Starting phenix.real_space_refine on Sun Jan 19 05:24:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yxz_39661/01_2025/8yxz_39661.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yxz_39661/01_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_39661/01_2025/8yxz_39661.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yxz_39661/01_2025/8yxz_39661.map" model { file = "/net/cci-nas-00/data/ceres_data/8yxz_39661/01_2025/8yxz_39661.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yxz_39661/01_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 6.55, per 1000 atoms: 0.49 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: 3.40 Conformation dependent library (CDL) restraints added in 2.4 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: 1.20 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: 4.24 Time building geometry restraints manager: 3.75 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: 26.560 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 28.600 Find NCS groups from input model: 0.290 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: 0.010 Load rotamer database and sin/cos tables:11.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.100 ------------------------------------------------------------------------------- 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 13689 Z= 0.693 Angle : 1.663 10.210 18556 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 *********************** 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 : 1.713 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: 1.8198 time to fit residues: 284.5753 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 : 2.205 ------------------------------------------------------------------------------- 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 13689 Z= 0.200 Angle : 0.628 9.284 18556 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 *********************** 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 : 1.435 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: 1.2074 time to fit residues: 137.1216 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 : 1.584 ------------------------------------------------------------------------------- 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 13689 Z= 0.439 Angle : 0.708 8.706 18556 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 *********************** 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 : 1.728 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: 1.0796 time to fit residues: 117.8503 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 : 1.657 ------------------------------------------------------------------------------- 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 13689 Z= 0.227 Angle : 0.557 7.919 18556 Z= 0.283 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 *********************** 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 : 1.556 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: 1.2114 time to fit residues: 130.7280 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 : 1.615 ------------------------------------------------------------------------------- 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 13689 Z= 0.186 Angle : 0.535 8.429 18556 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 *********************** 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 : 1.537 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: 1.2842 time to fit residues: 134.1534 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 : 1.448 ------------------------------------------------------------------------------- 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: 0.4980 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: 1.3182 ------------------------------------------------------------------------------- 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 = 0.3829 r_free = 0.3829 target = 0.094898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.061757 restraints weight = 33922.036| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.94 r_work: 0.2949 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13689 Z= 0.207 Angle : 0.546 9.372 18556 Z= 0.275 Chirality : 0.038 0.177 2224 Planarity : 0.004 0.040 2381 Dihedral : 3.701 18.928 1968 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.27 % Allowed : 18.50 % Favored : 79.23 % 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: 2.38 (0.20), residues: 1817 helix: 2.10 (0.14), residues: 1418 sheet: 2.06 (1.06), residues: 23 loop : -0.44 (0.35), residues: 376 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 0.015 0.001 PHE N 80 TYR 0.014 0.001 TYR M 7 ARG 0.005 0.000 ARG W 49 *********************** 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 93 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 64 time to evaluate : 1.430 Fit side-chains revert: symmetry clash REVERT: M 234 MET cc_start: 0.7665 (ttp) cc_final: 0.7303 (ptm) REVERT: N 315 ASP cc_start: 0.8860 (p0) cc_final: 0.7938 (t0) REVERT: N 540 LEU cc_start: 0.8477 (tt) cc_final: 0.8183 (mt) REVERT: P 47 GLU cc_start: 0.8554 (tm-30) cc_final: 0.8147 (tm-30) REVERT: S 48 ASP cc_start: 0.7535 (m-30) cc_final: 0.7290 (m-30) REVERT: U 19 MET cc_start: 0.8915 (ptp) cc_final: 0.8670 (ptm) REVERT: W 19 MET cc_start: 0.8851 (mtp) cc_final: 0.8619 (mtm) outliers start: 29 outliers final: 15 residues processed: 88 average time/residue: 1.0069 time to fit residues: 100.4011 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 : 1.460 ------------------------------------------------------------------------------- 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 V residue 66 VAL 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 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: 9.9990 chunk 11 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 55 optimal weight: 7.9990 chunk 137 optimal weight: 0.6980 chunk 124 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- 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 = 0.3816 r_free = 0.3816 target = 0.094141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.060650 restraints weight = 33833.722| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.99 r_work: 0.2927 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13689 Z= 0.250 Angle : 0.559 9.435 18556 Z= 0.280 Chirality : 0.039 0.176 2224 Planarity : 0.004 0.040 2381 Dihedral : 3.669 18.503 1968 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.74 % Allowed : 19.36 % Favored : 77.90 % 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: 2.36 (0.20), residues: 1817 helix: 2.08 (0.14), residues: 1414 sheet: 2.12 (1.08), residues: 23 loop : -0.46 (0.35), residues: 380 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 0.016 0.001 PHE N 80 TYR 0.015 0.001 TYR M 7 ARG 0.005 0.000 ARG W 49 *********************** 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 99 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 64 time to evaluate : 1.588 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 234 MET cc_start: 0.7718 (ttp) cc_final: 0.7325 (ptm) REVERT: N 315 ASP cc_start: 0.8872 (p0) cc_final: 0.7944 (t0) REVERT: N 540 LEU cc_start: 0.8481 (tt) cc_final: 0.8187 (mt) REVERT: P 47 GLU cc_start: 0.8556 (tm-30) cc_final: 0.8138 (tm-30) REVERT: S 48 ASP cc_start: 0.7528 (m-30) cc_final: 0.7202 (m-30) outliers start: 35 outliers final: 16 residues processed: 94 average time/residue: 1.0815 time to fit residues: 114.2623 Evaluate side-chains 75 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 59 time to evaluate : 1.445 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 98 optimal weight: 0.7980 chunk 173 optimal weight: 8.9990 chunk 77 optimal weight: 8.9990 chunk 71 optimal weight: 5.9990 chunk 112 optimal weight: 0.7980 chunk 145 optimal weight: 0.0470 chunk 85 optimal weight: 6.9990 chunk 14 optimal weight: 0.0170 chunk 147 optimal weight: 3.9990 overall best weight: 1.1318 ------------------------------------------------------------------------------- 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 = 0.3831 r_free = 0.3831 target = 0.095144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.061720 restraints weight = 33721.564| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.73 r_work: 0.2962 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13689 Z= 0.190 Angle : 0.550 9.293 18556 Z= 0.273 Chirality : 0.038 0.167 2224 Planarity : 0.004 0.041 2381 Dihedral : 3.662 18.132 1968 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.04 % Allowed : 20.61 % Favored : 77.35 % 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: 2.46 (0.20), residues: 1817 helix: 2.16 (0.14), residues: 1416 sheet: 2.19 (1.10), residues: 23 loop : -0.47 (0.35), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP N 420 HIS 0.003 0.000 HIS N 616 PHE 0.015 0.001 PHE N 80 TYR 0.013 0.001 TYR M 7 ARG 0.006 0.000 ARG S 49 *********************** 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 93 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 67 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 234 MET cc_start: 0.7678 (ttp) cc_final: 0.7328 (ptm) REVERT: N 315 ASP cc_start: 0.8863 (p0) cc_final: 0.7940 (t0) REVERT: N 540 LEU cc_start: 0.8484 (tt) cc_final: 0.8181 (mt) REVERT: P 47 GLU cc_start: 0.8526 (tm-30) cc_final: 0.8107 (tm-30) REVERT: S 48 ASP cc_start: 0.7554 (m-30) cc_final: 0.7324 (m-30) REVERT: W 19 MET cc_start: 0.8866 (mtp) cc_final: 0.8658 (mtm) outliers start: 26 outliers final: 15 residues processed: 87 average time/residue: 1.2623 time to fit residues: 122.0244 Evaluate side-chains 77 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 1.432 ------------------------------------------------------------------------------- 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 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 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: 40.0000 chunk 20 optimal weight: 9.9990 chunk 91 optimal weight: 20.0000 chunk 175 optimal weight: 5.9990 chunk 157 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 161 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 68 optimal weight: 0.8980 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 = 0.3817 r_free = 0.3817 target = 0.094255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.061209 