Starting phenix.real_space_refine on Thu May 15 16:07:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yxz_39661/05_2025/8yxz_39661.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yxz_39661/05_2025/8yxz_39661.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yxz_39661/05_2025/8yxz_39661.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yxz_39661/05_2025/8yxz_39661.map" model { file = "/net/cci-nas-00/data/ceres_data/8yxz_39661/05_2025/8yxz_39661.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yxz_39661/05_2025/8yxz_39661.cif" } resolution = 3.0 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= 0.002 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: 4 Type Number sf(0) Gaussians S 25 5.16 5 C 8757 2.51 5 N 2351 2.21 5 O 2345 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 114 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 13478 Number of models: 1 Model: "" Number of chains: 14 Chain: "M" Number of atoms: 2514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2514 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 12, 'TRANS': 307} Chain: "N" Number of atoms: 4868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 649, 4868 Classifications: {'peptide': 649} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 36, 'TRANS': 612} Unresolved non-hydrogen bonds: 227 Unresolved non-hydrogen angles: 289 Unresolved non-hydrogen dihedrals: 181 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 3, 'TYR:plan': 2, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 120 Chain: "O" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 508 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "P" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 508 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "Q" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 508 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "R" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 508 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "S" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 508 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "T" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 508 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "U" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 508 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "V" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 508 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "W" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 508 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "X" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 508 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "Y" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 508 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "Z" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 508 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Time building chain proxies: 8.74, per 1000 atoms: 0.65 Number of scatterers: 13478 At special positions: 0 Unit cell: (113.52, 110, 114.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 25 16.00 O 2345 8.00 N 2351 7.00 C 8757 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS M 267 " - pdb=" SG CYS M 322 " distance=2.06 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 3.04 Conformation dependent library (CDL) restraints added in 2.2 seconds 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3194 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 6 sheets defined 81.4% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'M' and resid 4 through 18 removed outlier: 3.825A pdb=" N THR M 18 " --> pdb=" O VAL M 14 " (cutoff:3.500A) Processing helix chain 'M' and resid 21 through 29 removed outlier: 3.856A pdb=" N PHE M 25 " --> pdb=" O LYS M 21 " (cutoff:3.500A) Processing helix chain 'M' and resid 32 through 43 Processing helix chain 'M' and resid 44 through 49 Processing helix chain 'M' and resid 53 through 70 Processing helix chain 'M' and resid 71 through 76 removed outlier: 3.648A pdb=" N VAL M 76 " --> pdb=" O LEU M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 78 through 86 removed outlier: 3.784A pdb=" N LEU M 86 " --> pdb=" O GLU M 82 " (cutoff:3.500A) Processing helix chain 'M' and resid 89 through 106 Processing helix chain 'M' and resid 108 through 112 Processing helix chain 'M' and resid 120 through 130 removed outlier: 4.157A pdb=" N TRP M 124 " --> pdb=" O ARG M 120 " (cutoff:3.500A) Processing helix chain 'M' and resid 132 through 141 Processing helix chain 'M' and resid 145 through 158 removed outlier: 3.792A pdb=" N ARG M 149 " --> pdb=" O HIS M 145 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG M 156 " --> pdb=" O ARG M 152 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU M 157 " --> pdb=" O ALA M 153 " (cutoff:3.500A) Processing helix chain 'M' and resid 163 through 182 removed outlier: 3.772A pdb=" N LEU M 167 " --> pdb=" O ARG M 163 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ALA M 169 " --> pdb=" O GLU M 165 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N LYS M 170 " --> pdb=" O ALA M 166 " (cutoff:3.500A) Processing helix chain 'M' and resid 185 through 208 removed outlier: 3.713A pdb=" N TYR M 191 " --> pdb=" O ALA M 187 " (cutoff:3.500A) Processing helix chain 'M' and resid 213 through 217 Processing helix chain 'M' and resid 226 through 235 Processing helix chain 'M' and resid 238 through 243 removed outlier: 3.915A pdb=" N ASP M 242 " --> pdb=" O TYR M 238 " (cutoff:3.500A) Processing helix chain 'M' and resid 247 through 253 removed outlier: 3.915A pdb=" N GLY M 251 " --> pdb=" O PRO M 248 " (cutoff:3.500A) Processing helix chain 'M' and resid 257 through 275 Processing helix chain 'M' and resid 276 through 279 Processing helix chain 'M' and resid 283 through 310 Processing helix chain 'M' and resid 312 through 316 Processing helix chain 'N' and resid 16 through 26 removed outlier: 3.518A pdb=" N GLN N 22 " --> pdb=" O LYS N 18 " (cutoff:3.500A) Processing helix chain 'N' and resid 46 through 70 Processing helix chain 'N' and resid 83 through 117 Proline residue: N 93 - end of helix removed outlier: 3.717A pdb=" N ALA N 117 " --> pdb=" O ALA N 113 " (cutoff:3.500A) Processing