Starting phenix.real_space_refine on Fri Jun 28 00:59:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x01_37964/06_2024/8x01_37964.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x01_37964/06_2024/8x01_37964.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x01_37964/06_2024/8x01_37964.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x01_37964/06_2024/8x01_37964.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x01_37964/06_2024/8x01_37964.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x01_37964/06_2024/8x01_37964.pdb" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.049 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1404 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 81 5.16 5 C 8105 2.51 5 N 2182 2.21 5 O 2372 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 384": "OE1" <-> "OE2" Residue "A ARG 459": "NH1" <-> "NH2" Residue "A GLU 539": "OE1" <-> "OE2" Residue "A PHE 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 687": "NH1" <-> "NH2" Residue "A ASP 727": "OD1" <-> "OD2" Residue "A ASP 779": "OD1" <-> "OD2" Residue "A GLU 811": "OE1" <-> "OE2" Residue "A ASP 969": "OD1" <-> "OD2" Residue "A TYR 1094": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1263": "OE1" <-> "OE2" Residue "B GLU 236": "OE1" <-> "OE2" Residue "B ASP 240": "OD1" <-> "OD2" Residue "C GLU 255": "OE1" <-> "OE2" Residue "C GLU 267": "OE1" <-> "OE2" Residue "C ASP 287": "OD1" <-> "OD2" Residue "E GLU 220": "OE1" <-> "OE2" Residue "E ASP 223": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 12742 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 10782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1350, 10782 Classifications: {'peptide': 1350} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 67, 'TRANS': 1282} Chain breaks: 5 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 517 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "C" Number of atoms: 642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 642 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 4, 'TRANS': 80} Chain: "D" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 387 Classifications: {'peptide': 50} Link IDs: {'TRANS': 49} Chain: "E" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 412 Classifications: {'peptide': 54} Link IDs: {'TRANS': 53} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9139 SG CYS A1187 15.673 94.179 45.655 1.00113.77 S ATOM 9164 SG CYS A1190 17.319 93.253 42.205 1.00110.61 S ATOM 8797 SG CYS A1142 26.288 109.947 52.146 1.00 76.21 S ATOM 10502 SG CYS A1379 23.718 109.223 50.767 1.00105.36 S ATOM 10508 SG CYS A1380 26.618 106.383 52.254 1.00 96.09 S Time building chain proxies: 8.60, per 1000 atoms: 0.67 Number of scatterers: 12742 At special positions: 0 Unit cell: (126.14, 138.33, 134.09, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 81 16.00 O 2372 8.00 N 2182 7.00 C 8105 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: 4.86 Conformation dependent library (CDL) restraints added in 3.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A3001 " pdb="ZN ZN A3001 " - pdb=" ND1 HIS A1372 " pdb="ZN ZN A3001 " - pdb=" NE2 HIS A1374 " pdb="ZN ZN A3001 " - pdb=" SG CYS A1190 " pdb="ZN ZN A3001 " - pdb=" SG CYS A1187 " pdb=" ZN A3002 " pdb="ZN ZN A3002 " - pdb=" SG CYS A1142 " pdb="ZN ZN A3002 " - pdb=" SG CYS A1380 " pdb="ZN ZN A3002 " - pdb=" SG CYS A1379 " Number of angles added : 2 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3070 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 8 sheets defined 61.9% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 19 through 30 removed outlier: 3.645A pdb=" N LEU A 23 " --> pdb=" O VAL A 19 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY A 30 " --> pdb=" O TYR A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 42 removed outlier: 3.547A pdb=" N GLY A 42 " --> pdb=" O PRO A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 47 removed outlier: 3.555A pdb=" N GLN A 47 " --> pdb=" O LEU A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 55 removed outlier: 3.509A pdb=" N ILE A 52 " --> pdb=" O ASN A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 74 Processing helix chain 'A' and resid 75 through 79 Processing helix chain 'A' and resid 90 through 98 removed outlier: 4.040A pdb=" N LEU A 95 " --> pdb=" O PRO A 92 " (cutoff:3.500A) Proline residue: A 96 - end of helix Processing helix chain 'A' and resid 108 through 122 Processing helix chain 'A' and resid 124 through 141 Processing helix chain 'A' and resid 162 through 172 Processing helix chain 'A' and resid 175 through 198 Processing helix chain 'A' and resid 237 through 260 Processing helix chain 'A' and resid 265 through 285 removed outlier: 4.246A pdb=" N ARG A 269 " --> pdb=" O PRO A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 305 removed outlier: 3.960A pdb=" N ILE A 291 " --> pdb=" O LYS A 287 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N TYR A 300 " --> pdb=" O GLU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 330 Processing helix chain 'A' and resid 335 through 348 Processing helix chain 'A' and resid 354 through 360 Processing helix chain 'A' and resid 361 through 362 No H-bonds generated for 'chain 'A' and resid 361 through 362' Processing helix chain 'A' and resid 363 through 367 removed outlier: 3.907A pdb=" N ARG A 366 " --> pdb=" O CYS A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 