Starting phenix.real_space_refine on Mon May 12 08:39:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kbz_37088/05_2025/8kbz_37088.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kbz_37088/05_2025/8kbz_37088.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8kbz_37088/05_2025/8kbz_37088.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kbz_37088/05_2025/8kbz_37088.map" model { file = "/net/cci-nas-00/data/ceres_data/8kbz_37088/05_2025/8kbz_37088.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kbz_37088/05_2025/8kbz_37088.cif" } resolution = 3.97 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= 0.013 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 13 5.16 5 C 5592 2.51 5 N 1645 2.21 5 O 1610 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 8860 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 2998 Classifications: {'peptide': 475} Incomplete info: {'truncation_to_alanine': 257} Link IDs: {'PTRANS': 17, 'TRANS': 457} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 955 Unresolved non-hydrogen angles: 1227 Unresolved non-hydrogen dihedrals: 788 Unresolved non-hydrogen chiralities: 110 Planarities with less than four sites: {'GLN:plan1': 10, 'ARG:plan': 18, 'TYR:plan': 8, 'ASN:plan1': 6, 'TRP:plan': 3, 'HIS:plan': 6, 'PHE:plan': 22, 'GLU:plan': 22, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 502 Chain: "B" Number of atoms: 2926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 2926 Classifications: {'peptide': 475} Incomplete info: {'truncation_to_alanine': 280} Link IDs: {'PTRANS': 17, 'TRANS': 457} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 1033 Unresolved non-hydrogen angles: 1332 Unresolved non-hydrogen dihedrals: 851 Unresolved non-hydrogen chiralities: 119 Planarities with less than four sites: {'GLN:plan1': 14, 'HIS:plan': 10, 'TYR:plan': 9, 'ASN:plan1': 9, 'TRP:plan': 3, 'ASP:plan': 7, 'PHE:plan': 22, 'GLU:plan': 22, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 549 Chain: "C" Number of atoms: 2936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 2936 Classifications: {'peptide': 475} Incomplete info: {'truncation_to_alanine': 275} Link IDs: {'PTRANS': 17, 'TRANS': 457} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 1011 Unresolved non-hydrogen angles: 1294 Unresolved non-hydrogen dihedrals: 818 Unresolved non-hydrogen chiralities: 120 Planarities with less than four sites: {'GLN:plan1': 17, 'ARG:plan': 22, 'TYR:plan': 5, 'ASN:plan1': 10, 'TRP:plan': 3, 'ASP:plan': 6, 'PHE:plan': 20, 'GLU:plan': 24, 'HIS:plan': 5} Unresolved non-hydrogen planarities: 529 Time building chain proxies: 9.99, per 1000 atoms: 1.13 Number of scatterers: 8860 At special positions: 0 Unit cell: (89.25, 124.1, 121.55, 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 13 16.00 O 1610 8.00 N 1645 7.00 C 5592 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 2.79 Conformation dependent library (CDL) restraints added in 1.4 seconds 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2718 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 6 sheets defined 75.2% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 42 through 56 removed outlier: 3.543A pdb=" N PHE A 46 " --> pdb=" O ASN A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 86 removed outlier: 3.617A pdb=" N PHE A 73 " --> pdb=" O GLU A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 94 Processing helix chain 'A' and resid 111 through 115 Processing helix chain 'A' and resid 118 through 128 removed outlier: 4.410A pdb=" N ALA A 124 " --> pdb=" O GLN A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 168 removed outlier: 4.287A pdb=" N GLU A 159 " --> pdb=" O CYS A 155 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE A 160 " --> pdb=" O CYS A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 191 removed outlier: 3.524A pdb=" N VAL A 183 " --> pdb=" O THR A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 225 removed outlier: 6.130A pdb=" N PHE A 215 " --> pdb=" O ARG A 211 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N GLN A 216 " --> pdb=" O ILE A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 256 Processing helix chain 'A' and resid 270 through 275 removed outlier: 3.530A pdb=" N LYS A 274 " --> pdb=" O ALA A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 323 Proline residue: A 302 - end of helix removed outlier: 4.063A pdb=" N GLU A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N VAL A 319 " --> pdb=" O SER A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 329 Processing helix chain 'A' and resid 333 through 338 Processing helix chain 'A' and resid 346 through 357 Processing helix chain 'A' and resid 357 through 366 removed outlier: 3.910A pdb=" N ALA A 361 " --> pdb=" O GLY A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 398 Processing helix chain 'A' and resid 404 through 425 removed outlier: 4.563A pdb=" N THR A 409 " --> pdb=" O GLU A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 446 removed outlier: 3.951A pdb=" N ALA A 443 " --> pdb=" O ARG A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 453 removed outlier: 3.861A pdb=" N GLN A 453 " --> pdb=" O ASP A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 470 removed outlier: 4.211A pdb=" N LEU A 468 " --> pdb=" O GLU A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 481 removed outlier: 3.578A pdb=" N PHE A 475 " --> pdb=" O TYR A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 493 Proline residue: A 487 - end of helix Processing helix chain 'A' and resid 494 through 496 No H-bonds generated for 'chain 'A' and resid 494 through 496' Processing helix chain 'A' and resid 497 through 508 Processing helix chain 'B' and resid 42 through 56 removed outlier: 3.954A pdb=" N PHE B 46 " --> pdb=" O ASN B 42 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ARG B 49 " --> pdb=" O LEU B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 86 removed outlier: 3.618A pdb=" N PHE B 73 " --> pdb=" O GLU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 94 Processing helix chain 'B' and resid 111 through 115 Processing helix chain 'B' and resid 118 through 128 removed outlier: 4.410A pdb=" N ALA B 124 " --> pdb=" O GLN B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 168 removed