helix chain 'N' and resid 118 through 129 Processing helix chain 'N' and resid 148 through 158 removed outlier: 4.166A pdb=" N LEU N 152 " --> pdb=" O LYS N 148 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA N 156 " --> pdb=" O LEU N 152 " (cutoff:3.500A) Processing helix chain 'N' and resid 183 through 197 removed outlier: 3.985A pdb=" N GLN N 189 " --> pdb=" O LYS N 185 " (cutoff:3.500A) Processing helix chain 'N' and resid 205 through 209 removed outlier: 3.813A pdb=" N LEU N 208 " --> pdb=" O PRO N 205 " (cutoff:3.500A) Processing helix chain 'N' and resid 212 through 266 removed outlier: 4.246A pdb=" N ALA N 217 " --> pdb=" O LEU N 213 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N ARG N 218 " --> pdb=" O SER N 214 " (cutoff:3.500A) Proline residue: N 228 - end of helix removed outlier: 6.008A pdb=" N SER N 247 " --> pdb=" O ARG N 243 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N THR N 248 " --> pdb=" O GLU N 244 " (cutoff:3.500A) Processing helix chain 'N' and resid 286 through 296 removed outlier: 3.775A pdb=" N VAL N 290 " --> pdb=" O ALA N 286 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA N 293 " --> pdb=" O LYS N 289 " (cutoff:3.500A) Processing helix chain 'N' and resid 313 through 316 Processing helix chain 'N' and resid 327 through 334 Processing helix chain 'N' and resid 350 through 364 Proline residue: N 356 - end of helix Processing helix chain 'N' and resid 365 through 385 removed outlier: 4.050A pdb=" N TYR N 382 " --> pdb=" O TRP N 378 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL N 383 " --> pdb=" O LEU N 379 " (cutoff:3.500A) Processing helix chain 'N' and resid 392 through 395 Processing helix chain 'N' and resid 399 through 425 removed outlier: 3.681A pdb=" N PHE N 415 " --> pdb=" O ASN N 411 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N TRP N 416 " --> pdb=" O TRP N 412 " (cutoff:3.500A) Processing helix chain 'N' and resid 430 through 434 Processing helix chain 'N' and resid 455 through 489 removed outlier: 6.553A pdb=" N ASN N 461 " --> pdb=" O ALA N 457 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N LEU N 462 " --> pdb=" O LYS N 458 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU N 463 " --> pdb=" O THR N 459 " (cutoff:3.500A) Processing helix chain 'N' and resid 491 through 516 Processing helix chain 'N' and resid 523 through 543 Processing helix chain 'N' and resid 546 through 560 removed outlier: 5.165A pdb=" N PHE N 552 " --> pdb=" O ILE N 548 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N THR N 553 " --> pdb=" O PRO N 549 " (cutoff:3.500A) Processing helix chain 'N' and resid 562 through 589 removed outlier: 4.244A pdb=" N GLY N 568 " --> pdb=" O ILE N 564 " (cutoff:3.500A) Processing helix chain 'N' and resid 590 through 592 No H-bonds generated for 'chain 'N' and resid 590 through 592' Processing helix chain 'N' and resid 593 through 626 removed outlier: 5.250A pdb=" N LEU N 614 " --> pdb=" O LEU N 610 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N GLY N 615 " --> pdb=" O LEU N 611 " (cutoff:3.500A) Proline residue: N 620 - end of helix removed outlier: 3.892A pdb=" N LEU N 623 " --> pdb=" O GLN N 619 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU N 624 " --> pdb=" O PRO N 620 " (cutoff:3.500A) Processing helix chain 'O' and resid 9 through 48 removed outlier: 3.744A pdb=" N ILE O 15 " --> pdb=" O ASP O 11 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA O 16 " --> pdb=" O ARG O 12 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL O 17 " --> pdb=" O GLY O 13 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA O 26 " --> pdb=" O ALA O 22 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ARG O 36 " --> pdb=" O VAL O 32 " (cutoff:3.500A) Processing helix chain 'O' and resid 51 through 61 Processing helix chain 'O' and resid 62 through 80 removed outlier: 4.358A pdb=" N VAL O 66 " --> pdb=" O PRO O 62 " (cutoff:3.500A) Processing helix chain 'P' and resid 9 through 48 removed outlier: 3.577A pdb=" N ALA P 16 " --> pdb=" O ARG P 12 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL P 17 " --> pdb=" O GLY P 13 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ARG P 36 " --> pdb=" O VAL P 32 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE P 37 " --> pdb=" O ALA P 33 " (cutoff:3.500A) Processing helix chain 'P' and resid 51 through 61 Processing helix chain 'P' and resid 63 through 79 removed outlier: 3.614A pdb=" N ARG P 79 " --> pdb=" O ILE P 75 " (cutoff:3.500A) Processing helix chain 'Q' and resid 9 through 48 removed outlier: 3.990A pdb=" N ALA Q 16 " --> pdb=" O ARG Q 12 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL Q 17 " --> pdb=" O GLY Q 13 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ARG Q 36 " --> pdb=" O VAL Q 32 " (cutoff:3.500A) Processing helix chain 'Q' and resid 51 through 61 Processing helix chain 'Q' and resid 63 through 78 Processing helix chain 'R' and resid 9 through 48 removed outlier: 3.636A pdb=" N ALA R 16 " --> pdb=" O ARG R 12 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL R 17 " --> pdb=" O GLY R 13 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ARG R 36 " --> pdb=" O VAL R 32 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU R 47 " --> pdb=" O GLY R 43 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP R 48 " --> pdb=" O ALA R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 51 through 61 Processing helix chain 'R' and resid 63 through 80 removed outlier: 3.515A pdb=" N ILE R 67 " --> pdb=" O GLU R 63 " (cutoff:3.500A) Processing helix chain 'S' and resid 9 through 48 removed outlier: 3.840A pdb=" N GLY S 13 " --> pdb=" O GLY S 9 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG S 36 " --> pdb=" O VAL S 32 " (cutoff:3.500A) Processing helix chain 'S' and resid 51 through 61 Processing helix chain 'S' and resid 63 through 80 Processing helix chain 'T' and resid 10 through 48 removed outlier: 3.808A pdb=" N ALA T 16 " --> pdb=" O ARG T 12 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ARG T 36 " --> pdb=" O VAL T 32 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE T 37 " --> pdb=" O ALA T 33 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA T 39 " --> pdb=" O ALA T 35 " (cutoff:3.500A) Processing helix chain 'T' and resid 51 through 61 Processing helix chain 'T' and resid 63 through 80 Processing helix chain 'U' and resid 10 through 48 removed outlier: 4.000A pdb=" N ARG U 36 " --> pdb=" O VAL U 32 " (cutoff:3.500A) Processing helix chain 'U' and resid 51 through 61 Processing helix chain 'U' and resid 63 through 80 Processing helix chain 'V' and resid 10 through 48 removed outlier: 4.185A pdb=" N ARG V 36 " --> pdb=" O VAL V 32 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE V 37 " --> pdb=" O ALA V 33 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA V 39 " --> pdb=" O ALA V 35 " (cutoff:3.500A) Processing helix chain 'V' and resid 51 through 61 Processing helix chain 'V' and resid 63 through 79 Processing helix chain 'W' and resid 9 through 48 removed outlier: 4.433A pdb=" N GLY W 13 " --> pdb=" O GLY W 9 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ARG W 36 " --> pdb=" O VAL W 32 " (cutoff:3.500A) Processing helix chain 'W' and resid 51 through 61 Processing helix chain 'W' and resid 63 through 78 Processing helix chain 'X' and resid 10 through 48 removed outlier: 4.060A pdb=" N ALA X 16 " --> pdb=" O ARG X 12 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL X 17 " --> pdb=" O GLY X 13 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY X 18 " --> pdb=" O LEU X 14 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ARG X 36 " --> pdb=" O VAL X 32 " (cutoff:3.500A) Processing helix chain 'X' and resid 51 through 61 removed outlier: 3.553A pdb=" N PHE X 58 " --> pdb=" O THR X 54 " (cutoff:3.500A) Processing helix chain 'X' and resid 63 through 80 Processing helix chain 'Y' and resid 10 through 48 removed outlier: 4.070A pdb=" N ARG Y 36 " --> pdb=" O VAL Y 32 " (cutoff:3.500A) Processing helix chain 'Y' and resid 51 through 61 Processing helix chain 'Y' and resid 63 through 78 removed outlier: 3.553A pdb=" N ILE Y 67 " --> pdb=" O GLU Y 63 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE Y 72 " --> pdb=" O PHE Y 68 " (cutoff:3.500A) Processing helix chain 'Z' and resid 10 through 48 removed outlier: 4.083A pdb=" N ARG Z 36 " --> pdb=" O VAL Z 32 " (cutoff:3.500A) Processing helix chain 'Z' and resid 51 through 61 Processing helix chain 'Z' and resid 63 through 79 removed outlier: 3.582A pdb=" N ILE Z 67 " --> pdb=" O GLU Z 63 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'N' and resid 31 through 33 removed outlier: 4.334A pdb=" N LEU N 279 " --> pdb=" O GLU N 33 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'N' and resid 31 through 33 removed outlier: 4.334A pdb=" N LEU N 279 " --> pdb=" O GLU N 33 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'N' and resid 176 through 177 removed outlier: 3.608A pdb=" N LEU N 144 " --> pdb=" O ALA N 200 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ALA N 200 " --> pdb=" O LEU N 144 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'N' and resid 318 through 319 Processing sheet with id=AA5, first strand: chain 'N' and resid 389 through 391 Processing sheet with id=AA6, first strand: chain 'N' and resid 438 through 439 1125 hydrogen bonds defined for protein. 3285 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: 4.80 Time building geometry restraints manager: 3.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3247 1.33 - 1.45: 2426 1.45 - 1.57: 7968 1.57 - 1.70: 0 1.70 - 1.82: 48 Bond restraints: 13689 Sorted by residual: bond pdb=" CZ ARG N 262 " pdb=" NH2 ARG N 262 " ideal model delta sigma weight residual 1.330 1.281 0.049 1.30e-02 5.92e+03 1.43e+01 bond pdb=" CZ ARG N 622 " pdb=" NH2 ARG N 622 " ideal model delta sigma weight residual 1.330 1.286 0.044 1.30e-02 5.92e+03 1.15e+01 bond pdb=" CZ ARG N 640 " pdb=" NH2 ARG N 640 " ideal model delta sigma weight residual 1.330 1.288 0.042 1.30e-02 5.92e+03 1.04e+01 bond pdb=" CA PRO N 324 " pdb=" C PRO N 324 " ideal model delta sigma weight residual 1.514 1.532 -0.018 5.50e-03 3.31e+04 1.03e+01 bond pdb=" CZ ARG M 256 " pdb=" NH2 ARG M 256 " ideal model delta sigma weight residual 1.330 1.288 0.042 1.30e-02 5.92e+03 1.02e+01 ... (remaining 13684 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 14599 2.04 - 4.08: 3574 4.08 - 6.13: 365 6.13 - 8.17: 13 8.17 - 10.21: 5 Bond angle restraints: 18556 Sorted by residual: angle pdb=" CA PHE N 629 " pdb=" CB PHE N 629 " pdb=" CG PHE N 629 " ideal model delta sigma weight residual 113.80 119.43 -5.63 1.00e+00 1.00e+00 3.17e+01 angle pdb=" CA VAL N 626 " pdb=" C VAL N 626 " pdb=" N GLU N 627 " ideal model delta sigma weight residual 117.15 121.39 -4.24 7.80e-01 1.64e+00 2.96e+01 angle pdb=" C ARG N 622 " pdb=" CA ARG N 622 " pdb=" CB ARG N 622 " ideal model delta sigma weight residual 110.68 101.97 8.71 1.70e+00 3.46e-01 2.63e+01 angle pdb=" CA ASP T 48 " pdb=" CB ASP T 48 " pdb=" CG ASP T 48 " ideal model delta sigma weight residual 112.60 117.69 -5.09 1.00e+00 1.00e+00 2.60e+01 angle pdb=" CA ASP Z 11 " pdb=" CB ASP Z 11 " pdb=" CG ASP Z 11 " ideal model delta sigma weight residual 112.60 117.68 -5.08 1.00e+00 1.00e+00 2.59e+01 ... (remaining 18551 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.09: 7343 17.09 - 34.17: 516 34.17 - 51.26: 114 51.26 - 68.34: 15 68.34 - 85.43: 9 Dihedral angle restraints: 7997 sinusoidal: 2949 harmonic: 5048 Sorted by residual: dihedral pdb=" CA VAL M 142 " pdb=" C VAL M 142 " pdb=" N PRO M 143 " pdb=" CA PRO M 143 " ideal model delta harmonic sigma weight residual 180.00 -151.50 -28.50 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA GLU N 299 " pdb=" C GLU N 299 " pdb=" N SER N 300 " pdb=" CA SER N 300 " ideal model delta harmonic sigma weight residual -180.00 -155.23 -24.77 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA GLU N 170 " pdb=" C GLU N 170 " pdb=" N ALA N 171 " pdb=" CA ALA N 171 " ideal model delta harmonic sigma weight residual 180.00 155.42 24.58 0 5.00e+00 4.00e-02 2.42e+01 ... (remaining 7994 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1432 0.078 - 0.156: 625 0.156 - 0.234: 140 0.234 - 0.311: 25 0.311 - 0.389: 2 Chirality restraints: 2224 Sorted by residual: chirality pdb=" CA PRO M 143 " pdb=" N PRO M 143 " pdb=" C PRO M 143 " pdb=" CB PRO M 143 " both_signs ideal