386 removed outlier: 3.629A pdb=" N LYS A 381 " --> pdb=" O GLN A 377 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL A 382 " --> pdb=" O ALA A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 413 Processing helix chain 'A' and resid 415 through 419 Processing helix chain 'A' and resid 430 through 440 Processing helix chain 'A' and resid 444 through 450 removed outlier: 3.648A pdb=" N LYS A 450 " --> pdb=" O GLU A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 456 Processing helix chain 'A' and resid 467 through 471 removed outlier: 4.426A pdb=" N ASP A 471 " --> pdb=" O PRO A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 477 removed outlier: 3.642A pdb=" N LYS A 477 " --> pdb=" O ILE A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 492 removed outlier: 4.118A pdb=" N VAL A 491 " --> pdb=" O TRP A 488 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE A 492 " --> pdb=" O MET A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 505 removed outlier: 4.527A pdb=" N GLN A 499 " --> pdb=" O SER A 495 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ARG A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 522 Processing helix chain 'A' and resid 527 through 532 Processing helix chain 'A' and resid 532 through 537 Processing helix chain 'A' and resid 568 through 585 removed outlier: 3.636A pdb=" N HIS A 585 " --> pdb=" O LEU A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 590 Processing helix chain 'A' and resid 598 through 611 Processing helix chain 'A' and resid 671 through 677 removed outlier: 4.014A pdb=" N CYS A 674 " --> pdb=" O THR A 671 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A 675 " --> pdb=" O LYS A 672 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TRP A 677 " --> pdb=" O CYS A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 694 Proline residue: A 684 - end of helix Processing helix chain 'A' and resid 700 through 709 removed outlier: 3.999A pdb=" N ARG A 708 " --> pdb=" O LEU A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 768 Processing helix chain 'A' and resid 794 through 820 removed outlier: 4.202A pdb=" N LEU A 808 " --> pdb=" O LYS A 804 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N PHE A 809 " --> pdb=" O ALA A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 858 removed outlier: 3.800A pdb=" N ASN A 855 " --> pdb=" O GLN A 851 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS A 858 " --> pdb=" O LYS A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 887 Processing helix chain 'A' and resid 890 through 912 Processing helix chain 'A' and resid 920 through 929 removed outlier: 3.546A pdb=" N HIS A 929 " --> pdb=" O ALA A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 939 removed outlier: 3.549A pdb=" N ILE A 933 " --> pdb=" O HIS A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 944 Processing helix chain 'A' and resid 951 through 955 Processing helix chain 'A' and resid 961 through 977 Processing helix chain 'A' and resid 980 through 989 removed outlier: 3.659A pdb=" N LEU A 984 " --> pdb=" O ASP A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1003 removed outlier: 3.533A pdb=" N LEU A1000 " --> pdb=" O LYS A 996 " (cutoff:3.500A) Processing helix chain 'A' and resid 1014 through 1031 Processing helix chain 'A' and resid 1033 through 1037 Processing helix chain 'A' and resid 1043 through 1057 Processing helix chain 'A' and resid 1062 through 1073 Processing helix chain 'A' and resid 1073 through 1084 Processing helix chain 'A' and resid 1088 through 1099 Processing helix chain 'A' and resid 1102 through 1111 Processing helix chain 'A' and resid 1111 through 1122 removed outlier: 3.748A pdb=" N GLU A1122 " --> pdb=" O SER A1118 " (cutoff:3.500A) Processing helix chain 'A' and resid 1131 through 1137 removed outlier: 3.564A pdb=" N ALA A1136 " --> pdb=" O PHE A1133 " (cutoff:3.500A) Processing helix chain 'A' and resid 1142 through 1155 Processing helix chain 'A' and resid 1155 through 1160 Processing helix chain 'A' and resid 1171 through 1176 removed outlier: 3.659A pdb=" N VAL A1176 " --> pdb=" O PRO A1172 " (cutoff:3.500A) Processing helix chain 'A' and resid 1187 through 1192 Processing helix chain 'A' and resid 1242 through 1260 Processing helix chain 'A' and resid 1262 through 1275 removed outlier: 3.515A pdb=" N GLU A1271 " --> pdb=" O GLN A1267 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A1272 " --> pdb=" O ASP A1268 " (cutoff:3.500A) Processing helix chain 'A' and resid 1280 through 1288 Processing helix chain 'A' and resid 1338 through 1358 Processing helix chain 'B' and resid 219 through 245 Processing helix chain 'B' and resid 246 through 276 removed outlier: 3.828A pdb=" N THR B 258 " --> pdb=" O ASN B 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 272 removed outlier: 4.122A pdb=" N GLY C 227 " --> pdb=" O ASP C 223 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N MET C 228 " --> pdb=" O LEU C 224 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA C 244 " --> pdb=" O ASP C 240 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLN C 245 " --> pdb=" O LYS C 241 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLY C 246 " --> pdb=" O VAL C 242 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER C 247 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR C 272 " --> pdb=" O GLY C 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 243 removed