Starting phenix.real_space_refine on Thu Jul 18 22:33:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtx_36655/07_2024/8jtx_36655.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtx_36655/07_2024/8jtx_36655.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtx_36655/07_2024/8jtx_36655.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtx_36655/07_2024/8jtx_36655.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtx_36655/07_2024/8jtx_36655.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtx_36655/07_2024/8jtx_36655.cif" } resolution = 3.28 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= -0.004 sd= 0.174 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 34 5.16 5 C 2777 2.51 5 N 699 2.21 5 O 743 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 137": "OE1" <-> "OE2" Residue "A PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 46": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 4253 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3360 Classifications: {'peptide': 448} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 22, 'TRANS': 425} Chain breaks: 1 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ASP:plan': 3, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 44 Chain: "B" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 893 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 3, 'TRANS': 114} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Time building chain proxies: 3.05, per 1000 atoms: 0.72 Number of scatterers: 4253 At special positions: 0 Unit cell: (60.2, 79.12, 126.42, 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 34 16.00 O 743 8.00 N 699 7.00 C 2777 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 121 " distance=2.03 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 102 " distance=2.03 Simple disulfide: pdb=" SG CYS A 88 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 95 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.56 Conformation dependent library (CDL) restraints added in 822.2 milliseconds 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1024 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 3 sheets defined 61.0% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 21 through 33 removed outlier: 4.288A pdb=" N LEU A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 37 Processing helix chain 'A' and resid 38 through 43 Processing helix chain 'A' and resid 54 through 63 removed outlier: 3.721A pdb=" N LEU A 58 " --> pdb=" O GLY A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 73 removed outlier: 3.902A pdb=" N TYR A 72 " --> pdb=" O GLU A 68 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR A 73 " --> pdb=" O GLU A 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 68 through 73' Processing helix chain 'A' and resid 82 through 88 Processing helix chain 'A' and resid 105 through 110 removed outlier: 4.117A pdb=" N LEU A 109 " --> pdb=" O PRO A 105 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 105 through 110' Processing helix chain 'A' and resid 133 through 139 Processing helix chain 'A' and resid 144 through 147 Processing helix chain 'A' and resid 148 through 182 removed outlier: 4.208A pdb=" N GLN A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU A 155 " --> pdb=" O PHE A 151 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER A 163 " --> pdb=" O PHE A 159 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LEU A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLY A 165 " --> pdb=" O PHE A 161 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLY A 167 " --> pdb=" O SER A 163 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N TYR A 168 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA A 170 " --> pdb=" O VAL A 166 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASP A 171 " --> pdb=" O GLY A 167 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ARG A 172 " --> pdb=" O TYR A 168 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N PHE A 173 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ARG A 175 " --> pdb=" O ASP A 171 " (cutoff:3.500A) removed outlier: 9.447A pdb=" N LYS A 176 " --> pdb=" O ARG A 172 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LEU A 177 " --> pdb=" O PHE A 173 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N CYS A 178 " --> pdb=" O GLY A 174 