model delta sigma weight residual False 2.72 2.33 0.39 2.00e-01 2.50e+01 3.79e+00 chirality pdb=" CA VAL N 626 " pdb=" N VAL N 626 " pdb=" C VAL N 626 " pdb=" CB VAL N 626 " both_signs ideal model delta sigma weight residual False 2.44 2.10 0.34 2.00e-01 2.50e+01 2.96e+00 chirality pdb=" CA LEU M 219 " pdb=" N LEU M 219 " pdb=" C LEU M 219 " pdb=" CB LEU M 219 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.38e+00 ... (remaining 2221 not shown) Planarity restraints: 2381 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR M 7 " 0.136 2.00e-02 2.50e+03 8.07e-02 1.30e+02 pdb=" CG TYR M 7 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR M 7 " -0.066 2.00e-02 2.50e+03 pdb=" CD2 TYR M 7 " -0.058 2.00e-02 2.50e+03 pdb=" CE1 TYR M 7 " -0.056 2.00e-02 2.50e+03 pdb=" CE2 TYR M 7 " -0.059 2.00e-02 2.50e+03 pdb=" CZ TYR M 7 " -0.011 2.00e-02 2.50e+03 pdb=" OH TYR M 7 " 0.136 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP N 358 " 0.091 2.00e-02 2.50e+03 4.82e-02 5.80e+01 pdb=" CG TRP N 358 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP N 358 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP N 358 " -0.055 2.00e-02 2.50e+03 pdb=" NE1 TRP N 358 " -0.030 2.00e-02 2.50e+03 pdb=" CE2 TRP N 358 " -0.016 2.00e-02 2.50e+03 pdb=" CE3 TRP N 358 " -0.063 2.00e-02 2.50e+03 pdb=" CZ2 TRP N 358 " 0.045 2.00e-02 2.50e+03 pdb=" CZ3 TRP N 358 " -0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP N 358 " 0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR N 424 " 0.083 2.00e-02 2.50e+03 4.51e-02 4.07e+01 pdb=" CG TYR N 424 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR N 424 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 TYR N 424 " -0.033 2.00e-02 2.50e+03 pdb=" CE1 TYR N 424 " -0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR N 424 " -0.028 2.00e-02 2.50e+03 pdb=" CZ TYR N 424 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR N 424 " 0.069 2.00e-02 2.50e+03 ... (remaining 2378 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 4506 2.90 - 3.40: 14551 3.40 - 3.90: 22161 3.90 - 4.40: 23790 4.40 - 4.90: 41714 Nonbonded interactions: 106722 Sorted by model distance: nonbonded pdb=" OD1 ASP Z 48 " pdb=" ND2 ASN Z 51 " model vdw 2.396 3.120 nonbonded pdb=" ND2 ASN N 518 " pdb=" O GLN N 520 " model vdw 2.495 3.120 nonbonded pdb=" OD1 ASP P 48 " pdb=" N ARG P 49 " model vdw 2.502 3.120 nonbonded pdb=" OD1 ASP U 48 " pdb=" OG SER U 50 " model vdw 2.544 3.040 nonbonded pdb=" OG SER N 46 " pdb=" OE1 GLU N 49 " model vdw 2.563 3.040 ... (remaining 106717 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } 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: 3.740 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: 0.020 Extract box with map and model: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.140 Process input model: 32.970 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.080 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:13.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 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 : 0.011 0.049 13690 Z= 0.669 Angle : 1.663 10.210 18558 Z= 1.122 Chirality : 0.087 0.389 2224 Planarity : 0.014 0.182 2381 Dihedral : 12.991 85.429 4800 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 0.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.48 % Favored : 97.47 % Rotamer: Outliers : 0.08 % Allowed : 9.09 % Favored : 90.83 % Cbeta Deviations : 0.13 % 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: -0.44 (0.19), residues: 1817 helix: -0.05 (0.13), residues: 1409 sheet: 1.54 (1.12), residues: 22 loop : -0.81 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.091 0.020 TRP N 358 HIS 0.016 0.003 HIS N 297 PHE 0.052 0.009 PHE N 431 TYR 0.136 0.015 TYR M 7 ARG 0.011 0.001 ARG R 79 Details of bonding type rmsd hydrogen bonds : bond 0.16199 ( 1122) hydrogen bonds : angle 5.71255 ( 3285) SS BOND : bond 0.02405 ( 1) SS BOND : angle 2.09917 ( 2) covalent geometry : bond 0.01057 (13689) covalent geometry : angle 1.66286 (18556) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 145 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 234 MET cc_start: 0.7369 (ttp) cc_final: 0.6969 (ptm) REVERT: M 279 ASP cc_start: 0.8408 (t0) cc_final: 0.7870 (t0) REVERT: N 5 MET cc_start: 0.8688 (mmt) cc_final: 0.8437 (mmp) REVERT: N 315 ASP cc_start: 0.8626 (p0) cc_final: 0.8056 (t0) REVERT: N 540 LEU cc_start: 0.8309 (tt) cc_final: 0.7999 (mt) REVERT: P 12 ARG cc_start: 0.7984 (mtt90) cc_final: 0.7024 (mtp-110) REVERT: P 47 GLU cc_start: 0.8171 (tm-30) cc_final: 0.7897 (tm-30) REVERT: Q 11 ASP cc_start: 0.8059 (t0) cc_final: 0.7651 (t70) REVERT: Q 48 ASP cc_start: 0.8050 (t0) cc_final: 0.7728 (t0) REVERT: S 48 ASP cc_start: 0.7654 (m-30) cc_final: 0.7388 (m-30) REVERT: V 49 ARG cc_start: 0.8395 (tpp-160) cc_final: 0.8158 (mmt-90) REVERT: V 57 ILE cc_start: 0.8835 (mt) cc_final: 0.8595 (mt) REVERT: W 63 GLU cc_start: 0.8576 (tt0) cc_final: 0.8327 (tt0) REVERT: X 48 ASP cc_start: 0.7910 (t0) cc_final: 0.7601 (t0) REVERT: X 50 SER cc_start: 0.8788 (t) cc_final: 0.8507 (p) REVERT: Y 11 ASP cc_start: 0.7795 (p0) cc_final: 0.7486 (p0) outliers start: 1 outliers final: 1 residues processed: 146 average time/residue: 1.6420 time to fit residues: 256.9413 Evaluate side-chains 73 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 72 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 57 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 0.6980 chunk 136 optimal weight: 0.4980 chunk 75 optimal weight: 0.9980 chunk 46 optimal weight: 50.0000 chunk 92 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 163 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 200 ASN N 25 GLN ** N 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 51 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.096929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.063349 restraints weight = 33669.626| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.80 r_work: 0.2995 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13690 Z= 0.149 Angle : 0.629 9.284 18558 Z= 0.319 Chirality : 0.041 0.208 2224 Planarity : 0.004 0.038 2381 Dihedral : 4.390 23.711 1970 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.25 % Allowed : 13.40 % Favored : 85.34 % 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: 1.64 (0.20), residues: 1817 helix: 1.51 (0.14), residues: 1417 sheet: -0.29 (0.93), residues: 36 loop : -0.25 (0.37), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 358 HIS 0.004 0.001 HIS N 561 PHE 0.018 0.001 PHE N 80 TYR 0.019 0.001 TYR M 128 ARG 0.008 0.001 ARG W 49 Details of bonding type rmsd hydrogen bonds : bond 0.05708 ( 1122) hydrogen bonds : angle 3.70135 ( 3285) SS BOND : bond 0.02190 ( 1) SS BOND : angle 1.42620 ( 2) covalent geometry : bond 0.00299 (13689) covalent geometry : angle 0.62836 (18556) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 1.446 Fit side-chains REVERT: N 5 MET cc_start: 0.8494 (mmt) cc_final: 0.8198 (mmp) REVERT: N 315 ASP cc_start: 0.8678 (p0) cc_final: 0.8078 (t0) REVERT: N 540 LEU cc_start: 0.8359 (tt) cc_final: 0.8077 (mt) REVERT: P 47 GLU cc_start: 0.8301 (tm-30) cc_final: 0.8052 (tm-30) REVERT: S 48 ASP cc_start: 0.7297 (m-30) cc_final: 0.6976 (m-30) REVERT: V 49 ARG cc_start: 0.8328 (tpp-160) cc_final: 0.8079 (mmt-90) REVERT: V 57 ILE cc_start: 0.8946 (mt) cc_final: 0.8707 (mt) REVERT: W 15 ILE cc_start: 0.8379 (pt) cc_final: 0.8143 (mt) REVERT: Y 11 ASP cc_start: 0.7874 (p0) cc_final: 0.7494 (p0) outliers start: 16 outliers final: 4 residues processed: 102 average time/residue: 1.1405 time to fit residues: 129.7796 Evaluate side-chains 65 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 72 ILE Chi-restraints excluded: chain S residue 54 THR Chi-restraints excluded: chain V residue 54 THR Chi-restraints excluded: chain Z residue 54 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 9 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 51 optimal weight: 40.0000 chunk 57 optimal weight: 9.9990 chunk 154 optimal weight: 4.9990 chunk 169 optimal weight: 8.9990 chunk 128 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 70 optimal weight: 0.5980 chunk 166 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 638 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.092036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.056158 restraints weight = 34069.946| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.40 r_work: 0.2876 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 13690 Z= 0.264 Angle : 0.709 8.706 18558 Z= 0.356 Chirality : 0.044 0.213 2224 Planarity : 0.005 0.043 2381 Dihedral : 4.146 21.362 1968 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.74 % Allowed : 15.20 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.20), residues: 1817 helix: 1.48 (0.14), residues: 1418 sheet: 2.67 (1.01), residues: 22 loop : -0.54 (0.35), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 326 HIS 0.006 0.001 HIS M 145 PHE 0.020 0.002 PHE N 80 TYR 0.016 0.002 TYR M 7 ARG 0.005 0.001 ARG W 49 Details of bonding type rmsd hydrogen bonds : bond 0.07045 ( 1122) hydrogen bonds : angle 3.89830 ( 3285) SS BOND : bond 0.01530 ( 1) SS BOND : angle 3.10190 ( 2) covalent geometry : bond 0.00655 (13689) covalent geometry : angle 0.70798 (18556) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 68 time to evaluate : 1.513 Fit side-chains REVERT: M 234 MET cc_start: 0.7749 (ttp) cc_final: 0.7322 (ptm) REVERT: N 5 MET cc_start: 0.8391 (mmt) cc_final: 0.8056 (mmp) REVERT: N 540 LEU cc_start: 0.8511 (tt) cc_final: 0.8231 (mt) REVERT: P 47 GLU cc_start: 0.8736 (tm-30) cc_final: 0.8452 (tm-30) REVERT: S 48 ASP cc_start: 0.7991 (m-30) cc_final: 0.7739 (m-30) REVERT: W 49 ARG cc_start: 0.8665 (mmm-85) cc_final: 0.8459 (mmt-90) REVERT: Y 11 ASP cc_start: 0.8109 (p0) cc_final: 0.7681 (p0) outliers start: 35 outliers final: 17 residues processed: 97 average time/residue: 0.9863 time to fit residues: 107.8497 Evaluate side-chains 77 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 41 SER Chi-restraints excluded: chain M residue 316 VAL Chi-restraints excluded: chain N residue 290 VAL Chi-restraints excluded: chain N residue 541 MET Chi-restraints excluded: chain Q residue 50 SER Chi-restraints excluded: chain S residue 19 MET Chi-restraints excluded: chain S residue 54 THR Chi-restraints excluded: chain T residue 23 VAL Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain V residue 66 VAL Chi-restraints excluded: chain W residue 14 LEU Chi-restraints excluded: chain W residue 75 ILE Chi-restraints excluded: chain X residue 30 THR Chi-restraints excluded: chain X residue 50 SER Chi-restraints excluded: chain Z residue 30 THR Chi-restraints excluded: chain Z residue 54 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 23 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 70 optimal weight: 20.0000 chunk 100 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 4 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 57 optimal weight: 9.9990 chunk 118 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 489 HIS N 638 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.094296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.060576 restraints weight = 33817.949| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.71 r_work: 0.2937 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13690 Z= 0.149 Angle : 0.562 8.432 18558 Z= 0.285 Chirality : 0.039 0.181 2224 Planarity : 0.004 0.041 2381 Dihedral : 3.914 20.444 1968 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.82 % Allowed : 16.38 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.20), residues: 1817 helix: 1.92 (0.14), residues: 1411 sheet: 2.33 (1.07), residues: 23 loop : -0.43 (0.35), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 295 HIS 0.003 0.001 HIS N 616 PHE 0.017 0.001 PHE N 80 TYR 0.012 0.001 TYR M 7 ARG 0.003 0.000 ARG W 49 Details of bonding type rmsd hydrogen bonds : bond 0.05614 ( 1122) hydrogen bonds : angle 3.51748 ( 3285) SS BOND : bond 0.00194 ( 1) SS BOND : angle 7.55854 ( 2) covalent geometry : bond 0.00338 (13689) covalent geometry : angle 0.55660 (18556) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 69 time to evaluate : 1.358 Fit side-chains revert: symmetry clash REVERT: M 234 MET cc_start: 0.7605 (ttp) cc_final: 0.7311 (ptm) REVERT: N 315 ASP cc_start: 0.8819 (p0) cc_final: 0.7968 (t0) REVERT: N 540 LEU cc_start: 0.8447 (tt) cc_final: 