restraints weight = 33679.386| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.90 r_work: 0.2937 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13689 Z= 0.242 Angle : 0.565 9.252 18556 Z= 0.280 Chirality : 0.039 0.172 2224 Planarity : 0.004 0.042 2381 Dihedral : 3.630 17.883 1968 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.80 % Allowed : 21.00 % Favored : 77.19 % 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: 2.44 (0.20), residues: 1817 helix: 2.15 (0.14), residues: 1416 sheet: 2.09 (1.09), residues: 23 loop : -0.48 (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 0.015 0.001 TYR M 7 ARG 0.004 0.000 ARG W 49 *********************** 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 86 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 63 time to evaluate : 1.616 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 234 MET cc_start: 0.7703 (ttp) cc_final: 0.7298 (ptm) REVERT: N 315 ASP cc_start: 0.8853 (p0) cc_final: 0.7926 (t0) REVERT: N 540 LEU cc_start: 0.8503 (tt) cc_final: 0.8198 (mt) REVERT: P 47 GLU cc_start: 0.8575 (tm-30) cc_final: 0.8143 (tm-30) REVERT: S 48 ASP cc_start: 0.7524 (m-30) cc_final: 0.7194 (m-30) REVERT: W 19 MET cc_start: 0.8879 (mtp) cc_final: 0.8644 (mtm) outliers start: 23 outliers final: 13 residues processed: 83 average time/residue: 1.1872 time to fit residues: 109.7395 Evaluate side-chains 72 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 138 GLN 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 S residue 54 THR Chi-restraints excluded: chain T residue 23 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 74 optimal weight: 4.9990 chunk 47 optimal weight: 20.0000 chunk 5 optimal weight: 0.9990 chunk 129 optimal weight: 0.5980 chunk 141 optimal weight: 0.9980 chunk 54 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 142 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 = 0.3805 r_free = 0.3805 target = 0.093557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.060061 restraints weight = 33768.218| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.97 r_work: 0.2912 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13689 Z= 0.278 Angle : 0.601 10.879 18556 Z= 0.298 Chirality : 0.040 0.196 2224 Planarity : 0.004 0.043 2381 Dihedral : 3.705 18.002 1968 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.72 % Allowed : 21.08 % Favored : 77.19 % 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: 2.33 (0.20), residues: 1817 helix: 2.06 (0.14), residues: 1417 sheet: 2.05 (1.10), 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 0.005 0.001 HIS N 97 PHE 0.015 0.001 PHE N 80 TYR 0.015 0.001 TYR M 7 ARG 0.006 0.000 ARG S 49 ********************** 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 83 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 61 time to evaluate : 1.450 Fit side-chains revert: symmetry clash REVERT: M 234 MET cc_start: 0.7768 (ttp) cc_final: 0.7341 (ptm) REVERT: N 315 ASP cc_start: 0.8860 (p0) cc_final: 0.7919 (t0) REVERT: N 540 LEU cc_start: 0.8507 (tt) cc_final: 0.8194 (mt) REVERT: N 547 MET cc_start: 0.8407 (mmm) cc_final: 0.8169 (mtp) REVERT: P 47 GLU cc_start: 0.8585 (tm-30) cc_final: 0.8160 (tm-30) REVERT: S 48 ASP cc_start: 0.7569 (m-30) cc_final: 0.7345 (m-30) REVERT: W 19 MET cc_start: 0.8919 (mtp) cc_final: 0.8695 (mtm) outliers start: 22 outliers final: 17 residues processed: 81 average time/residue: 1.2246 time to fit residues: 110.5341 Evaluate side-chains 75 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 58 time to evaluate : 1.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 321 VAL Chi-restraints excluded: chain N residue 290 VAL Chi-restraints excluded: chain N residue 335 SER 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 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 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: 2.9990 chunk 113 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 76 optimal weight: 9.9990 chunk 103 optimal weight: 0.9990 chunk 179 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 chunk 24 optimal weight: 8.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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** ** N 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.095324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.062276 restraints weight = 33687.398| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.65 r_work: 0.2982 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13689 Z= 0.183 Angle : 0.556 9.942 18556 Z= 0.274 Chirality : 0.038 0.170 2224 Planarity : 0.004 0.040 2381 Dihedral : 3.608 17.678 1968 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.57 % Allowed : 21.00 % 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: 2.54 (0.20), residues: 1817 helix: 2.23 (0.14), residues: 1417 sheet: 2.02 (1.09), residues: 23 loop : -0.47 (0.35), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 420 HIS 0.007 0.001 HIS N 97 PHE 0.015 0.001 PHE N 80 TYR 0.012 0.001 TYR M 7 ARG 0.006 0.000 ARG S 49 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8202.48 seconds wall clock time: 148 minutes 2.61 seconds (8882.61 seconds total)