outlier: 3.704A pdb=" N LEU D 243 " --> pdb=" O VAL D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 267 removed outlier: 4.620A pdb=" N MET D 248 " --> pdb=" O ALA D 244 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR D 265 " --> pdb=" O THR D 261 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE D 266 " --> pdb=" O THR D 262 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU D 267 " --> pdb=" O LEU D 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 219 through 271 removed outlier: 3.556A pdb=" N ALA E 271 " --> pdb=" O GLU E 267 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 89 removed outlier: 4.206A pdb=" N TYR A 234 " --> pdb=" O LEU A 89 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 390 through 393 Processing sheet with id=AA3, first strand: chain 'A' and resid 423 through 424 Processing sheet with id=AA4, first strand: chain 'A' and resid 563 through 566 Processing sheet with id=AA5, first strand: chain 'A' and resid 780 through 790 Processing sheet with id=AA6, first strand: chain 'A' and resid 835 through 838 removed outlier: 3.617A pdb=" N PHE A 836 " --> pdb=" O PHE A 843 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1180 through 1182 Processing sheet with id=AA8, first strand: chain 'A' and resid 1206 through 1207 removed outlier: 3.890A pdb=" N ILE A1206 " --> pdb=" O SER A1365 " (cutoff:3.500A) 718 hydrogen bonds defined for protein. 2055 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: 3.69 Time building geometry restraints manager: 5.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2108 1.31 - 1.44: 3226 1.44 - 1.56: 7510 1.56 - 1.69: 0 1.69 - 1.81: 133 Bond restraints: 12977 Sorted by residual: bond pdb=" C GLU A 554 " pdb=" N LYS A 555 " ideal model delta sigma weight residual 1.331 1.433 -0.102 1.36e-02 5.41e+03 5.61e+01 bond pdb=" C SER A 774 " pdb=" N MET A 775 " ideal model delta sigma weight residual 1.329 1.240 0.089 1.23e-02 6.61e+03 5.18e+01 bond pdb=" C GLU A 56 " pdb=" N SER A 57 " ideal model delta sigma weight residual 1.335 1.246 0.089 1.38e-02 5.25e+03 4.15e+01 bond pdb=" C LYS A 555 " pdb=" N GLU A 556 " ideal model delta sigma weight residual 1.331 1.246 0.084 1.34e-02 5.57e+03 3.94e+01 bond pdb=" C PHE C 293 " pdb=" N SER C 294 " ideal model delta sigma weight residual 1.333 1.250 0.084 1.34e-02 5.57e+03 3.90e+01 ... (remaining 12972 not shown) Histogram of bond angle deviations from ideal: 98.64 - 105.72: 294 105.72 - 112.81: 7184 112.81 - 119.89: 4361 119.89 - 126.97: 5600 126.97 - 134.06: 152 Bond angle restraints: 17591 Sorted by residual: angle pdb=" N LEU A 361 " pdb=" CA LEU A 361 " pdb=" C LEU A 361 " ideal model delta sigma weight residual 112.30 98.99 13.31 1.36e+00 5.41e-01 9.58e+01 angle pdb=" O SER A 774 " pdb=" C SER A 774 " pdb=" N MET A 775 " ideal model delta sigma weight residual 122.85 114.90 7.95 1.14e+00 7.69e-01 4.86e+01 angle pdb=" N LEU A 362 " pdb=" CA LEU A 362 " pdb=" C LEU A 362 " ideal model delta sigma weight residual 112.92 104.45 8.47 1.23e+00 6.61e-01 4.75e+01 angle pdb=" CA SER C 301 " pdb=" C SER C 301 " pdb=" N GLY C 302 " ideal model delta sigma weight residual 119.46 115.44 4.02 6.10e-01 2.69e+00 4.35e+01 angle pdb=" O GLU A 56 " pdb=" C GLU A 56 " pdb=" N SER A 57 " ideal model delta sigma weight residual 122.55 115.11 7.44 1.24e+00 6.50e-01 3.60e+01 ... (remaining 17586 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 6920 17.78 - 35.57: 804 35.57 - 53.35: 181 53.35 - 71.13: 38 71.13 - 88.91: 7 Dihedral angle restraints: 7950 sinusoidal: 3234 harmonic: 4716 Sorted by residual: dihedral pdb=" CA LEU A 849 " pdb=" C LEU A 849 " pdb=" N THR A 850 " pdb=" CA THR A 850 " ideal model delta harmonic sigma weight residual -180.00 -158.24 -21.76 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" C THR A 181 " pdb=" N THR A 181 " pdb=" CA THR A 181 " pdb=" CB THR A 181 " ideal model delta harmonic sigma weight residual -122.00 -111.64 -10.36 0 2.50e+00 1.60e-01 1.72e+01 dihedral pdb=" CA ILE A 865 " pdb=" C ILE A 865 " pdb=" N LEU A 866 " pdb=" CA LEU A 866 " ideal model delta harmonic sigma weight residual -180.00 -162.33 -17.67 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 7947 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1628 0.050 - 0.101: 317 0.101 - 0.151: 90 0.151 - 0.202: 23 0.202 - 0.252: 3 Chirality restraints: 2061 Sorted by residual: chirality pdb=" CA MET B 269 " pdb=" N MET B 269 " pdb=" C MET B 269 " pdb=" CB MET B 269 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CA ILE A 460 " pdb=" N ILE A 460 " pdb=" C ILE A 460 " pdb=" CB ILE A 460 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CG LEU C 243 " pdb=" CB LEU C 243 " pdb=" CD1 LEU C 243 " pdb=" CD2 LEU C 243 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 2058 not shown) Planarity restraints: 2226 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 358 " 0.028 2.00e-02 2.50e+03 5.45e-02 2.97e+01 pdb=" C THR A 358 " -0.094 2.00e-02 2.50e+03 pdb=" O THR A 358 " 0.035 2.00e-02 2.50e+03 pdb=" N ALA A 359 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 777 " -0.020 2.00e-02 2.50e+03 4.07e-02 1.66e+01 pdb=" C GLN A 777 " 0.070 2.00e-02 2.50e+03 pdb=" O GLN A 777 " -0.026 2.00e-02 2.50e+03 pdb=" N GLY A 778 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 301 " -0.018 2.00e-02 2.50e+03 3.82e-02 1.46e+01 pdb=" C SER C 301 " 0.066 2.00e-02 2.50e+03 pdb=" O SER C 301 " -0.025 