Starting phenix.real_space_refine on Fri Mar 15 00:36:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm5_13521/03_2024/7pm5_13521_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm5_13521/03_2024/7pm5_13521.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm5_13521/03_2024/7pm5_13521.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm5_13521/03_2024/7pm5_13521.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm5_13521/03_2024/7pm5_13521_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm5_13521/03_2024/7pm5_13521_updated.pdb" } resolution = 3.1 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 6474 2.51 5 N 1727 2.21 5 O 1901 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 ARG 12": "NH1" <-> "NH2" Residue "A ASP 17": "OD1" <-> "OD2" Residue "A TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 136": "OD1" <-> "OD2" Residue "A GLU 145": "OE1" <-> "OE2" Residue "A GLU 164": "OE1" <-> "OE2" 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 TYR 242": "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 442": "OE1" <-> "OE2" Residue "A GLU 450": "OE1" <-> "OE2" Residue "A PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 511": "OE1" <-> "OE2" Residue "A GLU 512": "OE1" <-> "OE2" Residue "A GLU 539": "OE1" <-> "OE2" Residue "A PHE 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 673": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 674": "OD1" <-> "OD2" Residue "A PHE 698": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 712": "NH1" <-> "NH2" Residue "A TYR 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 768": "NH1" <-> "NH2" Residue "A TYR 787": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 789": "NH1" <-> "NH2" Residue "A ARG 791": "NH1" <-> "NH2" Residue "A ARG 792": "NH1" <-> "NH2" Residue "C TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 72": "OE1" <-> "OE2" Residue "C ASP 80": "OD1" <-> "OD2" Residue "C ASP 184": "OD1" <-> "OD2" Residue "C PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 254": "NH1" <-> "NH2" Residue "C PHE 266": "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: 10171 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: 6092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 746, 6092 Classifications: {'peptide': 746} Link IDs: {'PTRANS': 27, 'TRANS': 718} Chain breaks: 4 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: 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: 6.35, per 1000 atoms: 0.62 Number of scatterers: 10171 At special positions: 0 Unit cell: (108.12, 140.98, 149.46, 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 1901 8.00 N 1727 7.00 C 6474 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: 4.32 Conformation dependent library (CDL) restraints added in 1.8 seconds 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 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: 2378 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 59 helices and 14 sheets defined 47.6% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.01 Creating SS restraints... Processing helix chain 'B' and resid 6 through 19 Processing helix chain 'B' and resid 29 through 38 removed outlier: 4.268A pdb=" N GLY B 33 " --> pdb=" O TYR B 29 " (cutoff:3.500A) removed outlier: 4.635A 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: 4.542A 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 74 through 76 No H-bonds generated for 'chain 'A' and resid 74 through 76' Processing helix chain 'A' and resid 82 through 94 Processing helix chain 'A' and resid 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 removed outlier: 3.544A pdb=" N ALA A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 183 removed outlier: 3.543A pdb=" N PHE A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 207 removed outlier: 3.568A 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 268 Processing helix chain 'A' and resid 272 through 274 No H-bonds generated for 'chain 'A' and resid 272 through 274' Processing helix chain 'A' and resid 301 through 314 removed outlier: 3.933A pdb=" N VAL A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 337 removed outlier: 3.870A pdb=" N ASN A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 364 