outlier: 4.287A pdb=" N GLU B 159 " --> pdb=" O CYS B 155 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE B 160 " --> pdb=" O CYS B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 194 removed outlier: 3.717A pdb=" N VAL B 188 " --> pdb=" O GLN B 184 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N LYS B 192 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLU B 193 " --> pdb=" O GLN B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 225 removed outlier: 6.127A pdb=" N PHE B 215 " --> pdb=" O ARG B 211 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N GLN B 216 " --> pdb=" O ILE B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 256 Processing helix chain 'B' and resid 270 through 275 removed outlier: 3.531A pdb=" N LYS B 274 " --> pdb=" O ALA B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 323 Proline residue: B 302 - end of helix removed outlier: 4.227A pdb=" N GLU B 318 " --> pdb=" O PHE B 314 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N VAL B 319 " --> pdb=" O SER B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 329 Processing helix chain 'B' and resid 333 through 338 Processing helix chain 'B' and resid 346 through 357 Processing helix chain 'B' and resid 357 through 368 removed outlier: 3.911A pdb=" N ALA B 361 " --> pdb=" O GLY B 357 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N PHE B 368 " --> pdb=" O TYR B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 398 removed outlier: 3.701A pdb=" N THR B 374 " --> pdb=" O SER B 370 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU B 375 " --> pdb=" O PRO B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 425 Processing helix chain 'B' and resid 433 through 446 removed outlier: 3.552A pdb=" N ILE B 441 " --> pdb=" O LEU B 437 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N LEU B 442 " --> pdb=" O LEU B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 467 removed outlier: 3.920A pdb=" N GLN B 467 " --> pdb=" O ASP B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 481 Processing helix chain 'B' and resid 481 through 493 Proline residue: B 487 - end of helix Processing helix chain 'B' and resid 494 through 496 No H-bonds generated for 'chain 'B' and resid 494 through 496' Processing helix chain 'B' and resid 497 through 508 Processing helix chain 'C' and resid 43 through 56 removed outlier: 4.898A pdb=" N ARG C 49 " --> pdb=" O LEU C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 86 removed outlier: 3.618A pdb=" N PHE C 73 " --> pdb=" O GLU C 69 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL C 84 " --> pdb=" O THR C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 94 Processing helix chain 'C' and resid 111 through 115 Processing helix chain 'C' and resid 118 through 128 removed outlier: 4.411A pdb=" N ALA C 124 " --> pdb=" O GLN C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 168 removed outlier: 4.207A pdb=" N GLU C 159 " --> pdb=" O CYS C 155 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE C 160 " --> pdb=" O CYS C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 194 removed outlier: 3.724A pdb=" N VAL C 183 " --> pdb=" O THR C 179 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLN C 189 " --> pdb=" O ALA C 185 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N LYS C 192 " --> pdb=" O VAL C 188 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N GLU C 193 " --> pdb=" O GLN C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 225 removed outlier: 6.127A pdb=" N PHE C 215 " --> pdb=" O ARG C 211 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N GLN C 216 " --> pdb=" O ILE C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 256 Processing helix chain 'C' and resid 270 through 275 removed outlier: 3.531A pdb=" N LYS C 274 " --> pdb=" O ALA C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 323 Proline residue: C 302 - end of helix removed outlier: 3.783A pdb=" N SER C 315 " --> pdb=" O TYR C 311 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA C 317 " --> pdb=" O PHE C 313 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLU C 318 " --> pdb=" O PHE C 314 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL C 319 " --> pdb=" O SER C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 329 Processing helix chain 'C' and resid 333 through 338 Processing helix chain 'C' and resid 346 through 357 Processing helix chain 'C' and resid 357 through 366 removed outlier: 3.912A pdb=" N ALA C 361 " --> pdb=" O GLY C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 398 removed outlier: 3.739A pdb=" N THR C 374 " --> pdb=" O SER C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 425 removed outlier: 4.100A pdb=" N VAL C 411 " --> pdb=" O VAL C 407 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N THR C 412 " --> pdb=" O LEU C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 446 removed outlier: 3.525A pdb=" N LEU C 437 " --> pdb=" O CYS C 433 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU C 438 " --> pdb=" O PRO C 434 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ARG C 439 " --> pdb=" O GLU C 435 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N VAL C 440 " --> pdb=" O GLN C 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 453 removed outlier: 3.708A pdb=" N GLN C 453 " --> pdb=" O ASP C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 467 removed outlier: 3.726A pdb=" N GLN C 467 " --> pdb=" O ASP C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 481 removed outlier: 3.502A pdb=" N PHE C 475 " --> pdb=" O TYR C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 493 Proline residue: C 487 - end of helix Processing helix chain 'C' and resid 494 through 496 No H-bonds generated for 'chain 'C' and resid 494 through 496' Processing helix chain 'C' and resid 497 through 508 Processing sheet with id=AA1, first strand: chain 'A' and resid 231 through 233 Processing sheet with id=AA2, first strand: chain 'A' and resid 510 through 512 Processing sheet with id=AA3, first strand: chain 'B' and resid 231 through 233 Processing sheet with id=AA4, first strand: chain 'B' and resid 510 through 512 Processing sheet with id=AA5, first strand: chain 'C' and resid 231 through 233 Processing sheet with id=AA6, first strand: chain 'C' and resid 510 through 512 736 hydrogen bonds defined for protein. 