 removed outlier: 4.284A pdb=" N GLY B 33 " --> pdb=" O TYR B 29 " (cutoff:3.500A) removed outlier: 4.597A 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: 4.266A 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 183 removed outlier: 3.781A pdb=" N PHE A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 207 Proline residue: A 201 - end of helix Processing helix chain 'A' and resid 246 through 249 Processing helix chain 'A' and resid 260 through 268 Processing helix chain 'A' and resid 274 through 277 Processing helix chain 'A' and resid 286 through 291 removed outlier: 3.967A pdb=" N GLN A 290 " --> pdb=" O HIS A 286 " (cutoff:3.500A) removed outlier: 5.292A 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: 4.027A pdb=" N VAL A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ASN A 307 " --> pdb=" O LYS A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 336 Processing helix chain 'A' and resid 355 through 364 removed outlier: 3.597A pdb=" N PHE A 360 " --> pdb=" O PRO A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 376 Processing helix chain 'A' and resid 393 through 423 removed outlier: 3.521A pdb=" N ASP A 417 " --> pdb=" O ASN A 413 " (cutoff:3.500A) removed outlier: 3.597A 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: 3.525A pdb=" N GLU A 512 " --> pdb=" O LEU A 508 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N CYS A 513 " --> pdb=" O LEU A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 531 removed outlier: 3.508A pdb=" N GLN A 525 " --> pdb=" O ASP A 521 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS A 526 " --> pdb=" O THR A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 568 No H-bonds generated for 'chain 'A' and resid 565 through 568' Processing helix chain 'A' and resid 574 through 581 removed outlier: 3.521A pdb=" N LEU A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 594 removed outlier: 3.993A pdb=" N PHE A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 633 No H-bonds generated for 'chain 'A' and resid 630 through 633' Processing helix chain 'A' and resid 636 through 652 removed outlier: 4.090A pdb=" N ARG A 641 " --> pdb=" O GLY A 637 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 684 removed outlier: 3.804A 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: 5.785A pdb=" N VAL A 713 " --> pdb=" O SER A 709 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LEU A 714 " --> pdb=" O ARG A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 719 No H-bonds generated for 'chain 'A' and resid 717 through 719' Processing helix chain 'A' and resid 724 through 735 removed outlier: 3.706A pdb=" N GLU A 733 " --> pdb=" O LYS A 729 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS A 734 " --> pdb=" O ASN A 730 " (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 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 92 removed outlier: 3.656A 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: 3.698A pdb=" N GLU C 117 " --> pdb=" O LYS C 113 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N MET C 123 " --> pdb=" O MET C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 144 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: 4.017A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 removed outlier: 3.535A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 232 Processing helix chain 'C' and resid 234 through 236 No H-bonds generated for 'chain 'C' and resid 234 through 236' Processing helix chain 'C' and resid 252 through 261 removed outlier: 4.123A pdb=" N CYS C 257 " --> pdb=" O ARG C 254 " (cutoff:3.500A) Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 274 through 284 removed outlier: 3.591A pdb=" N LYS C 284 " --> pdb=" O ASN C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 295 removed outlier: 3.969A pdb=" N TYR C 294 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 304 No H-bonds generated for 'chain 'C' and resid 302 through 304' Processing helix chain 'C' and resid 309 through 320 removed outlier: 3.779A pdb=" N ALA C 319 " --> pdb=" O LYS C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 348 removed outlier: 4.284A pdb=" N VAL C 339 " --> pdb=" O ARG C 335 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N TRP C 340 " --> pdb=" O LYS C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 354 removed outlier: 4.273A pdb=" N GLN C 354 " --> pdb=" O