Processing helix chain 'A' and resid 368 through 376 removed outlier: 3.801A pdb=" N CYS A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 423 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 512 Processing helix chain 'A' and resid 520 through 531 Processing helix chain 'A' and resid 564 through 568 Processing helix chain 'A' and resid 574 through 581 Processing helix chain 'A' and resid 587 through 593 removed outlier: 3.565A pdb=" N GLU A 591 " --> pdb=" O LYS A 587 " (cutoff:3.500A) removed outlier: 4.123A 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 Processing helix chain 'A' and resid 675 through 684 removed outlier: 3.599A 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: 6.596A pdb=" N VAL A 713 " --> pdb=" O SER A 709 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N LEU A 714 " --> pdb=" O ARG A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 735 removed outlier: 3.946A 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 Processing helix chain 'C' and resid 113 through 125 removed outlier: 3.822A pdb=" N MET C 123 " --> pdb=" O MET C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 removed outlier: 3.556A pdb=" N SER C 141 " --> pdb=" O GLN C 137 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.783A 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: 3.840A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 removed outlier: 3.777A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL C 209 " --> pdb=" O GLU C 205 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASP C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 230 Processing helix chain 'C' and resid 252 through 261 removed outlier: 4.259A 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 264 through 267 Processing helix chain 'C' and resid 274 through 284 removed outlier: 3.697A 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 304 No H-bonds generated for 'chain 'C' and resid 302 through 304' Processing helix chain 'C' and resid 309 through 318 Processing helix chain 'C' and resid 335 through 348 removed outlier: 5.031A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA C 347 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 354 removed outlier: 3.922A 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 372 Processing sheet with id= A, first strand: chain 'B' and resid 26 through 28 Processing sheet with id= B, first strand: chain 'B' and resid 103 through 105 Processing sheet with id= C, first strand: chain 'A' and resid 12 through 16 Processing sheet with id= D, first strand: chain 'A' and resid 37 through 40 removed outlier: 3.540A pdb=" N LEU A 38 " --> pdb=" O TYR A 50 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 100 through 103 removed outlier: 3.534A pdb=" N GLN A 157 " --> pdb=" O PHE A 432 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLY A 163 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY A 236 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 377 through 381 Processing sheet with id= G, first strand: chain 'A' and resid 547 through 551 Processing sheet with id= H, first strand: chain 'A' and resid 700 through 703 Processing sheet with id= I, first strand: chain 'A' and resid 340 through 344 removed outlier: 6.257A pdb=" N SER A 347 " --> pdb=" O ARG A 343 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 8 through 12 Processing sheet with id= K, first strand: chain 'C' and resid 34 through 38 Processing sheet with id= L, first strand: chain 'C' and resid 103 through 107 Processing sheet with id= M, first strand: chain 'C' and resid 297 through 300 removed outlier: 6.663A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 238 through 241 433 hydrogen bonds defined for protein. 