2130 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: 2.74 Time building geometry restraints manager: 3.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1553 1.31 - 1.43: 2506 1.43 - 1.56: 4972 1.56 - 1.68: 1 1.68 - 1.81: 17 Bond restraints: 9049 Sorted by residual: bond pdb=" CA TYR C 335 " pdb=" C TYR C 335 " ideal model delta sigma weight residual 1.527 1.467 0.060 1.35e-02 5.49e+03 1.98e+01 bond pdb=" C LEU A 53 " pdb=" O LEU A 53 " ideal model delta sigma weight residual 1.237 1.184 0.052 1.19e-02 7.06e+03 1.94e+01 bond pdb=" C LEU C 53 " pdb=" O LEU C 53 " ideal model delta sigma weight residual 1.237 1.184 0.052 1.19e-02 7.06e+03 1.92e+01 bond pdb=" C LEU B 53 " pdb=" O LEU B 53 " ideal model delta sigma weight residual 1.237 1.185 0.052 1.19e-02 7.06e+03 1.92e+01 bond pdb=" CA GLN A 184 " pdb=" C GLN A 184 " ideal model delta sigma weight residual 1.523 1.470 0.054 1.30e-02 5.92e+03 1.71e+01 ... (remaining 9044 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.87: 12204 3.87 - 7.74: 248 7.74 - 11.61: 31 11.61 - 15.48: 12 15.48 - 19.34: 6 Bond angle restraints: 12501 Sorted by residual: angle pdb=" N LEU B 369 " pdb=" CA LEU B 369 " pdb=" C LEU B 369 " ideal model delta sigma weight residual 111.28 130.62 -19.34 1.09e+00 8.42e-01 3.15e+02 angle pdb=" N CYS B 367 " pdb=" CA CYS B 367 " pdb=" C CYS B 367 " ideal model delta sigma weight residual 111.28 130.03 -18.75 1.09e+00 8.42e-01 2.96e+02 angle pdb=" N PHE A 465 " pdb=" CA PHE A 465 " pdb=" C PHE A 465 " ideal model delta sigma weight residual 113.50 95.84 17.66 1.23e+00 6.61e-01 2.06e+02 angle pdb=" N ILE A 40 " pdb=" CA ILE A 40 " pdb=" C ILE A 40 " ideal model delta sigma weight residual 110.62 124.07 -13.45 1.02e+00 9.61e-01 1.74e+02 angle pdb=" N PHE C 465 " pdb=" CA PHE C 465 " pdb=" C PHE C 465 " ideal model delta sigma weight residual 113.50 97.69 15.81 1.23e+00 6.61e-01 1.65e+02 ... (remaining 12496 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 4847 17.84 - 35.67: 261 35.67 - 53.51: 52 53.51 - 71.35: 13 71.35 - 89.18: 6 Dihedral angle restraints: 5179 sinusoidal: 1007 harmonic: 4172 Sorted by residual: dihedral pdb=" CA LYS B 56 " pdb=" C LYS B 56 " pdb=" N ASN B 57 " pdb=" CA ASN B 57 " ideal model delta harmonic sigma weight residual 180.00 -151.12 -28.88 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA LYS A 56 " pdb=" C LYS A 56 " pdb=" N ASN A 57 " pdb=" CA ASN A 57 " ideal model delta harmonic sigma weight residual -180.00 -151.15 -28.85 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA LYS C 56 " pdb=" C LYS C 56 " pdb=" N ASN C 57 " pdb=" CA ASN C 57 " ideal model delta harmonic sigma weight residual -180.00 -151.30 -28.70 0 5.00e+00 4.00e-02 3.29e+01 ... (remaining 5176 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1188 0.082 - 0.163: 240 0.163 - 0.245: 39 0.245 - 0.327: 10 0.327 - 0.409: 10 Chirality restraints: 1487 Sorted by residual: chirality pdb=" CA TRP A 37 " pdb=" N TRP A 37 " pdb=" C TRP A 37 " pdb=" CB TRP A 37 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.17e+00 chirality pdb=" CA LEU B 369 " pdb=" N LEU B 369 " pdb=" C LEU B 369 " pdb=" CB LEU B 369 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.74e+00 chirality pdb=" CA GLN C 453 " pdb=" N GLN C 453 " pdb=" C GLN C 453 " pdb=" CB GLN C 453 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.31e+00 ... (remaining 1484 not shown) Planarity restraints: 1699 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN B 308 " 0.028 2.00e-02 2.50e+03 5.79e-02 3.35e+01 pdb=" C GLN B 308 " -0.100 2.00e-02 2.50e+03 pdb=" O GLN B 308 " 0.038 2.00e-02 2.50e+03 pdb=" N ILE B 309 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 175 " -0.025 2.00e-02 2.50e+03 5.03e-02 2.53e+01 pdb=" C LEU C 175 " 0.087 2.00e-02 2.50e+03 pdb=" O LEU C 175 " -0.032 2.00e-02 2.50e+03 pdb=" N PRO C 176 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS C 429 " -0.024 2.00e-02 2.50e+03 4.73e-02 2.24e+01 pdb=" C HIS C 429 " 0.082 2.00e-02 2.50e+03 pdb=" O HIS C 429 " -0.031 2.00e-02 2.50e+03 pdb=" N MET C 430 " -0.027 2.00e-02 2.50e+03 ... (remaining 1696 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 105 2.58 - 3.16: 8001 3.16 - 3.74: 13914 3.74 - 4.32: 16456 4.32 - 4.90: 26746 Nonbonded interactions: 65222 Sorted by model distance: nonbonded pdb=" O ASN A 42 " pdb=" OD1 ASN A 42 " model vdw 2.003 3.040 nonbonded pdb=" NE2 HIS A 451 " pdb=" OE2 GLU A 464 " model vdw 2.223 3.120 nonbonded pdb=" NE2 HIS B 451 " pdb=" OE2 GLU B 464 " model vdw 2.224 3.120 nonbonded pdb=" OH TYR C 364 " pdb=" O ALA C 456 " model vdw 2.260 3.040 nonbonded pdb=" OH TYR A 364 " pdb=" O ALA A 456 " model vdw 2.261 3.040 ... (remaining 65217 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 'A' and (resid 36 through 38 or (resid 39 through 44 and (name N or name \ CA or name C or name O or name CB )) or resid 45 through 46 or (resid 47 through \ 50 and (name N or name CA or name C or name O or name CB )) or resid 51 or (res \ id 52 through 53 and (name N or name CA or name C or name O or name CB )) or res \ id 54 through 58 or (resid 59 through 64 and (name N or name CA or name C or nam \ e O or name CB )) or (resid 65 through 87 and (name N or name CA or name C or na \ me O or name CB )) or resid 88 through 110 or (resid 111 through 117 and (name N \ or name CA or name C or name O or name CB )) or resid 118 through 132 or (resid \ 133 through 139 and (name N or name CA or name C or name O or name CB )) or (re \ sid 140 through 162 and (name N or name CA or name C or name O or name CB )) or \ resid 163 or (resid 164 through 179 and (name N or name CA or name C or name O o \ r name CB )) or resid 180 through 183 or (resid 184 through 209 and (name N or n \ ame CA or name C or name O or name CB )) or resid 210 through 212 or (resid 213 \ through 217 and (name N or name CA or name C or name O or name CB )) or resid 21 \ 8 or (resid 219 through 221 and (name N or name CA or name C or name O or name C \ B )) or resid 222 or (resid 223 through 228 and (name N or name CA or name C or \ name O or name CB )) or resid 229 or (resid 230 through 235 and (name N or name \ CA or name C or name O or name CB )) or (resid 236 through 241 and (name N or na \ me CA or name C or name O or name CB )) or resid 242 through 251 or (resid 252 a \ nd (name N or name CA or name C or name O or name CB )) or resid 253 through 260 \ or (resid 261 through 263 and (name N or name CA or name C or name O or name CB \ )) or resid 264 through 265 or (resid 266 and (name N or name CA or name C or n \ ame O or name CB )) or resid 267 or (resid 268 through 271 and (name N or name C \ A or name C or name O or name CB )) or resid 272 through 279 or (resid 280 throu \ gh 293 and (name N or name CA or name C or name O or name CB )) or (resid 294 th \ rough 306 and (name N or name CA or name C or name O or name CB )) or resid 307 \ or (resid 308 through 314 and (name N or name CA or name C or name O or name CB \ )) or resid 315 through 318 or (resid 319 through 324 and (name N or name CA or \ name C or name O or name CB )) or (resid 325 through 331 and (name N or name CA \ or name C or name O or name CB )) or resid 332 through 333 or (resid 334 and (na \ me N or name CA or name C or name O or name CB )) or resid 335 through 336 or (r \ esid 337 through 338 and (name N or name CA or name C or name O or name CB )) or \ resid 339 through 343 or (resid 344 through 349 and (name N or name CA or name \ C or name O or name CB )) or resid 350 through 363 or (resid 364 through 365 and \ (name N or name CA or name C or name O or name CB )) or resid 366 through 367 o \ r (resid 368 through 370 and (name N or name CA or name C or name O or name CB ) \ ) or resid 371 through 373 or (resid 374 through 379 and (name N or name CA or n \ ame C or name O or name CB )) or (resid 380 through 414 and (name N or name CA o \ r name C or name O or name CB )) or (resid 415 through 444 and (name N or name C \ A or name C or name O or name CB )) or resid 445 or (resid 446 through 448 and ( \ name N or name CA or name C or name O or name CB )) or resid 449 through 451 or \ (resid 452 through 453 and (name N or name CA or name C or name O or name CB )) \ or resid 454 or (resid 455 through 460 and (name N or name CA or name C or name \ O or name CB )) or resid 461 through 463 or (resid 464 and (name N or name CA or \ name C or name O or name CB )) or resid 465 through 466 or (resid 467 and (name \ N or name CA or name C or name O or name CB )) or resid 468 through 469 or (res \ id 470 through 474 and (name N or name CA or name C or name O or name CB )) or r \ esid 475 through 491 or (resid 492 through 504 and (name N or name CA or name C \ or name O or name CB )) or resid 505 through 506 or (resid 507 through 509 and ( \ name N or name CA or name C or name O or name CB )) or resid 510 through 523)) selection = (chain 'B' and (resid 36 through 37 or (resid 38 through 44 and (name N or name \ CA or name C or name O or name CB )) or resid 45 or (resid 46 through 50 and (na \ me N or name CA or name C or name O or name CB )) or resid 51 through 90 or (res \ id 91 through 117 and (name N or name CA or name C or name O or name CB )) or re \ sid 118 through 120 or (resid 121 through 129 and (name N or name CA or name C o \ r name O or name CB )) or (resid 130 through 139 and (name N or name CA or name \ C or name O or name CB )) or resid 140 through 164 or (resid 165 through 179 and \ (name N or name CA or name C or name O or name CB )) or resid 180 through 183 o \ r (resid 184 through 209 and (name N or name CA or name C or name O or name CB ) \ ) or resid 210 through 213 or (resid 214 through 217 and (name N or name CA or n \ ame C or name O or name CB )) or resid 218 or (resid 219 through 221 and (name N \ or name CA or name C or name O or name CB )) or resid 222 or (resid 223 through \ 228 and (name N or name CA or name C or name O or name CB )) or resid 229 or (r \ esid 230 through 235 and (name N or name CA or name C or name O or name CB )) or \ resid 236 or (resid 237 and (name N or name CA or name C or name O or name CB ) \ ) or resid 238 or (resid 239 through 241 and (name N or name CA or name C or nam \ e O or name CB )) or resid 242 through 244 or (resid 245 and (name N or name CA \ or name C or name O or name CB )) or resid 246 through 250 or (resid 251 through \ 252 and (name N or name CA or name C or name O or name CB )) or resid 253 throu \ gh 256 or (resid 257 and (name N or name CA or name C or name O or name CB )) or \ resid 258 through 262 or (resid 263 and (name N or name CA or name C or name O \ or name CB )) or resid 264 through 267 or (resid 268 through 271 and (name N or \ name CA or name C or name O or name CB )) or resid 272 through 278 or (resid 279 \ through 293 and (name N or name CA or name C or name O or name CB )) or (resid \ 294 through 306 and (name N or name CA or name C or name O or name CB )) or resi \ d 307 through 309 or (resid 310 through 314 and (name N or name CA or name C or \ name O or name CB )) or resid 315 or (resid 316 through 324 and (name N or name \ CA or name C or name O or name CB )) or resid 325 through 333 or (resid 334 and \ (name N or name CA or name C or name O or name CB )) or resid 335 through 352 or \ (resid 353 through 354 and (name N or name CA or name C or name O or name CB )) \ or resid 355 through 366 or (resid 367 through 370 and (name N or name CA or na \ me C or name O or name CB )) or resid 371 through 386 or (resid 387 through 414 \ and (name N or name CA or name C or name O or name CB )) or (resid 415 through 4 \ 44 and (name N or name CA or name C or name O or name CB )) or resid 445 through \ 446 or (resid 447 through 448 and (name N or name CA or name C or name O or nam \ e CB )) or resid 449 through 452 or (resid 453 and (name N or name CA or name C \ or name O or name CB )) or resid 454 or (resid 455 through 460 and (name N or na \ me CA or name C or name O or name CB )) or resid 461 or (resid 462 through 464 a \ nd (name N or name CA or name C or name O or name CB )) or resid 465 through 466 \ or (resid 467 and (name N or name CA or name C or name O or name CB )) or resid \ 468 through 479 or (resid 480 through 482 and (name N or name CA or name C or n \ ame O or name CB )) or resid 483 through 485 or (resid 486 and (name N or name C \ A or name C or name O or name CB )) or resid 487 through 488 or (resid 489 throu \ gh 490 and (name N or name CA or name C or name O or name