SER C 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 350 through 354' Processing helix chain 'C' and resid 359 through 365 Processing helix chain 'C' and resid 367 through 374 removed outlier: 4.313A pdb=" N LYS C 373 " --> pdb=" O VAL C 370 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N CYS C 374 " --> pdb=" O HIS C 371 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 103 through 105 Processing sheet with id= B, first strand: chain 'A' and resid 12 through 16 Processing sheet with id= C, first strand: chain 'A' and resid 37 through 40 Processing sheet with id= D, first strand: chain 'A' and resid 100 through 103 removed outlier: 3.599A pdb=" N GLN A 157 " --> pdb=" O PHE A 432 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLY A 163 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER A 431 " --> pdb=" O PHE A 228 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY A 236 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 377 through 381 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: 3.761A 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 12 Processing sheet with id= I, first strand: chain 'C' and resid 34 through 38 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: 6.681A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.483A 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 241 428 hydrogen bonds defined for protein. 1227 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: 3.01 Time building geometry restraints manager: 4.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1690 1.32 - 1.44: 2741 1.44 - 1.57: 5826 1.57 - 1.69: 6 1.69 - 1.81: 102 Bond restraints: 10365 Sorted by residual: bond pdb=" CA EEP H 2 " pdb=" C EEP H 2 " ideal model delta sigma weight residual 1.572 1.451 0.121 2.00e-02 2.50e+03 3.69e+01 bond pdb=" C EEP H 2 " pdb=" O EEP H 2 " ideal model delta sigma weight residual 1.263 1.201 0.062 2.00e-02 2.50e+03 9.48e+00 bond pdb=" CA TRP H 1 " pdb=" C TRP H 1 " ideal model delta sigma weight residual 1.525 1.463 0.062 2.10e-02 2.27e+03 8.74e+00 bond pdb=" C HYP H 6 " pdb=" N ALA H 7 " ideal model delta sigma weight residual 1.329 1.370 -0.041 1.40e-02 5.10e+03 8.67e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.54e+00 ... (remaining 10360 not shown) Histogram of bond angle deviations from ideal: 98.55 - 106.09: 256 106.09 - 113.63: 5688 113.63 - 121.16: 5428 121.16 - 128.70: 2560 128.70 - 136.24: 71 Bond angle restraints: 14003 Sorted by residual: angle pdb=" C HYP H 6 " pdb=" N ALA H 7 " pdb=" CA ALA H 7 " ideal model delta sigma weight residual 121.70 109.79 11.91 1.80e+00 3.09e-01 4.38e+01 angle pdb=" N HYP H 6 " pdb=" CA HYP H 6 " pdb=" CB HYP H 6 " ideal model delta sigma weight residual 103.00 107.80 -4.80 1.10e+00 8.26e-01 1.90e+01 angle pdb=" C TRP H 1 " pdb=" CA TRP H 1 " pdb=" CB TRP H 1 " ideal model delta sigma weight residual 110.10 102.06 8.04 1.90e+00 2.77e-01 1.79e+01 angle pdb=" CD2 TRP H 1 " pdb=" CE2 TRP H 1 " pdb=" CZ2 TRP H 1 " ideal model delta sigma weight residual 122.40 118.28 4.12 1.00e+00 1.00e+00 1.69e+01 angle pdb=" N DTH H 4 " pdb=" CA DTH H 4 " pdb=" CB DTH H 4 " ideal model delta sigma weight residual 111.50 105.01 6.49 1.70e+00 3.46e-01 1.46e+01 ... (remaining 13998 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.71: 6079 32.71 - 65.42: 139 65.42 - 98.12: 27 98.12 - 130.83: 3 130.83 - 163.54: 1 Dihedral angle restraints: 6249 sinusoidal: 2568 harmonic: 3681 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 300.00 136.46 163.54 1 2.00e+01 2.50e-03 4.70e+01 dihedral pdb=" O1B ADP A1902 " pdb=" O3A ADP A1902 " pdb=" PB ADP A1902 " pdb=" PA ADP A1902 " ideal model delta sinusoidal sigma weight residual -60.00 66.38 -126.38 1 2.00e+01 2.50e-03 3.82e+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 300.00 176.15 123.85 1 2.00e+01 2.50e-03 3.74e+01 ... (remaining 6246 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1011 0.041 - 0.083: 353 0.083 - 0.124: 130 0.124 - 0.165: 27 0.165 - 0.207: 9 Chirality restraints: 1530 Sorted by residual: chirality pdb=" CA PHE C 255 " pdb=" N PHE C 255 " pdb=" C PHE C 255 " pdb=" CB PHE C 255 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA MET A 364 " pdb=" N MET A 364 " pdb=" C MET A 364 " pdb=" CB MET A 364 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA PHE C 124 " pdb=" N PHE C 124 " pdb=" C PHE C 124 " pdb=" CB PHE C 