2.00e-02 2.50e+03 pdb=" N GLY C 302 " -0.023 2.00e-02 2.50e+03 ... (remaining 2223 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2889 2.79 - 3.32: 12814 3.32 - 3.84: 21679 3.84 - 4.37: 25664 4.37 - 4.90: 43566 Nonbonded interactions: 106612 Sorted by model distance: nonbonded pdb=" NE2 HIS A 13 " pdb=" O THR A 862 " model vdw 2.259 2.520 nonbonded pdb=" OG SER A 952 " pdb=" OD1 ASP A1171 " model vdw 2.273 2.440 nonbonded pdb=" NH2 ARG A 841 " pdb=" O LEU A 849 " model vdw 2.279 2.520 nonbonded pdb=" OH TYR A 534 " pdb=" OD2 ASP A 543 " model vdw 2.283 2.440 nonbonded pdb=" N GLN A1131 " pdb=" OE1 GLN A1131 " model vdw 2.298 2.520 ... (remaining 106607 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'D' selection = (chain 'E' and resid 218 through 267) } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 17.860 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 38.170 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.060 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 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 0.102 12977 Z= 0.293 Angle : 0.746 13.309 17591 Z= 0.493 Chirality : 0.048 0.252 2061 Planarity : 0.005 0.073 2226 Dihedral : 15.840 88.914 4880 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.49 % Allowed : 19.14 % Favored : 80.38 % Cbeta Deviations : 0.07 % 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: 1.10 (0.21), residues: 1588 helix: 1.51 (0.17), residues: 889 sheet: -0.36 (0.61), residues: 81 loop : -0.18 (0.24), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 982 HIS 0.003 0.001 HIS A 697 PHE 0.022 0.001 PHE A 564 TYR 0.014 0.001 TYR A 289 ARG 0.005 0.000 ARG C 231 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 243 time to evaluate : 1.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 381 LYS cc_start: 0.8113 (mmmt) cc_final: 0.7806 (mttt) REVERT: A 810 PHE cc_start: 0.8324 (t80) cc_final: 0.8060 (t80) REVERT: A 1043 ASN cc_start: 0.7319 (p0) cc_final: 0.6599 (p0) REVERT: E 238 LYS cc_start: 0.8363 (pttm) cc_final: 0.7681 (ptmt) outliers start: 7 outliers final: 3 residues processed: 245 average time/residue: 0.2864 time to fit residues: 97.3103 Evaluate side-chains 214 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 211 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 1263 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 3.9990 chunk 120 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 124 optimal weight: 0.2980 chunk 48 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 144 optimal weight: 3.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 ASN A 818 HIS A 887 ASN ** A1008 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 233 GLN E 254 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 12977 Z= 0.324 Angle : 0.615 12.188 17591 Z= 0.312 Chirality : 0.043 0.182 2061 Planarity : 0.005 0.053 2226 Dihedral : 4.289 37.404 1740 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.02 % Allowed : 19.83 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.21), residues: 1588 helix: 1.66 (0.17), residues: 908 sheet: -0.37 (0.62), residues: 79 loop : -0.18 (0.25), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 182 HIS 0.008 0.001 HIS A1374 PHE 0.022 0.002 PHE A 394 TYR 0.019 0.002 TYR A 289 ARG 0.006 0.000 ARG B 231 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 222 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 256 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.7873 (mm) REVERT: E 238 LYS cc_start: 0.8381 (pttm) cc_final: 0.7704 (ptmt) REVERT: E 252 ILE cc_start: 0.8894 (tp) cc_final: 0.8582 (tt) outliers start: 29 outliers final: 17 residues processed: 239 average time/residue: 0.2679 time to fit residues: 89.3831 Evaluate side-chains 220 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 202 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 TRP Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 786 THR Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 956 ASN Chi-restraints excluded: chain A residue 999 THR Chi-restraints excluded: chain A residue 1370 THR Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 249 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 80 optimal weight: 0.5980 chunk 44 optimal weight: 8.9990 chunk 120 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 144 optimal weight: 0.8980 chunk 156 optimal weight: 10.0000 chunk 128 optimal weight: 3.9990 chunk 143 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 116 optimal weight: 0.0060 overall best weight: 1.1000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 599 GLN ** A1008 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1120 ASN B 233 GLN ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12977 Z= 0.215 Angle : 0.573 10.484 17591 Z= 0.288 Chirality : 0.041 0.169 2061 Planarity : 0.004 0.062 2226 Dihedral : 4.040 35.878 1735 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.55 % Allowed : 19.35 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.21), residues: 1588 helix: 1.79 (0.17), residues: 909 sheet: -0.42 (0.60), residues: 79 loop : -0.11 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 982 HIS 0.005 0.001 HIS A1374 PHE 0.016 0.001 PHE A 394 TYR 0.016 0.001 TYR A 289 ARG 0.005 0.000 ARG A 788 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 223 time to evaluate : 1.