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU A 180 " --> pdb=" O LYS A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 195 removed outlier: 3.764A pdb=" N GLY A 190 " --> pdb=" O ASN A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 211 removed outlier: 3.713A pdb=" N MET A 202 " --> pdb=" O ASN A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 226 Processing helix chain 'A' and resid 231 through 258 removed outlier: 4.012A pdb=" N ILE A 238 " --> pdb=" O ARG A 234 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N MET A 239 " --> pdb=" O THR A 235 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYR A 240 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLN A 241 " --> pdb=" O ALA A 237 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N PHE A 244 " --> pdb=" O TYR A 240 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N THR A 252 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLY A 253 " --> pdb=" O VAL A 249 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU A 254 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR A 256 " --> pdb=" O THR A 252 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA A 257 " --> pdb=" O GLY A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 277 removed outlier: 3.749A pdb=" N LEU A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) Proline residue: A 271 - end of helix Processing helix chain 'A' and resid 333 through 340 removed outlier: 3.884A pdb=" N PHE A 338 " --> pdb=" O PHE A 334 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ARG A 339 " --> pdb=" O ALA A 335 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N THR A 340 " --> pdb=" O ASP A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 369 removed outlier: 3.742A pdb=" N PHE A 348 " --> pdb=" O ARG A 344 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE A 349 " --> pdb=" O LYS A 345 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N TYR A 352 " --> pdb=" O PHE A 348 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU A 353 " --> pdb=" O ILE A 349 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TRP A 354 " --> pdb=" O LEU A 350 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N PHE A 355 " --> pdb=" O MET A 351 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE A 365 " --> pdb=" O TYR A 361 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU A 366 " --> pdb=" O GLN A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 385 removed outlier: 3.606A pdb=" N ASP A 378 " --> pdb=" O ASN A 374 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 380 " --> pdb=" O TYR A 376 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ALA A 383 " --> pdb=" O PHE A 379 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 396 removed outlier: 4.391A pdb=" N ALA A 390 " --> pdb=" O GLU A 386 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N PHE A 391 " --> pdb=" O ILE A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 421 removed outlier: 3.543A pdb=" N ALA A 413 " --> pdb=" O SER A 409 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLY A 414 " --> pdb=" O ASN A 410 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA A 415 " --> pdb=" O LEU A 411 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA A 416 " --> pdb=" O LEU A 412 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N CYS A 417 " --> pdb=" O ALA A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 457 removed outlier: 3.707A pdb=" N LEU A 430 " --> pdb=" O ASP A 426 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ILE A 432 " --> pdb=" O HIS A 428 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ILE A 433 " --> pdb=" O TRP A 429 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N CYS A 436 " --> pdb=" O ILE A 432 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN A 447 " --> pdb=" O THR A 443 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N MET A 448 " --> pdb=" O ILE A 444 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ILE A 449 " --> pdb=" O ALA A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 487 removed outlier: 3.756A pdb=" N ILE A 479 " --> pdb=" O ILE A 475 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR A 480 " --> pdb=" O GLY A 476 " (cutoff:3.500A) Proline residue: A 481 - end of helix Processing helix chain 'A' and resid 494 through 510 removed outlier: 3.877A pdb=" N LEU A 498 " --> pdb=" O