1209 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: 3.39 Time building geometry restraints manager: 4.64 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: 1741 1.32 - 1.45: 2709 1.45 - 1.57: 5830 1.57 - 1.69: 6 1.69 - 1.82: 102 Bond restraints: 10388 Sorted by residual: bond pdb=" CA EEP H 2 " pdb=" C EEP H 2 " ideal model delta sigma weight residual 1.572 1.450 0.122 2.00e-02 2.50e+03 3.71e+01 bond pdb=" C EEP H 2 " pdb=" O EEP H 2 " ideal model delta sigma weight residual 1.263 1.202 0.061 2.00e-02 2.50e+03 9.41e+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 8.64e+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 8.53e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.400 -0.053 2.00e-02 2.50e+03 7.02e+00 ... (remaining 10383 not shown) Histogram of bond angle deviations from ideal: 99.27 - 106.67: 322 106.67 - 114.07: 5855 114.07 - 121.47: 5494 121.47 - 128.87: 2291 128.87 - 136.27: 73 Bond angle restraints: 14035 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 121.70 109.82 11.88 1.80e+00 3.09e-01 4.36e+01 angle pdb=" N HYP H 6 " pdb=" CA HYP H 6 " pdb=" CB HYP H 6 " ideal model delta sigma weight residual 103.00 107.78 -4.78 1.10e+00 8.26e-01 1.89e+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 122.40 118.26 4.14 1.00e+00 1.00e+00 1.72e+01 angle pdb=" N TYR A 113 " pdb=" CA TYR A 113 " pdb=" CB TYR A 113 " ideal model delta sigma weight residual 113.15 106.47 6.68 1.63e+00 3.76e-01 1.68e+01 ... (remaining 14030 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.90: 6044 27.90 - 55.80: 181 55.80 - 83.71: 28 83.71 - 111.61: 6 111.61 - 139.51: 4 Dihedral angle restraints: 6263 sinusoidal: 2574 harmonic: 3689 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 -60.00 79.51 -139.51 1 2.00e+01 2.50e-03 4.23e+01 dihedral pdb=" O2A ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PA ADP C 401 " pdb=" PB ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 70.90 -130.90 1 2.00e+01 2.50e-03 3.97e+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 68.66 -128.66 1 2.00e+01 2.50e-03 3.90e+01 ... (remaining 6260 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1162 0.053 - 0.105: 295 0.105 - 0.158: 63 0.158 - 0.211: 9 0.211 - 0.264: 3 Chirality restraints: 1532 Sorted by residual: chirality pdb=" CG LEU A 782 " pdb=" CB LEU A 782 " pdb=" CD1 LEU A 782 " pdb=" CD2 LEU A 782 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA PHE B 19 " pdb=" N PHE B 19 " pdb=" C PHE B 19 " pdb=" CB PHE B 19 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA CYS C 257 " pdb=" N CYS C 257 " pdb=" C CYS C 257 " pdb=" CB CYS C 257 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 1529 not shown) Planarity restraints: 1792 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 113 " -0.037 2.00e-02 2.50e+03 3.28e-02 2.15e+01 pdb=" CG TYR A 113 " 0.069 2.00e-02 2.50e+03 pdb=" CD1 TYR A 113 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 TYR A 113 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 113 " 0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR A 113 " -0.013 2.00e-02 2.50e+03 pdb=" CZ TYR A 113 " 0.019 2.00e-02 2.50e+03 pdb=" OH TYR A 113 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 677 " 0.086 9.50e-02 1.11e+02 5.14e-02 1.54e+01 pdb=" NE ARG A 677 " -0.027 2.00e-02 2.50e+03 pdb=" CZ ARG A 677 " 0.065 2.00e-02 2.50e+03 pdb=" NH1 ARG A 677 " -0.023 2.00e-02 2.50e+03 pdb=" NH2 ARG A 677 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS C 88 " -0.018 2.00e-02 2.50e+03 3.67e-02 1.35e+01 pdb=" C HIS C 88 " 0.064 2.00e-02 2.50e+03 pdb=" O HIS C 88 " -0.024 2.00e-02 2.50e+03 pdb=" N THR C 89 " -0.022 2.00e-02 2.50e+03 ... (remaining 1789 not shown) Histogram of nonbonded interaction distances: 1.32 - 2.03: 2 2.03 - 2.75: 1138 2.75 - 3.47: 14425 3.47 - 4.18: 24005 4.18 - 4.90: 42906 Nonbonded interactions: 82476 Sorted by model distance: nonbonded pdb=" N TRP H 1 " pdb=" C ALA H 7 " model vdw 1.317 3.350 nonbonded pdb=" CD1 TRP H 1 " pdb=" SG CYS H 5 " model vdw 1.732 3.620 nonbonded pdb="MG MG A1901 " pdb=" O1B ADP A1902 " model vdw 2.037 2.170 nonbonded pdb=" OH TYR A 456 " pdb=" OE1 GLU A 500 " model vdw 2.056 2.440 nonbonded pdb=" O2B ADP C 401 " pdb="MG MG C 402 " model vdw 2.182 2.170 ... (remaining 82471 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: 1.760 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: 6.990 Check model and map are aligned: 0.150 Set scattering table: 0.110 Process input model: 31.650 Find NCS groups from input model: 0.250 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 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 : 0.005 0.122 10388 Z= 0.296 Angle : 0.833 11.883 14035 Z= 0.482 Chirality : 0.050 0.264 1532 