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 381 LYS cc_start: 0.8163 (mmmt) cc_final: 0.7847 (mttt) REVERT: A 435 GLU cc_start: 0.7526 (mp0) cc_final: 0.7238 (mp0) REVERT: A 810 PHE cc_start: 0.8319 (t80) cc_final: 0.8041 (t80) REVERT: A 1043 ASN cc_start: 0.7428 (p0) cc_final: 0.6840 (p0) REVERT: B 228 MET cc_start: 0.8142 (OUTLIER) cc_final: 0.7759 (mmm) REVERT: E 232 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7466 (tp) outliers start: 51 outliers final: 32 residues processed: 254 average time/residue: 0.2787 time to fit residues: 99.9011 Evaluate side-chains 234 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 200 time to evaluate : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 91 TRP Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 786 THR Chi-restraints excluded: chain A residue 956 ASN Chi-restraints excluded: chain A residue 999 THR Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1190 CYS Chi-restraints excluded: chain A residue 1310 THR Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1370 THR Chi-restraints excluded: chain A residue 1373 LEU Chi-restraints excluded: chain A residue 1398 LEU Chi-restraints excluded: chain A residue 1404 MET Chi-restraints excluded: chain A residue 1414 LEU Chi-restraints excluded: chain B residue 228 MET Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 252 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 142 optimal weight: 10.0000 chunk 108 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 16 optimal weight: 0.0060 chunk 69 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 chunk 145 optimal weight: 0.7980 chunk 153 optimal weight: 5.9990 chunk 137 optimal weight: 5.9990 chunk 41 optimal weight: 0.1980 chunk 127 optimal weight: 9.9990 overall best weight: 1.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN ** A1008 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1120 ASN B 233 GLN ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12977 Z= 0.226 Angle : 0.582 11.204 17591 Z= 0.292 Chirality : 0.042 0.174 2061 Planarity : 0.005 0.067 2226 Dihedral : 4.013 33.143 1735 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.99 % Allowed : 20.18 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.21), residues: 1588 helix: 1.79 (0.17), residues: 909 sheet: -0.48 (0.60), residues: 79 loop : -0.08 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 982 HIS 0.006 0.001 HIS B 234 PHE 0.011 0.001 PHE A 404 TYR 0.016 0.001 TYR A 289 ARG 0.007 0.000 ARG B 231 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 212 time to evaluate : 1.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TRP cc_start: 0.9036 (OUTLIER) cc_final: 0.8369 (t-100) REVERT: A 381 LYS cc_start: 0.8167 (mmmt) cc_final: 0.7847 (mttt) REVERT: A 539 GLU cc_start: 0.7875 (tp30) cc_final: 0.7586 (tp30) REVERT: A 810 PHE cc_start: 0.8313 (t80) cc_final: 0.8039 (t80) REVERT: A 1043 ASN cc_start: 0.7442 (p0) cc_final: 0.6862 (p0) REVERT: E 232 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7586 (tp) outliers start: 43 outliers final: 31 residues processed: 239 average time/residue: 0.2705 time to fit residues: 91.1164 Evaluate side-chains 231 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 198 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 91 TRP Chi-restraints excluded: chain A residue 170 TRP Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 786 THR Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain A residue 956 ASN Chi-restraints excluded: chain A residue 999 THR Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1190 CYS Chi-restraints excluded: chain A residue 1263 GLU Chi-restraints excluded: chain A residue 1310 THR Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1325 ASN Chi-restraints excluded: chain A residue 1370 THR Chi-restraints excluded: chain A residue 1398 LEU Chi-restraints excluded: chain A residue 1404 MET Chi-restraints excluded: chain A residue 1414 LEU Chi-restraints excluded: chain B residue 280 ASN Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 249 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 87 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 114 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 131 optimal weight: 7.9990 chunk 106 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 78 optimal weight: 0.7980 chunk 137 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN ** A1008 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1120 ASN B 233 GLN ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12977 Z= 0.194 Angle : 0.575 12.880 17591 Z= 0.287 Chirality : 0.041 0.154 2061 Planarity : 0.004 0.062 2226 Dihedral : 3.944 29.330 1735 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.13 % Allowed : 20.67 % Favored : 76.20 % 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: 1.50 (0.21), residues: 1588 helix: 1.85 (0.17), residues: 908 sheet: -0.45 (0.60), residues: 79 loop : -0.06 (0.25), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 982 HIS 0.005 0.001 HIS B 234 PHE 0.011 0.001 PHE A 404 TYR 0.015 0.001 TYR A 289 ARG 0.003 0.000 ARG B 231 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 213 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TRP cc_start: 0.9023 (OUTLIER) cc_final: 0.8378 (t-100) REVERT: A 381 LYS cc_start: 0.8162 (mmmt) cc_final: 0.7846 (mttt) REVERT: A 539 GLU cc_start: 0.7849 (tp30) cc_final: 0.7531 (tp30) REVERT: A 601 LYS cc_start: 0.7085 (ptpp) cc_final: 0.6658 (ptmt) REVERT: A 788 ARG cc_start: 0.7707 (mtp85) cc_final: 0.7456 (mtp85) REVERT: A 810 PHE cc_start: 0.8305 (t80) cc_final: 0.8034 (t80) REVERT: A 1043 ASN cc_start: 0.7442 (p0) cc_final: 0.6862 (p0) REVERT: E 238 LYS cc_start: 0.8424 (pttm) cc_final: 0.7952 (pttt) outliers start: 45 outliers final: 33 residues processed: 242 average time/residue: 0.2684 time to fit residues: 91.2268 Evaluate side-chains 236 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 202 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 91 TRP Chi-restraints excluded: chain A residue 170 TRP Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 786 THR Chi-restraints excluded: chain A residue 956 ASN Chi-restraints excluded: chain A residue 999 THR Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1190 CYS Chi-restraints excluded: chain A residue 1263 GLU Chi-restraints excluded: chain A residue 1310 THR Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1325 ASN Chi-restraints excluded: chain A residue 1370 THR Chi-restraints excluded: chain A residue 1373 LEU Chi-restraints excluded: chain A residue 1398 LEU Chi-restraints excluded: chain A residue 1404 MET Chi-restraints excluded: chain A residue 1414 LEU Chi-restraints excluded: chain B residue 280 ASN Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 255 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 138 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 chunk 90 optimal weight: 0.5980 chunk 37 optimal weight: 4.9990 chunk 153 optimal weight: 0.6980 chunk 127 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 148 optimal weight: 30.0000 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN A 887 ASN A1008 ASN ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12977 Z= 0.272 Angle : 0.621 12.167 17591 Z= 0.311 Chirality : 0.043 0.181 2061 Planarity : 0.005 0.063 2226 Dihedral : 4.057 23.880 1733 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.13 % Allowed : 21.09 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.21), residues: 1588 helix: 1.63 (0.17), residues: 928 sheet: -0.51 (0.60), residues: 79 loop : -0.15 (0.25), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 182 HIS 0.005 0.001 HIS B 234 PHE 0.011 0.001 PHE A 404 TYR 0.018 0.001 TYR A 289 ARG 0.003 0.000 ARG B 231 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 216 time to evaluate : 1.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TRP cc_start: 0.9054 (OUTLIER) cc_final: 0.8434 (t-100) REVERT: A 381 LYS cc_start: 0.8190 (mmmt) cc_final: 0.7910 (mttt) REVERT: A 431 LYS cc_start: 0.8208 (mmmm) cc_final: 0.7866 (mmmt) REVERT: A 810 PHE cc_start: 0.8320 (t80) cc_final: 0.8044 (t80) REVERT: A 1043 ASN cc_start: 0.7506 (p0) cc_final: 0.6976 (p0) outliers start: 45 outliers final: 34 residues processed: 247 average time/residue: 0.2907 time to fit residues: 100.0310 Evaluate side-chains 239 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 204 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 91 TRP Chi-restraints excluded: chain A residue 170 TRP Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 593 ASN Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 786 THR Chi-restraints excluded: chain A residue 873 SER Chi-restraints excluded: chain A residue 956 ASN Chi-restraints excluded: chain A residue 999 THR Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1263 GLU Chi-restraints excluded: chain A residue 1310 THR Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1325 ASN Chi-restraints excluded: chain A residue 1370 THR Chi-restraints excluded: chain A residue 1373 LEU Chi-restraints excluded: chain A residue 1398 LEU Chi-restraints excluded: chain A residue 1404 MET Chi-restraints excluded: chain A residue 1414 LEU Chi-restraints excluded: chain B residue 280 ASN Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain E residue 221 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 17 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 112 optimal weight: 0.7980 chunk 129 optimal weight: 0.4980 chunk 85 optimal weight: 0.6980 chunk 153 optimal weight: 0.2980 chunk 95 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 887 ASN A1120 ASN ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12977 Z= 0.180 Angle : 0.617 12.683 17591 Z= 0.303 Chirality : 0.042 0.314 2061 Planarity : 0.004 0.061 2226 Dihedral : 3.944 22.796 1733 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.92 % Allowed : 21.99 % Favored : 75.09 % 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: 1.44 (0.21), residues: 1588 helix: 1.78 (0.18), residues: 917 sheet: -0.45 (0.60), residues: 79 loop : -0.08 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 982 HIS 0.004 0.001 HIS B 234 PHE 0.010 0.001 PHE A 404 TYR 0.014 0.001 TYR A 289 ARG 0.009 0.000 ARG A 708 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 214 time to evaluate : 1.