LEU A 494 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHE A 499 " --> pdb=" O PRO A 495 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY A 508 " --> pdb=" O LEU A 504 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL A 509 " --> pdb=" O LEU A 505 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N THR A 510 " --> pdb=" O ALA A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 513 No H-bonds generated for 'chain 'A' and resid 511 through 513' Processing helix chain 'B' and resid 26 through 32 removed outlier: 4.151A pdb=" N TYR B 30 " --> pdb=" O GLY B 26 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N TYR B 31 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU B 32 " --> pdb=" O ILE B 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 26 through 32' Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 50 Processing sheet with id=AA2, first strand: chain 'B' and resid 5 through 6 removed outlier: 3.540A pdb=" N GLN B 5 " --> pdb=" O ALA B 23 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B 18 " --> pdb=" O MET B 82 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N MET B 82 " --> pdb=" O LEU B 18 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU B 80 " --> pdb=" O LEU B 20 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR B 77 " --> pdb=" O ASP B 72 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER B 70 " --> pdb=" O TYR B 79 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 57 through 59 removed outlier: 3.836A pdb=" N ASN B 58 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR B 50 " --> pdb=" O ASN B 58 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE B 51 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N MET B 34 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA B 96 " --> pdb=" O GLY B 35 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR B 116 " --> pdb=" O TYR B 93 " (cutoff:3.500A) 181 hydrogen bonds defined for protein. 537 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: 1.01 Time building geometry restraints manager: 1.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 658 1.32 - 1.44: 1235 1.44 - 1.57: 2416 1.57 - 1.69: 0 1.69 - 1.82: 51 Bond restraints: 4360 Sorted by residual: bond pdb=" CA TYR A 240 " pdb=" CB TYR A 240 " ideal model delta sigma weight residual 1.529 1.473 0.057 1.78e-02 3.16e+03 1.01e+01 bond pdb=" C TYR A 240 " pdb=" O TYR A 240 " ideal model delta sigma weight residual 1.236 1.196 0.040 1.29e-02 6.01e+03 9.59e+00 bond pdb=" C SER A 424 " pdb=" N PRO A 425 " ideal model delta sigma weight residual 1.334 1.367 -0.033 2.34e-02 1.83e+03 2.04e+00 bond pdb=" C TYR A 240 " pdb=" N GLN A 241 " ideal model delta sigma weight residual 1.333 1.313 0.020 1.45e-02 4.76e+03 1.92e+00 bond pdb=" C MET A 239 " pdb=" N TYR A 240 " ideal model delta sigma weight residual 1.334 1.349 -0.015 1.38e-02 5.25e+03 1.19e+00 ... (remaining 4355 not shown) Histogram of bond angle deviations from ideal: 100.34 - 107.10: 132 107.10 - 113.87: 2381 113.87 - 120.63: 1857 120.63 - 127.39: 1528 127.39 - 134.16: 51 Bond angle restraints: 5949 Sorted by residual: angle pdb=" N ILE B 110 " pdb=" CA ILE B 110 " pdb=" C ILE B 110 " ideal model delta sigma weight residual 113.20 109.38 3.82 9.60e-01 1.09e+00 1.58e+01 angle pdb=" CA TYR A 240 " pdb=" C TYR A 240 " pdb=" N GLN A 241 " ideal model delta sigma weight residual 118.43 123.55 -5.12 1.33e+00 5.65e-01 1.48e+01 angle pdb=" N VAL A 37 " pdb=" CA VAL A 37 " pdb=" C VAL A 37 " ideal model delta sigma weight residual 113.53 109.87 3.66 9.80e-01 1.04e+00 1.39e+01 angle pdb=" C TYR A 240 " pdb=" N GLN A 241 " pdb=" CA GLN A 241 " ideal model delta sigma weight residual 121.64 129.53 -7.89 2.13e+00 2.20e-01 1.37e+01 angle pdb=" C GLY B 113 " pdb=" N GLN B 114 " pdb=" CA GLN B 114 " ideal model delta sigma weight residual 121.54 128.30 -6.76 1.91e+00 2.74e-01 1.25e+01 ... (remaining 5944 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 2175 17.55 - 35.10: 264 35.10 - 52.65: 66 52.65 - 70.20: 12 70.20 - 87.75: 1 Dihedral angle restraints: 2518 sinusoidal: 908 harmonic: 1610 Sorted by residual: dihedral pdb=" CB CYS A 88 " pdb=" SG CYS A 88 " pdb=" SG CYS A 142 " pdb=" CB CYS A 142 " ideal model delta sinusoidal sigma weight residual 93.00 159.06 -66.06 1 1.00e+01 1.00e-02 5.70e+01 dihedral pdb=" CB CYS A 62 " pdb=" SG CYS A 62 " pdb=" SG