124 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.17e-01 ... (remaining 1527 not shown) Planarity restraints: 1786 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 248 " -0.114 9.50e-02 1.11e+02 6.65e-02 2.44e+01 pdb=" NE ARG A 248 " 0.034 2.00e-02 2.50e+03 pdb=" CZ ARG A 248 " -0.081 2.00e-02 2.50e+03 pdb=" NH1 ARG A 248 " 0.029 2.00e-02 2.50e+03 pdb=" NH2 ARG A 248 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 213 " 0.284 9.50e-02 1.11e+02 1.31e-01 2.06e+01 pdb=" NE ARG A 213 " 0.002 2.00e-02 2.50e+03 pdb=" CZ ARG A 213 " -0.060 2.00e-02 2.50e+03 pdb=" NH1 ARG A 213 " 0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG A 213 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 312 " -0.101 9.50e-02 1.11e+02 5.85e-02 1.85e+01 pdb=" NE ARG C 312 " 0.030 2.00e-02 2.50e+03 pdb=" CZ ARG C 312 " -0.071 2.00e-02 2.50e+03 pdb=" NH1 ARG C 312 " 0.025 2.00e-02 2.50e+03 pdb=" NH2 ARG C 312 " 0.020 2.00e-02 2.50e+03 ... (remaining 1783 not shown) Histogram of nonbonded interaction distances: 1.32 - 2.03: 2 2.03 - 2.75: 1045 2.75 - 3.47: 14804 3.47 - 4.18: 23707 4.18 - 4.90: 42429 Nonbonded interactions: 81987 Sorted by model distance: nonbonded pdb=" N TRP H 1 " pdb=" C ALA H 7 " model vdw 1.316 3.350 nonbonded pdb=" CD1 TRP H 1 " pdb=" SG CYS H 5 " model vdw 1.732 3.620 nonbonded pdb=" OG1 THR A 170 " pdb="MG MG A1901 " model vdw 2.140 2.170 nonbonded pdb=" OH TYR A 456 " pdb=" OE1 GLU A 500 " model vdw 2.141 2.440 nonbonded pdb=" O PHE A 698 " pdb=" NH1 ARG A 701 " model vdw 2.154 2.520 ... (remaining 81982 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.350 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: 6.950 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 31.830 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 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 : 0.004 0.121 10365 Z= 0.270 Angle : 0.853 11.913 14003 Z= 0.501 Chirality : 0.050 0.207 1530 Planarity : 0.008 0.131 1786 Dihedral : 15.669 163.540 3875 Min Nonbonded Distance : 1.316 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Rotamer: Outliers : 0.09 % Allowed : 0.46 % Favored : 99.44 % 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: -1.31 (0.21), residues: 1231 helix: -1.57 (0.17), residues: 589 sheet: 0.64 (0.39), residues: 148 loop : -0.16 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.004 TRP C 340 HIS 0.007 0.001 HIS C 371 PHE 0.032 0.002 PHE C 255 TYR 0.044 0.006 TYR A 113 ARG 0.083 0.011 ARG A 248 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 151 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 242 LEU cc_start: 0.8896 (mt) cc_final: 0.8164 (mp) outliers start: 1 outliers final: 1 residues processed: 152 average time/residue: 0.2629 time to fit residues: 54.9534 Evaluate side-chains 92 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 91 time to evaluate : 1.262 ------------------------------------------------------------------------------- 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: 125 random chunks: chunk 105 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 50 optimal weight: 0.0970 chunk 97 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 ASN A 191 ASN A 264 GLN A 354 HIS A 395 HIS A 462 GLN A 463 GLN A 730 ASN ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN C 162 ASN C 173 HIS C 280 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10365 Z= 0.243 Angle : 0.623 7.513 14003 Z= 0.324 Chirality : 0.044 0.227 1530 Planarity : 0.004 0.043 1786 Dihedral : 9.179 137.438 1405 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Rotamer: Outliers : 0.83 % Allowed : 6.11 % Favored : 93.06 % 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: 0.98 (0.24), residues: 1231 helix: 0.79 (0.21), residues: 607 sheet: 1.00 (0.38), residues: 161 loop : 0.56 (0.30), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 340 HIS 0.008 0.001 HIS C 275 PHE 0.021 0.002 PHE C 255 TYR 0.027 0.001 TYR A 102 ARG 0.008 0.001 ARG A 213 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 96 time to evaluate : 1.