CB )) or resid 491 thr \ ough 494 or (resid 495 through 504 and (name N or name CA or name C or name O or \ name CB )) or resid 505 through 506 or (resid 507 through 509 and (name N or na \ me CA or name C or name O or name CB )) or resid 510 through 518 or (resid 519 t \ hrough 523 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'C' and ((resid 36 and (name N or name CA or name C or name O or name CB \ )) or resid 37 or (resid 38 through 44 and (name N or name CA or name C or name \ O or name CB )) or resid 45 through 48 or (resid 49 through 50 and (name N or na \ me CA or name C or name O or name CB )) or resid 51 or (resid 52 through 53 and \ (name N or name CA or name C or name O or name CB )) or resid 54 through 56 or ( \ resid 57 and (name N or name CA or name C or name O or name CB )) or (resid 58 t \ hrough 64 and (name N or name CA or name C or name O or name CB )) or (resid 65 \ through 87 and (name N or name CA or name C or name O or name CB )) or resid 88 \ through 90 or (resid 91 through 117 and (name N or name CA or name C or name O o \ r name CB )) or resid 118 through 120 or (resid 121 through 129 and (name N or n \ ame CA or name C or name O or name CB )) or (resid 130 through 162 and (name N o \ r name CA or name C or name O or name CB )) or resid 163 or (resid 164 through 1 \ 79 and (name N or name CA or name C or name O or name CB )) or resid 180 through \ 189 or (resid 190 through 209 and (name N or name CA or name C or name O or nam \ e CB )) or resid 210 or (resid 211 through 217 and (name N or name CA or name C \ or name O or name CB )) or resid 218 through 225 or (resid 226 through 228 and ( \ name N or name CA or name C or name O or name CB )) or resid 229 through 250 or \ (resid 251 through 252 and (name N or name CA or name C or name O or name CB )) \ or resid 253 through 260 or (resid 261 through 263 and (name N or name CA or nam \ e C or name O or name CB )) or resid 264 through 265 or (resid 266 and (name N o \ r name CA or name C or name O or name CB )) or resid 267 through 301 or (resid 3 \ 02 through 306 and (name N or name CA or name C or name O or name CB )) or resid \ 307 or (resid 308 through 314 and (name N or name CA or name C or name O or nam \ e CB )) or resid 315 or (resid 316 through 324 and (name N or name CA or name C \ or name O or name CB )) or (resid 325 through 331 and (name N or name CA or name \ C or name O or name CB )) or resid 332 through 336 or (resid 337 through 338 an \ d (name N or name CA or name C or name O or name CB )) or resid 339 or (resid 34 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 341 through \ 342 or (resid 343 through 349 and (name N or name CA or name C or name O or name \ CB )) or resid 350 through 352 or (resid 353 through 354 and (name N or name CA \ or name C or name O or name CB )) or resid 355 through 363 or (resid 364 throug \ h 365 and (name N or name CA or name C or name O or name CB )) or resid 366 or ( \ resid 367 through 370 and (name N or name CA or name C or name O or name CB )) o \ r resid 371 through 377 or (resid 378 through 379 and (name N or name CA or name \ C or name O or name CB )) or (resid 380 through 384 and (name N or name CA or n \ ame C or name O or name CB )) or (resid 385 through 414 and (name N or name CA o \ r name C or name O or name CB )) or (resid 415 through 444 and (name N or name C \ A or name C or name O or name CB )) or resid 445 or (resid 446 through 448 and ( \ name N or name CA or name C or name O or name CB )) or resid 449 through 476 or \ (resid 477 through 482 and (name N or name CA or name C or name O or name CB )) \ or resid 483 through 484 or (resid 485 through 486 and (name N or name CA or nam \ e C or name O or name CB )) or resid 487 through 488 or (resid 489 through 490 a \ nd (name N or name CA or name C or name O or name CB )) or resid 491 or (resid 4 \ 92 through 504 and (name N or name CA or name C or name O or name CB )) or resid \ 505 through 519 or (resid 520 through 523 and (name N or name CA or name C or n \ ame O or name CB )))) } 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 group one per residue 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: 14.340 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: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 29.110 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5561 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 : 0.010 0.066 9049 Z= 0.662 Angle : 1.390 19.345 12501 Z= 0.995 Chirality : 0.075 0.409 1487 Planarity : 0.008 0.065 1699 Dihedral : 13.360 89.185 2461 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.71 % Favored : 91.93 % Rotamer: Outliers : 2.64 % Allowed : 9.25 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.20), residues: 1413 helix: -0.67 (0.16), residues: 936 sheet: None (None), residues: 0 loop : -2.22 (0.25), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 257 HIS 0.008 0.002 HIS A 348 PHE 0.020 0.002 PHE A 368 TYR 0.017 0.003 TYR C 177 ARG 0.004 0.001 ARG B 495 Details of bonding type rmsd hydrogen bonds : bond 0.17216 ( 736) hydrogen bonds : angle 7.08406 ( 2130) covalent geometry : bond 0.00995 ( 9049) covalent geometry : angle 1.38974 (12501) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 184 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ASN cc_start: 0.4803 (p0) cc_final: 0.4418 (p0) REVERT: B 186 ARG cc_start: 0.5902 (tpt170) cc_final: 0.5307 (tpt170) outliers start: 12 outliers final: 3 residues processed: 188 average time/residue: 0.1990 time to fit residues: 51.6717 Evaluate side-chains 155 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 152 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain B residue 356 ARG Chi-restraints excluded: chain C residue 79 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 119 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 59 optimal weight: 0.2980 chunk 36 optimal weight: 0.8980 chunk 72 optimal weight: 0.2980 chunk 57 optimal weight: 0.7980 chunk 110 optimal weight: 0.5980 chunk 42 optimal weight: 0.6980 chunk 67 optimal weight: 0.0980 chunk 82 optimal weight: 1.9990 chunk 128 optimal weight: 7.