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TRP cc_start: 0.9025 (OUTLIER) cc_final: 0.8488 (t-100) REVERT: A 381 LYS cc_start: 0.8157 (mmmt) cc_final: 0.7887 (mttt) REVERT: A 431 LYS cc_start: 0.8189 (mmmm) cc_final: 0.7877 (mmmt) REVERT: A 459 ARG cc_start: 0.7113 (ttm-80) cc_final: 0.6743 (mmt-90) REVERT: A 539 GLU cc_start: 0.7820 (tp30) cc_final: 0.7518 (tp30) REVERT: A 601 LYS cc_start: 0.6898 (pttm) cc_final: 0.6388 (ptpp) REVERT: A 810 PHE cc_start: 0.8289 (t80) cc_final: 0.8027 (t80) REVERT: A 1043 ASN cc_start: 0.7480 (p0) cc_final: 0.6962 (p0) REVERT: A 1190 CYS cc_start: 0.6234 (OUTLIER) cc_final: 0.5567 (m) outliers start: 42 outliers final: 31 residues processed: 239 average time/residue: 0.2794 time to fit residues: 93.2320 Evaluate side-chains 235 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 202 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 170 TRP Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 579 GLU Chi-restraints excluded: chain A residue 593 ASN Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 786 THR Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain A residue 956 ASN Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1138 ASN Chi-restraints excluded: chain A residue 1190 CYS Chi-restraints excluded: chain A residue 1263 GLU Chi-restraints excluded: chain A residue 1310 THR Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1325 ASN Chi-restraints excluded: chain A residue 1370 THR Chi-restraints excluded: chain A residue 1373 LEU Chi-restraints excluded: chain A residue 1404 MET Chi-restraints excluded: chain A residue 1414 LEU Chi-restraints excluded: chain B residue 280 ASN Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 232 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 91 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 30 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 14 optimal weight: 0.4980 chunk 120 optimal weight: 6.9990 chunk 139 optimal weight: 5.9990 chunk 146 optimal weight: 0.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12977 Z= 0.229 Angle : 0.664 21.381 17591 Z= 0.321 Chirality : 0.043 0.270 2061 Planarity : 0.004 0.060 2226 Dihedral : 3.995 23.256 1733 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.99 % Allowed : 22.06 % Favored : 74.95 % 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: 1.28 (0.21), residues: 1588 helix: 1.67 (0.18), residues: 921 sheet: -0.45 (0.60), residues: 79 loop : -0.20 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 182 HIS 0.004 0.001 HIS B 234 PHE 0.012 0.001 PHE A 394 TYR 0.017 0.001 TYR A 289 ARG 0.008 0.000 ARG A 708 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 203 time to evaluate : 1.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TRP cc_start: 0.9041 (OUTLIER) cc_final: 0.8433 (t-100) REVERT: A 381 LYS cc_start: 0.8183 (mmmt) cc_final: 0.7904 (mttt) REVERT: A 431 LYS cc_start: 0.8203 (mmmm) cc_final: 0.7903 (mmmt) REVERT: A 539 GLU cc_start: 0.7876 (tp30) cc_final: 0.7581 (tp30) REVERT: A 601 LYS cc_start: 0.6853 (pttm) cc_final: 0.6360 (ptpp) REVERT: A 810 PHE cc_start: 0.8291 (t80) cc_final: 0.8024 (t80) REVERT: A 1043 ASN cc_start: 0.7518 (p0) cc_final: 0.7052 (p0) REVERT: E 238 LYS cc_start: 0.8285 (pttt) cc_final: 0.7711 (pttt) outliers start: 43 outliers final: 32 residues processed: 231 average time/residue: 0.2758 time to fit residues: 89.2265 Evaluate side-chains 232 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 199 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 170 TRP Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 593 ASN Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 786 THR Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain A residue 956 ASN Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1138 ASN Chi-restraints excluded: chain A residue 1190 CYS Chi-restraints excluded: chain A residue 1263 GLU Chi-restraints excluded: chain A residue 1310 THR Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1325 ASN Chi-restraints excluded: chain A residue 1370 THR Chi-restraints excluded: chain A residue 1404 MET Chi-restraints excluded: chain A residue 1414 LEU Chi-restraints excluded: chain B residue 280 ASN Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain E residue 221 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 133 optimal weight: 10.0000 chunk 142 optimal weight: 4.9990 chunk 146 optimal weight: 8.9990 chunk 85 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 112 optimal weight: 0.8980 chunk 43 optimal weight: 0.0980 chunk 129 optimal weight: 0.8980 chunk 135 optimal weight: 9.9990 chunk 93 optimal weight: 4.9990 chunk 151 optimal weight: 4.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 816 ASN A1120 ASN ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 12977 Z= 0.243 Angle : 0.660 16.382 17591 Z= 0.324 Chirality : 0.043 0.254 2061 Planarity : 0.004 0.060 2226 Dihedral : 4.064 23.562 1733 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.92 % Allowed : 22.55 % Favored : 74.53 % 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: 1.20 (0.21), residues: 1588 helix: 1.57 (0.18), residues: 922 sheet: -0.50 (0.60), residues: 79 loop : -0.17 (0.25), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 182 HIS 0.005 0.001 HIS B 234 PHE 0.010 0.001 PHE A 403 TYR 0.017 0.001 TYR A 289 ARG 0.008 0.000 ARG E 231 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 200 time to evaluate : 1.