0.8155 (mt) REVERT: P 47 GLU cc_start: 0.8517 (tm-30) cc_final: 0.8191 (tm-30) REVERT: S 48 ASP cc_start: 0.7656 (m-30) cc_final: 0.7381 (m-30) outliers start: 36 outliers final: 10 residues processed: 96 average time/residue: 1.0439 time to fit residues: 112.1364 Evaluate side-chains 66 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 290 VAL Chi-restraints excluded: chain Q residue 50 SER Chi-restraints excluded: chain Q residue 61 LEU Chi-restraints excluded: chain R residue 19 MET Chi-restraints excluded: chain S residue 54 THR Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain V residue 66 VAL Chi-restraints excluded: chain X residue 19 MET Chi-restraints excluded: chain X residue 50 SER Chi-restraints excluded: chain Y residue 30 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 19 optimal weight: 7.9990 chunk 158 optimal weight: 0.4980 chunk 66 optimal weight: 0.2980 chunk 92 optimal weight: 2.9990 chunk 137 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 35 optimal weight: 10.0000 chunk 76 optimal weight: 4.9990 chunk 39 optimal weight: 9.9990 chunk 171 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.095140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.062242 restraints weight = 33537.420| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 2.93 r_work: 0.2960 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13690 Z= 0.129 Angle : 0.536 8.429 18558 Z= 0.270 Chirality : 0.038 0.173 2224 Planarity : 0.004 0.040 2381 Dihedral : 3.730 19.553 1968 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.43 % Allowed : 17.63 % Favored : 79.94 % 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: 2.40 (0.20), residues: 1817 helix: 2.10 (0.14), residues: 1417 sheet: 2.20 (1.04), residues: 23 loop : -0.41 (0.35), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP N 420 HIS 0.003 0.001 HIS N 616 PHE 0.016 0.001 PHE N 80 TYR 0.012 0.001 TYR M 7 ARG 0.008 0.000 ARG W 49 Details of bonding type rmsd hydrogen bonds : bond 0.05076 ( 1122) hydrogen bonds : angle 3.36957 ( 3285) SS BOND : bond 0.01354 ( 1) SS BOND : angle 1.58377 ( 2) covalent geometry : bond 0.00279 (13689) covalent geometry : angle 0.53537 (18556) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 68 time to evaluate : 1.455 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 234 MET cc_start: 0.7645 (ttp) cc_final: 0.7310 (ptm) REVERT: N 315 ASP cc_start: 0.8844 (p0) cc_final: 0.7950 (t0) REVERT: N 540 LEU cc_start: 0.8454 (tt) cc_final: 0.8167 (mt) REVERT: P 47 GLU cc_start: 0.8529 (tm-30) cc_final: 0.8127 (tm-30) REVERT: S 48 ASP cc_start: 0.7528 (m-30) cc_final: 0.7201 (m-30) REVERT: U 19 MET cc_start: 0.8878 (ptp) cc_final: 0.8580 (ptm) REVERT: W 10 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7982 (tp) REVERT: W 19 MET cc_start: 0.8848 (mtp) cc_final: 0.8607 (mtm) outliers start: 31 outliers final: 12 residues processed: 94 average time/residue: 1.1915 time to fit residues: 124.0966 Evaluate side-chains 73 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 290 VAL Chi-restraints excluded: chain Q residue 50 SER Chi-restraints excluded: chain Q residue 61 LEU Chi-restraints excluded: chain S residue 54 THR Chi-restraints excluded: chain T residue 23 VAL Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 76 LEU Chi-restraints excluded: chain V residue 66 VAL Chi-restraints excluded: chain W residue 10 LEU Chi-restraints excluded: chain W residue 75 ILE Chi-restraints excluded: chain X residue 19 MET Chi-restraints excluded: chain X residue 50 SER Chi-restraints excluded: chain Z residue 61 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 141 optimal weight: 1.9990 chunk 163 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 23 optimal weight: 6.9990 chunk 59 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 chunk 52 optimal weight: 0.0970 chunk 179 optimal weight: 4.9990 chunk 153 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 106 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.094806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.061589 restraints weight = 33929.218| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.89 r_work: 0.2947 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13690 Z= 0.138 Angle : 0.550 8.909 18558 Z= 0.277 Chirality : 0.038 0.173 2224 Planarity : 0.004 0.040 2381 Dihedral : 3.708 18.934 1968 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.51 % Allowed : 18.18 % Favored : 79.31 % 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: 2.37 (0.20), residues: 1817 helix: 2.09 (0.14), residues: 1417 sheet: 2.06 (1.06), residues: 23 loop : -0.45 (0.35), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP N 420 HIS 0.003 0.001 HIS N 616 PHE 0.016 0.001 PHE N 80 TYR 0.014 0.001 TYR M 7 ARG 0.006 0.000 ARG W 49 Details of bonding type rmsd hydrogen bonds : bond 0.05136 ( 1122) hydrogen bonds : angle 3.42110 ( 3285) SS BOND : bond 0.00847 ( 1) SS BOND : angle 5.55329 ( 2) covalent geometry : bond 0.00314 (13689) covalent geometry : angle 0.54678 (18556) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 64 time to evaluate : 1.516 Fit side-chains revert: symmetry clash REVERT: M 234 MET cc_start: 0.7667 (ttp) cc_final: 0.7303 (ptm) REVERT: N 315 ASP cc_start: 0.8858 (p0) cc_final: 0.7936 (t0) REVERT: N 540 LEU cc_start: 0.8477 (tt) cc_final: 0.8183 (mt) REVERT: P 47 GLU cc_start: 0.8555 (tm-30) cc_final: 0.8148 (tm-30) REVERT: S 48 ASP cc_start: 0.7541 (m-30) cc_final: 0.7296 (m-30) REVERT: U 19 MET cc_start: 0.8918 (ptp) cc_final: 0.8676 (ptm) REVERT: W 19 MET cc_start: 0.8853 (mtp) cc_final: 0.8616 (mtm) outliers start: 32 outliers final: 15 residues processed: 90 average time/residue: 0.9953 time to fit residues: 101.5710 Evaluate side-chains 74 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 138 GLN Chi-restraints excluded: chain M residue 321 VAL Chi-restraints excluded: chain N residue 290 VAL Chi-restraints excluded: chain N residue 528 MET Chi-restraints excluded: chain N residue 558 ILE Chi-restraints excluded: chain Q residue 50 SER Chi-restraints excluded: chain Q residue 61 LEU Chi-restraints excluded: chain S residue 54 THR Chi-restraints excluded: chain T residue 23 VAL Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain V residue 66 VAL Chi-restraints excluded: chain W residue 75 ILE Chi-restraints excluded: chain X residue 50 SER Chi-restraints excluded: chain Z residue 61 LEU Chi-restraints excluded: chain Z residue 63 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 115 optimal weight: 0.7980 chunk 38 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 55 optimal weight: 9.9990 chunk 137 optimal weight: 0.9980 chunk 124 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 51 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.093551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.059955 restraints weight = 33898.695| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.96 r_work: 0.2911 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13690 Z= 0.173 Angle : 0.576 10.041 18558 Z= 0.289 Chirality : 0.039 0.179 2224 Planarity : 0.004 0.041 2381 Dihedral : 3.697 18.511 1968 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.51 % Allowed : 19.83 % Favored : 77.66 % 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: 2.28 (0.20), residues: 1817 helix: 2.03 (0.14), residues: 1414 sheet: 2.10 (1.07), residues: 23 loop : -0.47 (0.35), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP M 295 HIS 0.003 0.001 HIS M 145 PHE 0.016 0.001 PHE N 80 TYR 0.016 0.001 TYR M 7 ARG 0.005 0.000 ARG W 49 Details of bonding type rmsd hydrogen bonds : bond 0.05569 ( 1122) hydrogen bonds : angle 3.48320 ( 3285) SS BOND : bond 0.01314 ( 1) SS BOND : angle 1.22524 ( 2) covalent geometry : bond 0.00418 (13689) covalent geometry : angle 0.57590 (18556) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 65 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 234 MET cc_start: 0.7707 (ttp) cc_final: 0.7289 (ptm) REVERT: N 540 LEU cc_start: 0.8484 (tt) cc_final: 0.8190 (mt) REVERT: P 47 GLU cc_start: 0.8545 (tm-30) cc_final: 0.8133 (tm-30) REVERT: S 48 ASP cc_start: 0.7569 (m-30) cc_final: 0.7240 (m-30) outliers start: 32 outliers final: 17 residues processed: 93 average time/residue: 1.1335 time to fit residues: 117.7630 Evaluate side-chains 77 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 321 VAL Chi-restraints excluded: chain N residue 290 VAL Chi-restraints excluded: chain P residue 75 ILE Chi-restraints excluded: chain Q residue 50 SER Chi-restraints excluded: chain R residue 19 MET Chi-restraints excluded: chain S residue 54 THR Chi-restraints excluded: chain T residue 23 VAL Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain V residue 66 VAL Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 66 VAL Chi-restraints excluded: chain W residue 75 ILE Chi-restraints excluded: chain X residue 50 SER Chi-restraints excluded: chain Y residue 30 THR Chi-restraints excluded: chain Z residue 54 THR Chi-restraints excluded: chain Z residue 61 LEU Chi-restraints excluded: chain Z residue 63 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 106 optimal weight: 4.9990 chunk 176 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 173 optimal weight: 9.9990 chunk 77 optimal weight: 8.9990 chunk 71 optimal weight: 5.9990 chunk 112 optimal weight: 0.9980 chunk 145 optimal weight: 0.9980 chunk 85 optimal weight: 5.9990 chunk 14 optimal weight: 0.0770 chunk 147 optimal weight: 0.7980 overall best weight: 0.7738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.095803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.062801 restraints weight = 33644.299| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 3.02 r_work: 0.2976 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13690 Z= 0.121 Angle : 0.549 9.574 18558 Z= 0.273 Chirality : 0.038 0.191 2224 Planarity : 0.004 0.041 2381 Dihedral : 3.635 18.152 1968 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.80 % Allowed : 20.77 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.20), residues: 1817 helix: 2.21 (0.14), residues: 1417 sheet: 2.16 (1.09), residues: 23 loop : -0.46 (0.35), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 420 HIS 0.003 0.000 HIS N 616 PHE 0.015 0.001 PHE N 80 TYR 0.012 0.001 TYR M 7 ARG 0.006 0.000 ARG S 49 Details of bonding type rmsd hydrogen bonds : bond 0.04717 ( 1122) hydrogen bonds : angle 3.33404 ( 3285) SS BOND : bond 0.00374 ( 1) SS BOND : angle 8.00097 ( 2) covalent geometry : bond 0.00254 (13689) covalent geometry : angle 0.54288 (18556) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 66 time to evaluate : 1.397 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 234 MET cc_start: 0.7716 (ttp) cc_final: 0.7322 (ptm) REVERT: N 315 ASP cc_start: 0.8841 (p0) cc_final: 0.7947 (t0) REVERT: N 540 LEU cc_start: 0.8499 (tt) cc_final: 0.8206 (mt) REVERT: P 47 GLU cc_start: 0.8521 (tm-30) cc_final: 0.8103 (tm-30) REVERT: S 48 ASP cc_start: 0.7529 (m-30) cc_final: 0.7289 (m-30) outliers start: 23 outliers final: 11 residues processed: 85 average time/residue: 1.1429 time to fit residues: 108.2044 Evaluate side-chains 72 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 321 VAL Chi-restraints excluded: chain N residue 290 VAL Chi-restraints excluded: chain Q residue 50 SER Chi-restraints excluded: chain R residue 19 MET Chi-restraints excluded: chain V residue 66 VAL Chi-restraints excluded: chain W residue 66 VAL Chi-restraints excluded: chain X residue 50 SER Chi-restraints excluded: chain Y residue 30 THR Chi-restraints excluded: chain Z residue 54 THR Chi-restraints excluded: chain Z residue 61 LEU Chi-restraints excluded: chain Z residue 63 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 123 optimal weight: 3.9990 chunk 49 optimal weight: 30.0000 chunk 20 optimal weight: 4.9990 chunk 91 optimal weight: 20.0000 chunk 175 optimal weight: 6.9990 chunk 157 optimal weight: 0.8980 chunk 88 optimal weight: 5.9990 chunk 109 optimal weight: 0.8980 chunk 161 optimal weight: 3.9990 chunk 38 optimal weight: 20.0000 chunk 68 optimal weight: 0.0670 overall best weight: 1.