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN A 308 GLN A 366 ASN A 467 GLN ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 ASN B 55 GLN B 216 GLN B 217 ASN B 366 ASN C 145 HIS ** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.152395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.127405 restraints weight = 20085.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.130927 restraints weight = 13281.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.133461 restraints weight = 9724.525| |-----------------------------------------------------------------------------| r_work (final): 0.3936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6681 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9049 Z= 0.179 Angle : 0.647 10.428 12501 Z= 0.361 Chirality : 0.043 0.170 1487 Planarity : 0.006 0.074 1699 Dihedral : 5.745 46.701 1488 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.46 % Favored : 95.47 % Rotamer: Outliers : 3.74 % Allowed : 19.60 % Favored : 76.65 % 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: 0.03 (0.22), residues: 1413 helix: 0.90 (0.16), residues: 963 sheet: None (None), residues: 0 loop : -1.91 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 267 HIS 0.015 0.002 HIS A 451 PHE 0.037 0.002 PHE C 383 TYR 0.021 0.002 TYR A 51 ARG 0.013 0.001 ARG C 353 Details of bonding type rmsd hydrogen bonds : bond 0.04738 ( 736) hydrogen bonds : angle 4.51252 ( 2130) covalent geometry : bond 0.00335 ( 9049) covalent geometry : angle 0.64740 (12501) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 154 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 219 MET cc_start: 0.7408 (ttm) cc_final: 0.7196 (ttp) REVERT: C 68 PHE cc_start: 0.8047 (m-80) cc_final: 0.7792 (m-80) REVERT: C 179 THR cc_start: 0.8379 (m) cc_final: 0.8160 (p) REVERT: C 353 ARG cc_start: 0.7083 (ttm-80) cc_final: 0.6869 (ttm110) REVERT: C 383 PHE cc_start: 0.7885 (m-80) cc_final: 0.7684 (m-80) REVERT: C 446 HIS cc_start: 0.7466 (m90) cc_final: 0.7146 (m90) outliers start: 17 outliers final: 11 residues processed: 162 average time/residue: 0.1988 time to fit residues: 44.5686 Evaluate side-chains 157 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 146 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain B residue 216 GLN Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 292 TRP Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 114 ASP Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 489 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 132 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 119 optimal weight: 0.7980 chunk 128 optimal weight: 3.9990 chunk 19 optimal weight: 0.1980 chunk 56 optimal weight: 0.5980 chunk 100 optimal weight: 0.0030 chunk 61 optimal weight: 5.9990 chunk 66 optimal weight: 0.6980 chunk 112 optimal weight: 0.9990 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 55 GLN A 444 HIS A 470 GLN C 210 HIS C 348 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.145767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.121256 restraints weight = 20434.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.124682 restraints weight = 13270.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.127199 restraints weight = 9623.340| |-----------------------------------------------------------------------------| r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 moved from start: 0.4314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9049 Z= 0.188 Angle : 0.646 9.730 12501 Z= 0.357 Chirality : 0.043 0.139 1487 Planarity : 0.005 0.056 1699 Dihedral : 5.137 30.287 1481 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.45 % Favored : 94.48 % Rotamer: Outliers : 4.19 % Allowed : 19.82 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.84 (0.22), residues: 1413 helix: 1.52 (0.17), residues: 954 sheet: None (None), residues: 0 loop : -1.55 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 267 HIS 0.013 0.002 HIS B 39 PHE 0.022 0.002 PHE B 215 TYR 0.029 0.002 TYR A 51 ARG 0.005 0.001 ARG A 214 Details of bonding type rmsd hydrogen bonds : bond 0.04577 ( 736) hydrogen bonds : angle 4.43308 ( 2130) covalent geometry : bond 0.00363 ( 9049) covalent geometry : angle 0.64630 (12501) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 154 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 TRP cc_start: 0.7415 (m100) cc_final: 0.6678 (m100) REVERT: B 334 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8185 (mp) REVERT: B 519 CYS cc_start: 0.7098 (t) cc_final: 0.6767 (t) REVERT: C 383 PHE cc_start: 0.7919 (m-80) cc_final: 0.7649 (m-80) outliers start: 19 outliers final: 9 residues processed: 163 average time/residue: 0.2157 time to fit residues: 49.0560 Evaluate side-chains 158 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 148 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 342 HIS Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 114 ASP Chi-restraints excluded: chain C residue 489 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 106 optimal weight: 0.8980 chunk 87 optimal weight: 0.0040 chunk 131 optimal weight: 1.9990 chunk 119 optimal weight: 0.5980 chunk 128 optimal weight: 3.9990 chunk 135 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 84 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 55 GLN A 348 HIS C 145 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.139290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.115037 restraints weight = 20516.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.118345 restraints weight = 13348.