CYS A 102 " pdb=" CB CYS A 102 " ideal model delta sinusoidal sigma weight residual -86.00 -145.88 59.88 1 1.00e+01 1.00e-02 4.78e+01 dihedral pdb=" CB CYS A 50 " pdb=" SG CYS A 50 " pdb=" SG CYS A 121 " pdb=" CB CYS A 121 " ideal model delta sinusoidal sigma weight residual -86.00 -44.62 -41.38 1 1.00e+01 1.00e-02 2.40e+01 ... (remaining 2515 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 382 0.026 - 0.053: 192 0.053 - 0.079: 69 0.079 - 0.105: 29 0.105 - 0.131: 15 Chirality restraints: 687 Sorted by residual: chirality pdb=" CA THR A 480 " pdb=" N THR A 480 " pdb=" C THR A 480 " pdb=" CB THR A 480 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.13 2.00e-01 2.50e+01 4.29e-01 chirality pdb=" CA PRO A 425 " pdb=" N PRO A 425 " pdb=" C PRO A 425 " pdb=" CB PRO A 425 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 3.91e-01 chirality pdb=" CA THR A 111 " pdb=" N THR A 111 " pdb=" C THR A 111 " pdb=" CB THR A 111 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.12 2.00e-01 2.50e+01 3.83e-01 ... (remaining 684 not shown) Planarity restraints: 746 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 240 " 0.017 2.00e-02 2.50e+03 3.30e-02 1.09e+01 pdb=" C TYR A 240 " -0.057 2.00e-02 2.50e+03 pdb=" O TYR A 240 " 0.020 2.00e-02 2.50e+03 pdb=" N GLN A 241 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 270 " -0.031 5.00e-02 4.00e+02 4.69e-02 3.52e+00 pdb=" N PRO A 271 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 271 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 271 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 74 " -0.027 5.00e-02 4.00e+02 4.16e-02 2.77e+00 pdb=" N PRO A 75 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 75 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 75 " -0.023 5.00e-02 4.00e+02 ... (remaining 743 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1245 2.82 - 3.34: 3700 3.34 - 3.86: 6236 3.86 - 4.38: 6683 4.38 - 4.90: 12377 Nonbonded interactions: 30241 Sorted by model distance: nonbonded pdb=" OH TYR B 37 " pdb=" O TRP B 106 " model vdw 2.297 2.440 nonbonded pdb=" OH TYR A 127 " pdb=" OD1 ASN A 139 " model vdw 2.318 2.440 nonbonded pdb=" O PRO A 405 " pdb=" OG SER A 409 " model vdw 2.322 2.440 nonbonded pdb=" O MET A 368 " pdb=" OG SER A 372 " model vdw 2.360 2.440 nonbonded pdb=" OG1 THR A 182 " pdb=" OD1 ASN A 216 " model vdw 2.373 2.440 ... (remaining 30236 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.280 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 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 : 0.003 0.057 4360 Z= 0.189 Angle : 0.701 9.956 5949 Z= 0.391 Chirality : 0.040 0.131 687 Planarity : 0.004 0.047 746 Dihedral : 15.904 87.752 1482 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.46 % Allowed : 22.92 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.35), residues: 560 helix: 0.03 (0.33), residues: 280 sheet: -0.64 (0.78), residues: 53 loop : -1.84 (0.35), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 217 HIS 0.001 0.001 HIS A 48 PHE 0.010 0.001 PHE A 355 TYR 0.019 0.001 TYR A 91 ARG 0.006 0.000 ARG A 486 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 60 time to evaluate : 0.456 Fit side-chains REVERT: A 240 TYR cc_start: 0.7803 (OUTLIER) cc_final: 0.6797 (m-80) outliers start: 2 outliers final: 0 residues processed: 62 average time/residue: 0.2096 time to fit residues: 15.7340 Evaluate side-chains 57 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 56 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 46 optimal weight: 0.0770 chunk 41 optimal weight: 0.2980 chunk 23 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 26 optimal weight: 0.2980 chunk 32 optimal weight: 0.4980 chunk 49 optimal weight: 0.9990 overall best weight: 0.3738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.0825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 4360 Z= 0.135 Angle : 0.525 11.214 5949 Z= 0.263 Chirality : 0.038 0.131 687 Planarity : 0.004 0.061 746 Dihedral : 4.899 58.561 612 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.62 % Allowed : 24.77 % Favored : 73.