Planarity : 0.007 0.053 1792 Dihedral : 14.892 139.511 3885 Min Nonbonded Distance : 1.317 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Rotamer: Outliers : 0.09 % Allowed : 0.28 % Favored : 99.63 % 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: -1.20 (0.21), residues: 1236 helix: -1.48 (0.17), residues: 590 sheet: -0.25 (0.40), residues: 150 loop : 0.27 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP C 79 HIS 0.010 0.001 HIS B 147 PHE 0.033 0.002 PHE B 19 TYR 0.069 0.006 TYR A 113 ARG 0.066 0.010 ARG A 677 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 132 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 105 MET cc_start: 0.7943 (mmp) cc_final: 0.7232 (ttt) REVERT: A 305 MET cc_start: 0.8785 (tpp) cc_final: 0.8037 (tpp) REVERT: C 299 MET cc_start: 0.9064 (mmp) cc_final: 0.8834 (mmt) outliers start: 1 outliers final: 1 residues processed: 133 average time/residue: 0.2558 time to fit residues: 46.8910 Evaluate side-chains 80 residues out of total 1094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 79 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.6980 chunk 93 optimal weight: 0.0970 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN A 191 ASN A 264 GLN A 418 HIS ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 HIS C 162 ASN C 280 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10388 Z= 0.293 Angle : 0.648 14.032 14035 Z= 0.331 Chirality : 0.045 0.274 1532 Planarity : 0.005 0.075 1792 Dihedral : 9.705 138.888 1409 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 1.02 % Allowed : 4.52 % Favored : 94.46 % 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: 0.63 (0.23), residues: 1236 helix: 0.39 (0.21), residues: 597 sheet: 0.17 (0.38), residues: 171 loop : 0.88 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 79 HIS 0.018 0.001 HIS B 147 PHE 0.022 0.002 PHE C 255 TYR 0.031 0.002 TYR A 113 ARG 0.005 0.001 ARG A 779 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 84 time to evaluate : 1.277 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 105 MET cc_start: 0.7942 (mmp) cc_final: 0.7181 (ttt) REVERT: A 191 ASN cc_start: 0.7043 (OUTLIER) cc_final: 0.5791 (p0) REVERT: A 305 MET cc_start: 0.8629 (tpp) cc_final: 0.8218 (tpp) REVERT: A 503 MET cc_start: 0.8565 (mmm) cc_final: 0.8345 (mmm) REVERT: A 788 MET cc_start: 0.5206 (mtt) cc_final: 0.4659 (tpt) outliers start: 11 outliers final: 5 residues processed: 91 average time/residue: 0.2077 time to fit residues: 28.1455 Evaluate side-chains 75 residues out of total 1094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 69 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 PHE Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain A residue 191 ASN Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain H residue 5 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 93 optimal weight: 0.0070 chunk 76 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 112 optimal weight: 0.4980 chunk 121 optimal weight: 0.0770 chunk 100 optimal weight: 0.9990 chunk 111 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 overall best weight: 0.3956 ------------------------------------------------------------------------------- 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 C 225 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10388 Z= 0.161 Angle : 0.551 11.828 14035 Z= 0.278 Chirality : 0.042 0.250 1532 Planarity : 0.004 0.052 1792 Dihedral : 8.688 138.169 1409 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 1.11 % Allowed : 4.99 % Favored : 93.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.24), residues: 1236 helix: 0.98 (0.21), residues: 601 sheet: 0.35 (0.39), residues: 165 loop : 0.84 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 79 HIS 0.010 0.001 HIS B 147 PHE 0.023 0.001 PHE C 255 TYR 0.025 0.001 TYR A 787 ARG 0.007 0.000 ARG A 343 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 83 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 105 MET cc_start: 0.8028 (mmp) cc_final: 0.7293 (ttt) REVERT: B 120 MET cc_start: 0.4064 (mtm) cc_final: 0.3606 (mmm) REVERT: A 135 MET cc_start: 0.8887 (mmm) cc_final: 0.8375 (mmm) REVERT: A 305 MET cc_start: 0.8512 (tpp) cc_final: 0.8232 (tpp) REVERT: A 788 MET cc_start: 0.5214 (mtt) cc_final: 0.4872 (tpt) REVERT: H 1 TRP cc_start: 0.8415 (m100) cc_final: 0.8038 (m100) outliers start: 12 outliers final: 4 residues processed: 91 average time/residue: 0.1942 time to fit residues: 27.0294 Evaluate side-chains 79 residues out of total 1094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 75 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain H residue 5 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 58 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 75 optimal weight: 0.4980 chunk 113 optimal weight: 0.4980 chunk 119 optimal weight: 6.9990 chunk 59 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10388 Z= 0.192 Angle : 0.532 9.640 14035 Z= 0.266 Chirality : 0.042 0.235 1532 Planarity : 0.004 0.055 1792 Dihedral : 8.015 137.171 1409 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 1.11 % Allowed : 6.19 % Favored : 92.71 % 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: 1.38 (0.24), residues: 1236 helix: 1.35 (0.22), residues: 594 sheet: 0.59 (0.40), residues: 159 loop : 0.67 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 79 HIS 0.008 0.001 HIS B 147 PHE 0.015 0.001 PHE C 255 TYR 0.025 0.001 TYR A 787 ARG 0.003 0.000 ARG A 542 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 77 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 105 MET cc_start: 0.8088 (mmp) cc_final: 0.7300 (ttt) REVERT: B 120 MET cc_start: 0.3946 (mtm) cc_final: 0.3574 (mmm) REVERT: A 135 MET cc_start: 0.8829 (mmm) cc_final: 0.8374 (mmm) REVERT: A 305 MET cc_start: 0.8550 (tpp) cc_final: 0.8252 (tpp) REVERT: H 1 TRP cc_start: 0.8575 (m100) cc_final: 0.8171 (m100) outliers start: 12 outliers final: 6 residues processed: 86 average time/residue: 0.1989 time to fit residues: 26.0107 Evaluate side-chains 75 residues out of total 1094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 69 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain H residue 5 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 89 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10388 Z= 0.314 Angle : 0.577 8.303 14035 Z= 0.286 Chirality : 0.043 0.192 1532 Planarity : 0.004 0.056 1792 Dihedral : 7.972 132.548 1409 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.57 % Allowed : 6.37 % Favored : 92.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.24), residues: 1236 helix: 1.34 (0.22), residues: 594 sheet: 0.64 (0.41), residues: 159 loop : 0.56 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 79 HIS 0.005 0.001 HIS B 147 PHE 0.014 0.001 PHE C 255 TYR 0.032 0.001 TYR A 787 ARG 0.004 0.000 ARG C 335 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 72 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 105 MET cc_start: 0.8150 (mmp) cc_final: 0.7342 (ttt) REVERT: A 43 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7574 (tp30) REVERT: A 135 MET cc_start: 0.8817 (mmm) cc_final: 0.8430 (mmm) REVERT: A 305 MET cc_start: 0.8537 (tpp) cc_final: 0.8304 (tpp) REVERT: A 767 LEU cc_start: 0.9134 (tt) cc_final: 0.8876 (pp) outliers start: 17 outliers final: 7 residues processed: 86 average time/residue: 0.1824 time to fit residues: 24.2155 Evaluate side-chains 75 residues out of total 1094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 67 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain H residue 5 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 119 optimal weight: 0.0870 chunk 99 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 39 optimal weight: 0.2980 chunk 62 optimal weight: 1.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10388 Z= 0.178 Angle : 0.524 8.484 14035 Z= 0.257 Chirality : 0.041 0.181 1532 Planarity : 0.003 0.052 1792 Dihedral : 7.528 130.469 1409 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.02 % Allowed : 7.29 % Favored : 91.