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.120680 restraints weight = 9703.790| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 0.5940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9049 Z= 0.235 Angle : 0.694 7.803 12501 Z= 0.389 Chirality : 0.046 0.192 1487 Planarity : 0.006 0.061 1699 Dihedral : 5.503 28.393 1481 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.44 % Favored : 93.42 % Rotamer: Outliers : 6.83 % Allowed : 20.48 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.22), residues: 1413 helix: 1.19 (0.17), residues: 973 sheet: None (None), residues: 0 loop : -1.53 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 292 HIS 0.009 0.002 HIS B 38 PHE 0.034 0.003 PHE A 47 TYR 0.030 0.002 TYR A 164 ARG 0.006 0.001 ARG A 497 Details of bonding type rmsd hydrogen bonds : bond 0.04977 ( 736) hydrogen bonds : angle 4.76136 ( 2130) covalent geometry : bond 0.00448 ( 9049) covalent geometry : angle 0.69418 (12501) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 149 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 38 HIS cc_start: 0.8121 (p90) cc_final: 0.7905 (p90) REVERT: B 219 MET cc_start: 0.7497 (ttt) cc_final: 0.7115 (ttp) REVERT: C 38 HIS cc_start: 0.6377 (OUTLIER) cc_final: 0.5886 (p90) REVERT: C 383 PHE cc_start: 0.7969 (m-80) cc_final: 0.7648 (m-80) outliers start: 31 outliers final: 13 residues processed: 167 average time/residue: 0.1838 time to fit residues: 43.4507 Evaluate side-chains 163 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 149 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 342 HIS Chi-restraints excluded: chain B residue 469 PHE Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 114 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 50 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 42 optimal weight: 0.1980 chunk 136 optimal weight: 0.0670 chunk 109 optimal weight: 3.9990 chunk 67 optimal weight: 0.3980 chunk 34 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 overall best weight: 0.3718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN A 224 ASN ** B 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 GLN C 145 HIS C 181 GLN ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 366 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.141459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.117147 restraints weight = 20391.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.120612 restraints weight = 13129.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.123043 restraints weight = 9434.156| |-----------------------------------------------------------------------------| r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.6229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9049 Z= 0.155 Angle : 0.597 9.218 12501 Z= 0.322 Chirality : 0.042 0.164 1487 Planarity : 0.005 0.067 1699 Dihedral : 4.920 29.373 1481 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.10 % Favored : 94.69 % Rotamer: Outliers : 5.29 % Allowed : 22.47 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.23), residues: 1413 helix: 1.83 (0.17), residues: 962 sheet: None (None), residues: 0 loop : -1.39 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 267 HIS 0.010 0.001 HIS B 39 PHE 0.027 0.002 PHE C 79 TYR 0.020 0.002 TYR C 364 ARG 0.005 0.001 ARG A 337 Details of bonding type rmsd hydrogen bonds : bond 0.04113 ( 736) hydrogen bonds : angle 4.25233 ( 2130) covalent geometry : bond 0.00298 ( 9049) covalent geometry : angle 0.59663 (12501) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 152 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 247 LEU cc_start: 0.8254 (tp) cc_final: 0.7973 (tt) REVERT: B 255 LEU cc_start: 0.6865 (OUTLIER) cc_final: 0.6531 (tp) REVERT: B 272 GLU cc_start: 0.8038 (pm20) cc_final: 0.7705 (pm20) REVERT: C 383 PHE cc_start: 0.7970 (m-80) cc_final: 0.7644 (m-80) outliers start: 24 outliers final: 14 residues processed: 163 average time/residue: 0.1909 time to fit residues: 43.9496 Evaluate side-chains 160 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 145 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 342 HIS Chi-restraints excluded: chain B residue 469 PHE Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 114 ASP Chi-restraints excluded: chain C residue 218 TYR Chi-restraints excluded: chain C residue 264 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 136 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 61 optimal weight: 0.0050 chunk 74 optimal weight: 0.5980 chunk 90 optimal weight: 0.5980 chunk 93 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN B 39 HIS B 55 GLN C 145 HIS C 342 HIS ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.139187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.115339 restraints weight = 20443.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.118640 restraints weight = 13237.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.120929 restraints weight = 9591.807| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.6714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9049 Z= 0.186 Angle : 0.621 6.528 12501 Z= 0.341 Chirality : 0.043 0.161 1487 Planarity : 0.005 0.075 1699 Dihedral : 4.982 27.978 1481 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.58 % Favored : 93.21 % Rotamer: Outliers : 6.17 % Allowed : 21.81 % Favored : 72.03 % 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: 1.17 (0.23), residues: 1413 helix: 1.75 (0.17), residues: 969 sheet: None (None), residues: 0 loop : -1.47 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 267 HIS 0.007 0.001 HIS A 451 PHE 0.024 0.002 PHE C 79 TYR 0.024 0.002 TYR C 152 ARG 0.006 0.001 ARG C 353 Details of bonding type rmsd hydrogen bonds : bond 0.04325 ( 736) hydrogen bonds : angle 4.37048 ( 2130) covalent geometry : bond 0.00362 ( 9049) covalent geometry : angle 0.62132 (12501) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 153 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 255 LEU cc_start: 0.6991 (OUTLIER) cc_final: 0.6712 (tp) REVERT: B 272 GLU cc_start: 0.8029 (pm20) cc_final: 0.7766 (pm20) REVERT: C 143 TRP cc_start: 0.7733 (t60) cc_final: 0.6695 (t60) REVERT: C 383 PHE cc_start: 0.7960 (m-80) cc_final: 0.7643 (m-80) outliers start: 28 outliers final: 20 residues processed: 168 average time/residue: 0.1986 time to fit residues: 46.6036 Evaluate side-chains 177 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 156 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 TYR Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 284 GLN Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 239 GLU Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain B residue 469 PHE Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 114 ASP Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 451 HIS Chi-restraints excluded: chain C residue 489 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 40 optimal weight: 0.8980 chunk 120 optimal weight: 0.6980 chunk 80 optimal weight: 0.6980 chunk 100 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 107 optimal weight: 0.5980 chunk 88 optimal weight: 0.3980 chunk 82 optimal weight: 0.0170 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN A 224 ASN B 342 HIS C 145 HIS ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.139083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.115162 restraints weight = 20442.