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.36), residues: 560 helix: 0.52 (0.33), residues: 280 sheet: -0.57 (0.72), residues: 57 loop : -1.67 (0.37), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 217 HIS 0.004 0.001 HIS A 48 PHE 0.008 0.001 PHE A 355 TYR 0.011 0.001 TYR A 91 ARG 0.003 0.000 ARG A 486 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 57 time to evaluate : 0.338 Fit side-chains REVERT: A 240 TYR cc_start: 0.7612 (OUTLIER) cc_final: 0.6776 (m-80) REVERT: A 277 LEU cc_start: 0.6350 (OUTLIER) cc_final: 0.6118 (tp) REVERT: B 81 GLN cc_start: 0.7047 (OUTLIER) cc_final: 0.6712 (tp40) outliers start: 7 outliers final: 3 residues processed: 63 average time/residue: 0.1471 time to fit residues: 11.6187 Evaluate side-chains 61 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 55 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain B residue 81 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 27 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 17 optimal weight: 0.0970 chunk 40 optimal weight: 0.8980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 4360 Z= 0.280 Angle : 0.588 10.182 5949 Z= 0.305 Chirality : 0.042 0.157 687 Planarity : 0.004 0.066 746 Dihedral : 5.095 57.677 612 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 3.70 % Allowed : 22.69 % Favored : 73.61 % 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: -1.00 (0.35), residues: 560 helix: 0.31 (0.33), residues: 283 sheet: -0.63 (0.71), residues: 57 loop : -1.94 (0.36), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 217 HIS 0.003 0.001 HIS A 49 PHE 0.010 0.001 PHE A 355 TYR 0.012 0.001 TYR A 352 ARG 0.002 0.000 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 58 time to evaluate : 0.445 Fit side-chains REVERT: A 240 TYR cc_start: 0.7948 (OUTLIER) cc_final: 0.6988 (m-80) REVERT: A 277 LEU cc_start: 0.6383 (OUTLIER) cc_final: 0.6174 (tp) REVERT: A 374 ASN cc_start: 0.7693 (OUTLIER) cc_final: 0.7312 (p0) REVERT: B 81 GLN cc_start: 0.7043 (mm-40) cc_final: 0.6753 (tp40) outliers start: 16 outliers final: 11 residues processed: 69 average time/residue: 0.1734 time to fit residues: 14.9868 Evaluate side-chains 72 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 58 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 69 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 49 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 25 optimal weight: 0.3980 chunk 5 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4360 Z= 0.181 Angle : 0.535 11.385 5949 Z= 0.272 Chirality : 0.040 0.150 687 Planarity : 0.004 0.067 746 Dihedral : 4.942 57.012 612 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.70 % Allowed : 23.38 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.36), residues: 560 helix: 0.45 (0.33), residues: 282 sheet: -0.48 (0.72), residues: 57 loop : -1.70 (0.37), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 217 HIS 0.002 0.001 HIS A 49 PHE 0.009 0.001 PHE A 355 TYR 0.010 0.001 TYR A 352 ARG 0.001 0.000 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 56 time to evaluate : 0.470 Fit side-chains REVERT: A 240 TYR cc_start: 0.7868 (OUTLIER) cc_final: 0.6969 (m-80) REVERT: A 277 LEU cc_start: 0.6265 (OUTLIER) cc_final: 0.5899 (tp) REVERT: A 374 ASN cc_start: 0.7670 (OUTLIER) cc_final: 0.7303 (p0) REVERT: B 81 GLN cc_start: 0.7077 (OUTLIER) cc_final: 0.6789 (tp40) outliers start: 16 outliers final: 8 residues processed: 66 average time/residue: 0.1795 time to fit residues: 14.8137 Evaluate side-chains 67 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 55 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 81 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 44 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 39 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 36 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 17 optimal weight: 0.3980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4360 Z= 0.213 Angle : 0.555 10.771 5949 Z= 0.283 Chirality : 0.041 0.153 687 Planarity : 0.004 0.068 746 Dihedral : 4.906 55.744 612 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 4.40 % Allowed : 24.07 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.36), residues: 560 helix: 0.52 (0.33), residues: 279 sheet: -0.39 (0.74), residues: 57 loop : -1.77 (0.37), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 217 HIS 0.002 0.001 HIS A 49 PHE 0.009 0.001 PHE A 355 TYR 0.011 0.001 TYR A 352 ARG 0.002 0.000 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 57 time to evaluate : 0.470 Fit side-chains REVERT: A 240 TYR cc_start: 0.7921 (OUTLIER) cc_final: 0.6856 (m-80) REVERT: A 277 LEU cc_start: 0.6202 (OUTLIER) cc_final: 0.5973 (tp) REVERT: A 374 ASN cc_start: 0.7699 (OUTLIER) cc_final: 0.7306 (p0) outliers start: 19 outliers final: 11 residues processed: 69 average time/residue: 0.2046 time to fit residues: 17.7657 Evaluate side-chains 71 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 57 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain B residue 69 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 47 optimal weight: 0.6980 chunk 10 optimal weight: 0.0040 chunk 31 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 24 optimal weight: 0.5980 chunk 4 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4360 Z= 0.146 Angle : 0.518 11.598 5949 Z= 0.259 Chirality : 0.039 0.144 687 Planarity : 0.004 0.068 746 Dihedral : 4.722 55.165 612 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.63 % Allowed : 23.84 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.36), residues: 560 helix: 0.69 (0.33), residues: 283 sheet: -0.33 (0.73), residues: 57 loop : -1.60 (0.38), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 217 HIS 0.002 0.001 HIS A 49 PHE 0.009 0.001 PHE A 355 TYR 0.009 0.001 TYR A 352 ARG 0.002 0.000 ARG A 90 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 60 time to evaluate : 0.418 Fit side-chains REVERT: A 147 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7759 (mtpt) REVERT: A 240 TYR cc_start: 0.7817 (OUTLIER) cc_final: 0.6824 (m-80) REVERT: A 374 ASN cc_start: 0.7608 (OUTLIER) cc_final: 0.7250 (p0) REVERT: A 519 VAL cc_start: 0.3889 (OUTLIER) cc_final: 0.3550 (t) outliers start: 20 outliers final: 11 residues processed: 76 average time/residue: 0.1724 time to fit residues: 16.3621 Evaluate side-chains 73 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 58 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain B residue 69 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 5 optimal weight: 7.9990 chunk 30 optimal weight: 0.1980 chunk 38 optimal weight: 0.0370 chunk 44 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4360 Z= 0.138 Angle : 0.524 11.719 5949 Z= 0.261 Chirality : 0.039 0.141 687 Planarity : 0.004 0.069 746 Dihedral : 4.631 54.524 612 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.47 % Allowed : 25.23 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.36), residues: 560 helix: 0.81 (0.34), residues: 283 sheet: -0.33 (0.73), residues: 57 loop : -1.52 (0.38), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 217 HIS 0.001 0.001 HIS A 49 PHE 0.009 0.001 PHE A 355 TYR 0.010 0.001 TYR A 361 ARG 0.002 0.000 ARG A 90 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 57 time to evaluate : 0.478 Fit side-chains REVERT: A 147 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7747 (mtpt) REVERT: A 240 TYR cc_start: 0.7770 (OUTLIER) cc_final: 0.6737 (m-80) REVERT: A 374 ASN cc_start: 0.7591 (OUTLIER) cc_final: 0.7208 (p0) REVERT: A 519 VAL cc_start: 0.3893 (OUTLIER) cc_final: 0.3554 (t) outliers start: 15 outliers final: 10 residues processed: 68 average time/residue: 0.1872 time to fit residues: 15.9514 Evaluate side-chains 71 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 57 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain B residue 18 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 15 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 33 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 4 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 50 optimal weight: 0.1980 chunk 46 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 4360 Z= 0.157 Angle : 0.523 10.995 5949 Z= 0.262 Chirality : 0.039 0.146 687 Planarity : 0.004 0.067 746 Dihedral : 4.573 53.370 612 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 4.86 % Allowed : 23.84 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.36), residues: 560 helix: 0.63 (0.33), residues: 294 sheet: -0.33 (0.74), residues: 57 loop : -1.64 (0.39), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 217 HIS 0.001 0.001 HIS A 49 PHE 0.010 0.001 PHE A 355 TYR 0.010 0.001 TYR A 361 ARG 0.002 0.000 ARG A 90 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 62 time to evaluate : 0.477 Fit side-chains REVERT: A 147 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7732 (mtpt) REVERT: A 240 TYR cc_start: 0.7857 (OUTLIER) cc_final: 0.6739 (m-80) REVERT: A 374 ASN cc_start: 0.7626 (OUTLIER) cc_final: 0.7227 (p0) REVERT: A 519 VAL cc_start: 0.3958 (OUTLIER) cc_final: 0.3616 (t) outliers start: 21 outliers final: 14 residues processed: 78 average time/residue: 0.1899 time to fit residues: 18.7491 Evaluate side-chains 79 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 61 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 69 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 50 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 38 optimal weight: 0.0770 chunk 15 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 overall best weight: 0.