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 478 MET cc_start: 0.8066 (mmp) cc_final: 0.7642 (mmp) REVERT: A 484 TRP cc_start: 0.6242 (m-10) cc_final: 0.5813 (m-10) outliers start: 9 outliers final: 5 residues processed: 102 average time/residue: 0.1945 time to fit residues: 29.7863 Evaluate side-chains 88 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 83 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 374 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 63 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 77 optimal weight: 0.4980 chunk 31 optimal weight: 1.9990 chunk 113 optimal weight: 0.4980 chunk 122 optimal weight: 0.8980 chunk 101 optimal weight: 0.7980 chunk 112 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 775 GLN ** 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: 0.8300 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10365 Z= 0.191 Angle : 0.563 7.628 14003 Z= 0.286 Chirality : 0.041 0.189 1530 Planarity : 0.004 0.051 1786 Dihedral : 7.344 82.947 1405 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.39 % Allowed : 7.86 % Favored : 90.75 % 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: 1.60 (0.24), residues: 1231 helix: 1.44 (0.21), residues: 606 sheet: 1.24 (0.38), residues: 161 loop : 0.67 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 340 HIS 0.006 0.001 HIS C 275 PHE 0.019 0.001 PHE C 255 TYR 0.019 0.001 TYR A 102 ARG 0.006 0.000 ARG B 110 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 87 time to evaluate : 1.320 Fit side-chains REVERT: A 135 MET cc_start: 0.7887 (mmm) cc_final: 0.7642 (mmm) REVERT: A 478 MET cc_start: 0.7922 (mmp) cc_final: 0.7633 (mmp) outliers start: 15 outliers final: 11 residues processed: 96 average time/residue: 0.2197 time to fit residues: 30.9086 Evaluate side-chains 78 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 67 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 283 MET Chi-restraints excluded: chain C residue 311 ASP Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 374 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 54 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 114 optimal weight: 0.0270 chunk 120 optimal weight: 5.9990 chunk 108 optimal weight: 0.5980 chunk 32 optimal weight: 0.0970 chunk 100 optimal weight: 3.9990 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10365 Z= 0.154 Angle : 0.543 6.867 14003 Z= 0.272 Chirality : 0.040 0.186 1530 Planarity : 0.004 0.053 1786 Dihedral : 6.535 70.259 1405 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.39 % Allowed : 8.88 % Favored : 89.73 % 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: 1.88 (0.25), residues: 1231 helix: 1.69 (0.22), residues: 601 sheet: 1.34 (0.38), residues: 167 loop : 0.80 (0.31), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 484 HIS 0.004 0.001 HIS C 275 PHE 0.017 0.001 PHE C 255 TYR 0.015 0.001 TYR A 102 ARG 0.007 0.000 ARG A 779 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 77 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 MET cc_start: 0.4990 (mmm) cc_final: 0.4649 (tpp) outliers start: 15 outliers final: 10 residues processed: 85 average time/residue: 0.1963 time to fit residues: 25.8182 Evaluate side-chains 77 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 67 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 283 MET Chi-restraints excluded: chain C residue 311 ASP Chi-restraints excluded: chain C residue 374 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 68 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 89 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 83 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 30 optimal weight: 0.1980 chunk 40 optimal weight: 0.1980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 406 HIS A 418 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10365 Z= 0.235 Angle : 0.567 7.187 14003 Z= 0.283 Chirality : 0.042 0.187 1530 Planarity : 0.004 0.052 1786 Dihedral : 6.252 69.624 1405 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.67 % Allowed : 8.88 % Favored : 89.45 % 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: 1.86 (0.25), residues: 1231 helix: 1.74 (0.22), residues: 603 sheet: 1.26 (0.39), residues: 167 loop : 0.70 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 484 HIS 0.004 0.001 HIS A 354 PHE 0.017 0.001 PHE C 255 TYR 0.009 0.001 TYR C 143 ARG 0.008 0.000 ARG B 110 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 66 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 MET cc_start: 0.6339 (tmm) cc_final: 0.5138 (tmm) outliers start: 18 outliers final: 12 residues processed: 79 average time/residue: 0.2034 time to fit residues: 24.5567 Evaluate side-chains 72 