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.24), residues: 1236 helix: 1.55 (0.22), residues: 591 sheet: 0.78 (0.41), residues: 157 loop : 0.51 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 79 HIS 0.007 0.001 HIS C 275 PHE 0.014 0.001 PHE C 255 TYR 0.032 0.001 TYR A 787 ARG 0.002 0.000 ARG A 724 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 76 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 105 MET cc_start: 0.8085 (mmp) cc_final: 0.7241 (ttt) REVERT: A 135 MET cc_start: 0.8786 (mmm) cc_final: 0.8395 (mmm) REVERT: A 305 MET cc_start: 0.8537 (tpp) cc_final: 0.8277 (tpp) REVERT: A 767 LEU cc_start: 0.9172 (tt) cc_final: 0.8889 (pp) REVERT: C 176 MET cc_start: 0.8305 (mmt) cc_final: 0.7873 (mmt) REVERT: H 1 TRP cc_start: 0.8724 (m100) cc_final: 0.8412 (m100) outliers start: 11 outliers final: 8 residues processed: 85 average time/residue: 0.1875 time to fit residues: 24.9617 Evaluate side-chains 80 residues out of total 1094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 72 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain H residue 5 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 0.6980 chunk 13 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 119 optimal weight: 0.4980 chunk 74 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10388 Z= 0.207 Angle : 0.530 7.615 14035 Z= 0.261 Chirality : 0.041 0.181 1532 Planarity : 0.003 0.049 1792 Dihedral : 7.356 125.527 1409 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.02 % Allowed : 8.59 % Favored : 90.40 % 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: 1.49 (0.24), residues: 1236 helix: 1.58 (0.22), residues: 591 sheet: 0.79 (0.42), residues: 157 loop : 0.47 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 79 HIS 0.007 0.001 HIS C 275 PHE 0.013 0.001 PHE C 255 TYR 0.027 0.001 TYR A 787 ARG 0.002 0.000 ARG B 64 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 70 time to evaluate : 1.357 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 105 MET cc_start: 0.8101 (mmp) cc_final: 0.7296 (ttt) REVERT: B 120 MET cc_start: 0.2504 (mmm) cc_final: 0.2105 (mmm) REVERT: A 135 MET cc_start: 0.8787 (mmm) cc_final: 0.8413 (mmm) REVERT: A 305 MET cc_start: 0.8544 (tpp) cc_final: 0.8278 (tpp) REVERT: A 767 LEU cc_start: 0.9185 (tt) cc_final: 0.8911 (pp) REVERT: C 176 MET cc_start: 0.8277 (mmt) cc_final: 0.7842 (mmt) REVERT: H 1 TRP cc_start: 0.8807 (m100) cc_final: 0.8495 (m100) outliers start: 11 outliers final: 10 residues processed: 80 average time/residue: 0.1901 time to fit residues: 23.7688 Evaluate side-chains 77 residues out of total 1094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 67 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain H residue 5 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 81 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 chunk 11 optimal weight: 0.0070 chunk 93 optimal weight: 0.2980 chunk 108 optimal weight: 2.9990 overall best weight: 0.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 GLN ** A 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10388 Z= 0.169 Angle : 0.521 7.879 14035 Z= 0.255 Chirality : 0.040 0.179 1532 Planarity : 0.003 0.043 1792 Dihedral : 7.040 122.369 1409 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.11 % Allowed : 8.77 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.24), residues: 1236 helix: 1.65 (0.22), residues: 592 sheet: 0.83 (0.42), residues: 157 loop : 0.41 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 781 HIS 0.007 0.001 HIS C 275 PHE 0.016 0.001 PHE B 96 TYR 0.029 0.001 TYR A 787 ARG 0.002 0.000 ARG B 64 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 74 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 105 MET cc_start: 0.8161 (mmp) cc_final: 0.7343 (ttt) REVERT: B 120 MET cc_start: 0.2765 (mmm) cc_final: 0.2319 (mmm) REVERT: A 135 MET cc_start: 0.8767 (mmm) cc_final: 0.8386 (mmm) REVERT: A 305 MET cc_start: 0.8518 (tpp) cc_final: 0.8262 (tpp) REVERT: A 767 LEU cc_start: 0.9207 (tt) cc_final: 0.8965 (pp) REVERT: C 176 MET cc_start: 0.8261 (mmt) cc_final: 0.7832 (mmt) REVERT: H 1 TRP cc_start: 0.8753 (m100) cc_final: 0.8501 (m100) outliers start: 12 outliers final: 10 residues processed: 83 average time/residue: 0.1888 time to fit residues: 24.1238 Evaluate side-chains 80 residues out of total 1094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 70 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain H residue 5 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 87 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 105 optimal weight: 0.7980 chunk 110 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10388 