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4360 Z= 0.199 Angle : 0.544 10.325 5949 Z= 0.277 Chirality : 0.040 0.152 687 Planarity : 0.004 0.065 746 Dihedral : 4.683 52.629 612 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.63 % Allowed : 24.07 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.36), residues: 560 helix: 0.64 (0.33), residues: 288 sheet: -0.37 (0.74), residues: 57 loop : -1.66 (0.38), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 217 HIS 0.002 0.001 HIS A 49 PHE 0.009 0.001 PHE A 355 TYR 0.010 0.001 TYR A 352 ARG 0.002 0.000 ARG A 90 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 59 time to evaluate : 0.452 Fit side-chains REVERT: A 147 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7768 (mtpt) REVERT: A 374 ASN cc_start: 0.7754 (OUTLIER) cc_final: 0.7350 (p0) REVERT: A 519 VAL cc_start: 0.3979 (OUTLIER) cc_final: 0.3638 (t) outliers start: 20 outliers final: 15 residues processed: 74 average time/residue: 0.1775 time to fit residues: 16.3719 Evaluate side-chains 77 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 59 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 69 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 24 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 4 optimal weight: 10.0000 chunk 33 optimal weight: 0.8980 chunk 26 optimal weight: 0.0980 chunk 34 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4360 Z= 0.154 Angle : 0.521 10.937 5949 Z= 0.262 Chirality : 0.039 0.146 687 Planarity : 0.004 0.066 746 Dihedral : 4.570 52.283 612 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 4.40 % Allowed : 24.54 % Favored : 71.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.37), residues: 560 helix: 0.79 (0.33), residues: 283 sheet: -0.33 (0.74), residues: 57 loop : -1.45 (0.39), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 217 HIS 0.001 0.001 HIS A 49 PHE 0.009 0.001 PHE A 355 TYR 0.009 0.001 TYR A 352 ARG 0.002 0.000 ARG A 90 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 59 time to evaluate : 0.453 Fit side-chains REVERT: A 147 LYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7756 (mtpt) REVERT: A 240 TYR cc_start: 0.7865 (OUTLIER) cc_final: 0.6707 (m-80) REVERT: A 374 ASN cc_start: 0.7611 (OUTLIER) cc_final: 0.7212 (p0) REVERT: A 519 VAL cc_start: 0.3898 (OUTLIER) cc_final: 0.3553 (t) outliers start: 19 outliers final: 13 residues processed: 74 average time/residue: 0.1861 time to fit residues: 17.1463 Evaluate side-chains 76 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 59 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 69 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 40 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 8 optimal weight: 9.9990 chunk 38 optimal weight: 0.0570 chunk 2 optimal weight: 2.9990 chunk 31 optimal weight: 0.0770 overall best weight: 0.5456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.207764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.164288 restraints weight = 4553.022| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 1.81 r_work: 0.3522 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4360 Z= 0.149 Angle : 0.512 10.660 5949 Z= 0.257 Chirality : 0.039 0.147 687 Planarity : 0.004 0.067 746 Dihedral : 4.440 51.219 612 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.94 % Allowed : 25.23 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.37), residues: 560 helix: 0.69 (0.33), residues: 294 sheet: -0.29 (0.74), residues: 57 loop : -1.60 (0.39), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 217 HIS 0.001 0.001 HIS A 49 PHE 0.009 0.001 PHE A 355 TYR 0.009 0.001 TYR A 352 ARG 0.001 0.000 ARG A 486 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1412.23 seconds wall clock time: 26 minutes 17.19 seconds (1577.19 seconds total)