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 60 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 775 GLN Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 374 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 40 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 116 optimal weight: 0.2980 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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: 0.8356 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10365 Z= 0.261 Angle : 0.583 8.367 14003 Z= 0.291 Chirality : 0.042 0.189 1530 Planarity : 0.004 0.054 1786 Dihedral : 6.043 68.300 1405 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.48 % Allowed : 9.81 % Favored : 88.71 % 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: 1.83 (0.25), residues: 1231 helix: 1.74 (0.22), residues: 603 sheet: 1.18 (0.39), residues: 167 loop : 0.67 (0.31), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 484 HIS 0.005 0.001 HIS C 275 PHE 0.021 0.001 PHE A 470 TYR 0.009 0.001 TYR C 143 ARG 0.008 0.000 ARG B 110 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 68 time to evaluate : 1.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 MET cc_start: 0.5902 (tmm) cc_final: 0.5376 (tmm) REVERT: B 110 ARG cc_start: 0.9222 (tmm160) cc_final: 0.8973 (ppt170) REVERT: B 120 MET cc_start: 0.4635 (tpt) cc_final: 0.4127 (tpp) outliers start: 16 outliers final: 10 residues processed: 82 average time/residue: 0.2040 time to fit residues: 25.3343 Evaluate side-chains 75 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 65 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 775 GLN Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 374 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 13 optimal weight: 5.9990 chunk 68 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 120 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 297 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10365 Z= 0.252 Angle : 0.577 7.877 14003 Z= 0.287 Chirality : 0.042 0.190 1530 Planarity : 0.004 0.056 1786 Dihedral : 5.838 67.365 1405 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.94 % Allowed : 9.81 % Favored : 88.25 % 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: 1231 helix: 1.81 (0.22), residues: 602 sheet: 1.10 (0.39), residues: 167 loop : 0.60 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 484 HIS 0.004 0.001 HIS A 354 PHE 0.017 0.001 PHE C 255 TYR 0.008 0.001 TYR C 143 ARG 0.004 0.000 ARG B 110 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 69 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 330 ILE cc_start: 0.9122 (mt) cc_final: 0.8868 (tp) outliers start: 21 outliers final: 15 residues processed: 85 average time/residue: 0.2024 time to fit residues: 25.9116 Evaluate side-chains 79 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 64 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 775 GLN Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 374 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 71 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 94 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 10365 Z= 0.314 Angle : 0.614 9.600 14003 Z= 0.307 Chirality : 0.042 0.198 1530 Planarity : 0.004 0.056 1786 Dihedral : 5.898 68.010 1405 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.57 % Allowed : 10.36 % Favored : 88.07 % 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: 1.69 (0.25), residues: 1231 helix: 1.68 (0.22), residues: 605 sheet: 0.98 (0.38), residues: 177 loop : 0.57 (0.31), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 484 HIS 0.005 0.001 HIS A 354 PHE 0.017 0.001 PHE C 255 TYR 0.009 0.001 TYR A 711 ARG 0.003 0.000 ARG B 110 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 70 time to evaluate : 1.