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TRP cc_start: 0.9046 (OUTLIER) cc_final: 0.8451 (t-100) REVERT: A 381 LYS cc_start: 0.8181 (mmmt) cc_final: 0.7903 (mttt) REVERT: A 431 LYS cc_start: 0.8215 (mmmm) cc_final: 0.7910 (mmmt) REVERT: A 459 ARG cc_start: 0.7151 (ttm-80) cc_final: 0.6801 (mmt-90) REVERT: A 539 GLU cc_start: 0.7907 (tp30) cc_final: 0.7604 (tp30) REVERT: A 601 LYS cc_start: 0.6839 (pttm) cc_final: 0.6350 (ptpp) REVERT: A 810 PHE cc_start: 0.8295 (t80) cc_final: 0.8023 (t80) REVERT: A 1043 ASN cc_start: 0.7551 (p0) cc_final: 0.6999 (p0) REVERT: B 228 MET cc_start: 0.8226 (mmt) cc_final: 0.7899 (mmp) REVERT: D 248 MET cc_start: 0.4668 (ppp) cc_final: 0.4433 (ppp) REVERT: E 238 LYS cc_start: 0.8253 (pttt) cc_final: 0.7701 (pttt) outliers start: 42 outliers final: 35 residues processed: 227 average time/residue: 0.2852 time to fit residues: 91.4746 Evaluate side-chains 235 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 199 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 170 TRP Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 593 ASN Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 786 THR Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain A residue 956 ASN Chi-restraints excluded: chain A residue 999 THR Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1138 ASN Chi-restraints excluded: chain A residue 1190 CYS Chi-restraints excluded: chain A residue 1263 GLU Chi-restraints excluded: chain A residue 1310 THR Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1325 ASN Chi-restraints excluded: chain A residue 1370 THR Chi-restraints excluded: chain A residue 1404 MET Chi-restraints excluded: chain A residue 1414 LEU Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 280 ASN Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain E residue 221 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 92 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 158 optimal weight: 0.9990 chunk 145 optimal weight: 0.6980 chunk 126 optimal weight: 7.9990 chunk 13 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 100 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 816 ASN A 887 ASN ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12977 Z= 0.283 Angle : 0.688 21.024 17591 Z= 0.335 Chirality : 0.044 0.244 2061 Planarity : 0.005 0.060 2226 Dihedral : 4.176 24.368 1733 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.85 % Allowed : 22.69 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.21), residues: 1588 helix: 1.53 (0.17), residues: 924 sheet: -0.52 (0.60), residues: 79 loop : -0.19 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 182 HIS 0.005 0.001 HIS B 234 PHE 0.026 0.001 PHE A 319 TYR 0.018 0.001 TYR A 289 ARG 0.010 0.000 ARG E 231 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 197 time to evaluate : 1.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TRP cc_start: 0.9055 (OUTLIER) cc_final: 0.8547 (t-100) REVERT: A 381 LYS cc_start: 0.8172 (mmmt) cc_final: 0.7897 (mttt) REVERT: A 431 LYS cc_start: 0.8240 (mmmm) cc_final: 0.7938 (mmmt) REVERT: A 601 LYS cc_start: 0.6817 (pttm) cc_final: 0.6343 (ptpp) REVERT: A 810 PHE cc_start: 0.8323 (t80) cc_final: 0.8035 (t80) REVERT: A 1043 ASN cc_start: 0.7594 (p0) cc_final: 0.7023 (p0) REVERT: A 1190 CYS cc_start: 0.6183 (OUTLIER) cc_final: 0.5511 (m) REVERT: E 235 LEU cc_start: 0.9097 (pp) cc_final: 0.8764 (pp) outliers start: 41 outliers final: 38 residues processed: 224 average time/residue: 0.2831 time to fit residues: 89.1995 Evaluate side-chains 233 residues out of total 1441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 193 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 170 TRP Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 593 ASN Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 786 THR Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain A residue 873 SER Chi-restraints excluded: chain A residue 956 ASN Chi-restraints excluded: chain A residue 999 THR Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1138 ASN Chi-restraints excluded: chain A residue 1190 CYS Chi-restraints excluded: chain A residue 1263 GLU Chi-restraints excluded: chain A residue 1310 THR Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1325 ASN Chi-restraints excluded: chain A residue 1366 VAL Chi-restraints excluded: chain A residue 1370 THR Chi-restraints excluded: chain A residue 1373 LEU Chi-restraints excluded: chain A residue 1404 MET Chi-restraints excluded: chain A residue 1414 LEU Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 280 ASN Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain E residue 221 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 38 optimal weight: 4.9990 chunk 116 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 126 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 129 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 110 optimal weight: 0.0970 chunk 7 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 816 ASN A 887 ASN A1120 ASN ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.157954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.121796 restraints weight = 17198.583| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.15 r_work: 0.3342 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12977 Z= 0.187 Angle : 0.673 20.185 17591 Z= 0.324 Chirality : 0.043 0.229 2061 Planarity : 0.004 0.060 2226 Dihedral : 4.028 23.037 1733 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.13 % Allowed : 22.48 % Favored : 74.39 % 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: 1.28 (0.21), residues: 1588 helix: 1.64 (0.18), residues: 921 sheet: -0.46 (0.60), residues: 79 loop : -0.14 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 982 HIS 0.005 0.001 HIS B 234 PHE 0.023 0.001 PHE A 319 TYR 0.014 0.001 TYR A 289 ARG 0.008 0.000 ARG E 231 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3421.51 seconds wall clock time: 61 minutes 37.58 seconds (3697.58 seconds total)