Z= 0.212 Angle : 0.547 12.044 14035 Z= 0.266 Chirality : 0.041 0.181 1532 Planarity : 0.003 0.043 1792 Dihedral : 6.988 117.987 1409 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.92 % Allowed : 9.23 % Favored : 89.84 % 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: 1.54 (0.24), residues: 1236 helix: 1.66 (0.22), residues: 594 sheet: 0.82 (0.42), residues: 157 loop : 0.43 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 79 HIS 0.007 0.001 HIS C 275 PHE 0.013 0.001 PHE C 255 TYR 0.028 0.001 TYR A 787 ARG 0.002 0.000 ARG B 64 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 73 time to evaluate : 1.298 Fit side-chains REVERT: B 105 MET cc_start: 0.8172 (mmp) cc_final: 0.7322 (ttt) REVERT: B 120 MET cc_start: 0.2689 (mmm) cc_final: 0.2301 (mmm) REVERT: A 135 MET cc_start: 0.8768 (mmm) cc_final: 0.8396 (mmm) REVERT: A 305 MET cc_start: 0.8554 (tpp) cc_final: 0.8300 (tpp) REVERT: A 751 PHE cc_start: 0.8510 (m-10) cc_final: 0.8152 (m-10) REVERT: A 767 LEU cc_start: 0.9193 (tt) cc_final: 0.8982 (pp) REVERT: C 176 MET cc_start: 0.8264 (mmt) cc_final: 0.7863 (mmt) REVERT: H 1 TRP cc_start: 0.8853 (m100) cc_final: 0.8632 (m100) outliers start: 10 outliers final: 10 residues processed: 82 average time/residue: 0.1859 time to fit residues: 24.0392 Evaluate side-chains 82 residues out of total 1094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 72 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain H residue 5 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 113 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10388 Z= 0.224 Angle : 0.551 8.586 14035 Z= 0.269 Chirality : 0.041 0.183 1532 Planarity : 0.003 0.043 1792 Dihedral : 6.923 115.984 1409 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.02 % Allowed : 9.14 % Favored : 89.84 % 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: 1.52 (0.24), residues: 1236 helix: 1.69 (0.22), residues: 593 sheet: 0.76 (0.42), residues: 157 loop : 0.37 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 781 HIS 0.007 0.001 HIS C 275 PHE 0.013 0.001 PHE C 255 TYR 0.028 0.001 TYR A 787 ARG 0.003 0.000 ARG B 64 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 74 time to evaluate : 1.249 Fit side-chains REVERT: B 105 MET cc_start: 0.8146 (mmp) cc_final: 0.7305 (ttt) REVERT: B 120 MET cc_start: 0.2669 (mmm) cc_final: 0.2249 (mmm) REVERT: A 135 MET cc_start: 0.8759 (mmm) cc_final: 0.8370 (mmm) REVERT: A 305 MET cc_start: 0.8579 (tpp) cc_final: 0.8360 (tpp) REVERT: A 751 PHE cc_start: 0.8504 (m-10) cc_final: 0.8156 (m-10) REVERT: A 767 LEU cc_start: 0.9203 (tt) cc_final: 0.8991 (pp) REVERT: C 176 MET cc_start: 0.8265 (mmt) cc_final: 0.7860 (mmt) outliers start: 11 outliers final: 10 residues processed: 83 average time/residue: 0.1858 time to fit residues: 24.2468 Evaluate side-chains 79 residues out of total 1094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 69 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain H residue 5 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 41 optimal weight: 0.0270 chunk 101 optimal weight: 0.9980 chunk 12 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 86 optimal weight: 9.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** 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 = 0.3610 r_free = 0.3610 target = 0.092403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.057202 restraints weight = 24811.477| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 3.33 r_work: 0.2707 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10388 Z= 0.184 Angle : 0.541 10.197 14035 Z= 0.262 Chirality : 0.040 0.185 1532 Planarity : 0.003 0.042 1792 Dihedral : 6.855 117.115 1409 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.02 % Allowed : 9.14 % Favored : 89.84 % 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: 1236 helix: 1.72 (0.22), residues: 593 sheet: 0.97 (0.43), residues: 147 loop : 0.41 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 781 HIS 0.007 0.001 HIS C 275 PHE 0.016 0.001 PHE B 96 TYR 0.027 0.001 TYR A 787 ARG 0.003 0.000 ARG B 64 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2301.19 seconds wall clock time: 42 minutes 12.10 seconds (2532.10 seconds total)