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.094018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.060455 restraints weight = 33660.146| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.93 r_work: 0.2927 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13690 Z= 0.162 Angle : 0.576 10.051 18558 Z= 0.285 Chirality : 0.039 0.173 2224 Planarity : 0.004 0.042 2381 Dihedral : 3.604 17.897 1968 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.65 % Allowed : 21.24 % Favored : 77.12 % 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: 2.41 (0.20), residues: 1817 helix: 2.12 (0.14), residues: 1416 sheet: 2.10 (1.10), residues: 23 loop : -0.47 (0.35), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP M 295 HIS 0.002 0.001 HIS N 616 PHE 0.015 0.001 PHE N 80 TYR 0.016 0.001 TYR M 7 ARG 0.004 0.000 ARG W 49 Details of bonding type rmsd hydrogen bonds : bond 0.05290 ( 1122) hydrogen bonds : angle 3.40748 ( 3285) SS BOND : bond 0.01403 ( 1) SS BOND : angle 0.31040 ( 2) covalent geometry : bond 0.00390 (13689) covalent geometry : angle 0.57553 (18556) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 64 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 234 MET cc_start: 0.7738 (ttp) cc_final: 0.7295 (ptm) REVERT: N 315 ASP cc_start: 0.8849 (p0) cc_final: 0.7933 (t0) REVERT: N 540 LEU cc_start: 0.8508 (tt) cc_final: 0.8201 (mt) REVERT: P 47 GLU cc_start: 0.8590 (tm-30) cc_final: 0.8162 (tm-30) REVERT: S 48 ASP cc_start: 0.7546 (m-30) cc_final: 0.7215 (m-30) outliers start: 21 outliers final: 15 residues processed: 84 average time/residue: 1.1061 time to fit residues: 103.6033 Evaluate side-chains 76 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 138 GLN Chi-restraints excluded: chain M residue 321 VAL Chi-restraints excluded: chain N residue 290 VAL Chi-restraints excluded: chain P residue 75 ILE Chi-restraints excluded: chain Q residue 50 SER Chi-restraints excluded: chain Q residue 61 LEU Chi-restraints excluded: chain R residue 19 MET Chi-restraints excluded: chain V residue 66 VAL Chi-restraints excluded: chain W residue 10 LEU Chi-restraints excluded: chain W residue 66 VAL Chi-restraints excluded: chain X residue 50 SER Chi-restraints excluded: chain Y residue 30 THR Chi-restraints excluded: chain Z residue 54 THR Chi-restraints excluded: chain Z residue 61 LEU Chi-restraints excluded: chain Z residue 63 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 74 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 129 optimal weight: 0.0470 chunk 141 optimal weight: 1.9990 chunk 54 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 overall best weight: 1.7884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 237 HIS ** 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 = 0.3815 r_free = 0.3815 target = 0.094069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.060501 restraints weight = 33761.834| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.75 r_work: 0.2933 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13690 Z= 0.154 Angle : 0.585 10.939 18558 Z= 0.288 Chirality : 0.039 0.171 2224 Planarity : 0.004 0.042 2381 Dihedral : 3.620 17.765 1968 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.49 % Allowed : 21.47 % Favored : 77.04 % 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: 2.40 (0.20), residues: 1817 helix: 2.12 (0.14), residues: 1417 sheet: 2.19 (1.13), residues: 23 loop : -0.48 (0.35), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP M 295 HIS 0.008 0.001 HIS N 97 PHE 0.015 0.001 PHE N 80 TYR 0.014 0.001 TYR M 7 ARG 0.004 0.000 ARG W 49 Details of bonding type rmsd hydrogen bonds : bond 0.05257 ( 1122) hydrogen bonds : angle 3.40421 ( 3285) SS BOND : bond 0.00057 ( 1) SS BOND : angle 2.42318 ( 2) covalent geometry : bond 0.00366 (13689) covalent geometry : angle 0.58434 (18556) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 63 time to evaluate : 1.364 Fit side-chains revert: symmetry clash REVERT: M 234 MET cc_start: 0.7787 (ttp) cc_final: 0.7370 (ptm) REVERT: N 315 ASP cc_start: 0.8835 (p0) cc_final: 0.7910 (t0) REVERT: N 540 LEU cc_start: 0.8501 (tt) cc_final: 0.8190 (mt) REVERT: P 47 GLU cc_start: 0.8584 (tm-30) cc_final: 0.8151 (tm-30) REVERT: S 48 ASP cc_start: 0.7579 (m-30) cc_final: 0.7362 (m-30) outliers start: 19 outliers final: 13 residues processed: 80 average time/residue: 1.1220 time to fit residues: 100.7883 Evaluate side-chains 73 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 290 VAL Chi-restraints excluded: chain P residue 75 ILE Chi-restraints excluded: chain Q residue 50 SER Chi-restraints excluded: chain Q residue 61 LEU Chi-restraints excluded: chain R residue 19 MET Chi-restraints excluded: chain V residue 66 VAL Chi-restraints excluded: chain W residue 10 LEU Chi-restraints excluded: chain W residue 66 VAL Chi-restraints excluded: chain X residue 50 SER Chi-restraints excluded: chain Y residue 30 THR Chi-restraints excluded: chain Z residue 54 THR Chi-restraints excluded: chain Z residue 61 LEU Chi-restraints excluded: chain Z residue 63 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 118 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 76 optimal weight: 8.9990 chunk 103 optimal weight: 0.9990 chunk 179 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 237 HIS ** 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 = 0.3815 r_free = 0.3815 target = 0.094081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.060459 restraints weight = 33863.102| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 2.75 r_work: 0.2933 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13690 Z= 0.153 Angle : 0.593 10.556 18558 Z= 0.293 Chirality : 0.039 0.196 2224 Planarity : 0.004 0.042 2381 Dihedral : 3.677 17.800 1968 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.65 % Allowed : 20.92 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.20), residues: 1817 helix: 2.09 (0.14), residues: 1417 sheet: 2.19 (1.14), residues: 23 loop : -0.49 (0.35), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP M 295 HIS 0.008 0.001 HIS N 97 PHE 0.015 0.001 PHE N 80 TYR 0.014 0.001 TYR M 7 ARG 0.004 0.000 ARG W 49 Details of bonding type rmsd hydrogen bonds : bond 0.05260 ( 1122) hydrogen bonds : angle 3.43369 ( 3285) SS BOND : bond 0.00213 ( 1) SS BOND : angle 8.06791 ( 2) covalent geometry : bond 0.00363 (13689) covalent geometry : angle 0.58738 (18556) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8266.83 seconds wall clock time: 143 minutes 7.14 seconds (8587.14 seconds total)