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 110 ARG cc_start: 0.9153 (ppt170) cc_final: 0.8903 (ppt170) REVERT: B 120 MET cc_start: 0.5323 (tpp) cc_final: 0.5011 (tpp) REVERT: C 330 ILE cc_start: 0.9137 (mt) cc_final: 0.8871 (tp) outliers start: 17 outliers final: 14 residues processed: 80 average time/residue: 0.2145 time to fit residues: 27.2029 Evaluate side-chains 80 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 66 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 775 GLN Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 374 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 429 GLN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10365 Z= 0.279 Angle : 0.613 10.288 14003 Z= 0.305 Chirality : 0.042 0.196 1530 Planarity : 0.004 0.057 1786 Dihedral : 5.849 67.435 1405 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.39 % Allowed : 10.92 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.25), residues: 1231 helix: 1.69 (0.22), residues: 605 sheet: 0.95 (0.38), residues: 177 loop : 0.56 (0.31), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 484 HIS 0.004 0.001 HIS A 354 PHE 0.017 0.001 PHE C 255 TYR 0.008 0.001 TYR A 31 ARG 0.003 0.000 ARG B 64 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 69 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 36 MET cc_start: 0.7363 (tmm) cc_final: 0.6407 (tpp) REVERT: B 110 ARG cc_start: 0.9189 (ppt170) cc_final: 0.8853 (ppt170) REVERT: C 330 ILE cc_start: 0.9143 (mt) cc_final: 0.8890 (tp) outliers start: 15 outliers final: 15 residues processed: 80 average time/residue: 0.1971 time to fit residues: 24.2652 Evaluate side-chains 80 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 65 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 775 GLN Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 374 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 72 optimal weight: 3.9990 chunk 56 optimal weight: 0.3980 chunk 82 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 chunk 60 optimal weight: 0.5980 chunk 78 optimal weight: 0.8980 chunk 105 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.4047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10365 Z= 0.176 Angle : 0.579 11.107 14003 Z= 0.284 Chirality : 0.041 0.191 1530 Planarity : 0.004 0.059 1786 Dihedral : 5.607 66.781 1405 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.30 % Allowed : 11.29 % Favored : 87.42 % 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: 1.83 (0.25), residues: 1231 helix: 1.81 (0.22), residues: 606 sheet: 1.03 (0.38), residues: 177 loop : 0.62 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 340 HIS 0.004 0.001 HIS C 275 PHE 0.016 0.001 PHE A 360 TYR 0.008 0.001 TYR A 259 ARG 0.003 0.000 ARG B 37 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 75 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 36 MET cc_start: 0.7375 (tmm) cc_final: 0.6326 (tpp) REVERT: B 110 ARG cc_start: 0.9154 (ppt170) cc_final: 0.8812 (ppt170) REVERT: A 354 HIS cc_start: 0.8323 (OUTLIER) cc_final: 0.8114 (t-170) REVERT: C 154 ASP cc_start: 0.7713 (t70) cc_final: 0.7340 (t0) REVERT: C 330 ILE cc_start: 0.9109 (mt) cc_final: 0.8876 (tp) outliers start: 14 outliers final: 11 residues processed: 85 average time/residue: 0.2028 time to fit residues: 25.9410 Evaluate side-chains 80 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 68 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain A residue 354 HIS Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 775 GLN Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 374 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 30 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 41 optimal weight: 0.0670 chunk 101 optimal weight: 0.8980 chunk 12 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 5 optimal weight: 0.0270 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.073322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.053033 restraints weight = 36187.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.055065 restraints weight = 17015.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.056405 restraints weight = 10474.290| |-----------------------------------------------------------------------------| r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.4138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10365 Z= 0.165 Angle : 0.580 11.307 14003 Z= 0.284 Chirality : 0.041 0.190 1530 Planarity : 0.004 0.060 1786 Dihedral : 5.540 67.589 1405 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.20 % Allowed : 11.75 % Favored : 87.05 % 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: 1231 helix: 1.87 (0.22), residues: 605 sheet: 0.94 (0.38), residues: 161 loop : 0.56 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 340 HIS 0.004 0.001 HIS C 87 PHE 0.016 0.001 PHE A 360 TYR 0.008 0.001 TYR A 179 ARG 0.003 0.000 ARG A 213 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2047.54 seconds wall clock time: 37 minutes 50.25 seconds (2270.25 seconds total)