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.118457 restraints weight = 13291.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.120771 restraints weight = 9645.041| |-----------------------------------------------------------------------------| r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.7130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9049 Z= 0.180 Angle : 0.619 8.468 12501 Z= 0.338 Chirality : 0.043 0.158 1487 Planarity : 0.005 0.073 1699 Dihedral : 4.945 29.169 1481 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.80 % Favored : 93.98 % Rotamer: Outliers : 6.39 % Allowed : 23.13 % Favored : 70.48 % 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: 1.18 (0.23), residues: 1413 helix: 1.76 (0.17), residues: 965 sheet: None (None), residues: 0 loop : -1.45 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 267 HIS 0.007 0.001 HIS B 39 PHE 0.023 0.002 PHE C 79 TYR 0.019 0.002 TYR C 51 ARG 0.008 0.001 ARG A 337 Details of bonding type rmsd hydrogen bonds : bond 0.04271 ( 736) hydrogen bonds : angle 4.36124 ( 2130) covalent geometry : bond 0.00352 ( 9049) covalent geometry : angle 0.61945 (12501) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 153 time to evaluate : 0.994 Fit side-chains revert: symmetry clash REVERT: A 284 GLN cc_start: 0.8350 (OUTLIER) cc_final: 0.8030 (tp-100) REVERT: B 255 LEU cc_start: 0.7000 (OUTLIER) cc_final: 0.6710 (tp) REVERT: B 272 GLU cc_start: 0.8057 (pm20) cc_final: 0.7808 (pm20) REVERT: C 38 HIS cc_start: 0.6044 (OUTLIER) cc_final: 0.5628 (p90) REVERT: C 143 TRP cc_start: 0.7924 (t60) cc_final: 0.7296 (t60) REVERT: C 383 PHE cc_start: 0.8015 (m-80) cc_final: 0.7674 (m-80) outliers start: 29 outliers final: 24 residues processed: 166 average time/residue: 0.1870 time to fit residues: 43.8679 Evaluate side-chains 176 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 149 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 TYR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 284 GLN Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 239 GLU Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 464 GLU Chi-restraints excluded: chain B residue 469 PHE Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 114 ASP Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 218 TYR Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 451 HIS Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 489 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 49 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 chunk 79 optimal weight: 0.0170 chunk 85 optimal weight: 0.0870 chunk 10 optimal weight: 0.4980 chunk 64 optimal weight: 0.3980 chunk 119 optimal weight: 0.7980 chunk 137 optimal weight: 0.5980 chunk 140 optimal weight: 0.9980 chunk 7 optimal weight: 0.0980 chunk 109 optimal weight: 3.9990 overall best weight: 0.2196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN B 55 GLN B 467 GLN C 145 HIS C 210 HIS C 342 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.141419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.117436 restraints weight = 20742.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.120798 restraints weight = 13518.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.123089 restraints weight = 9811.764| |-----------------------------------------------------------------------------| r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.7239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9049 Z= 0.125 Angle : 0.572 7.853 12501 Z= 0.303 Chirality : 0.042 0.153 1487 Planarity : 0.005 0.074 1699 Dihedral : 4.661 27.928 1481 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.73 % Favored : 94.13 % Rotamer: Outliers : 4.63 % Allowed : 25.55 % Favored : 69.82 % 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: 1.55 (0.23), residues: 1413 helix: 2.09 (0.17), residues: 964 sheet: None (None), residues: 0 loop : -1.41 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 267 HIS 0.007 0.001 HIS B 39 PHE 0.021 0.001 PHE C 79 TYR 0.017 0.001 TYR A 364 ARG 0.004 0.000 ARG A 337 Details of bonding type rmsd hydrogen bonds : bond 0.03807 ( 736) hydrogen bonds : angle 4.09842 ( 2130) covalent geometry : bond 0.00242 ( 9049) covalent geometry : angle 0.57169 (12501) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 154 time to evaluate : 0.974 Fit side-chains revert: symmetry clash REVERT: A 284 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.8039 (tp-100) REVERT: B 272 GLU cc_start: 0.8062 (pm20) cc_final: 0.7860 (pm20) REVERT: B 353 ARG cc_start: 0.8021 (tpp80) cc_final: 0.7504 (tpp80) REVERT: C 143 TRP cc_start: 0.7726 (t60) cc_final: 0.7013 (t60) REVERT: C 383 PHE cc_start: 0.8005 (m-80) cc_final: 0.7701 (m-80) outliers start: 21 outliers final: 19 residues processed: 160 average time/residue: 0.1952 time to fit residues: 43.3726 Evaluate side-chains 170 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 150 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 TYR Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 284 GLN Chi-restraints excluded: chain A residue 332 TRP Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 239 GLU Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain B residue 453 GLN Chi-restraints excluded: chain B residue 469 PHE Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 114 ASP Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 218 TYR Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 451 HIS Chi-restraints excluded: chain C residue 489 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 55 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 chunk 114 optimal weight: 0.5980 chunk 71 optimal weight: 0.6980 chunk 136 optimal weight: 0.2980 chunk 139 optimal weight: 0.5980 chunk 108 optimal weight: 0.9990 chunk 69 optimal weight: 0.3980 chunk 21 optimal weight: 0.3980 chunk 37 optimal weight: 0.0170 chunk 77 optimal weight: 0.0370 overall best weight: 0.2296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN A 224 ASN C 145 HIS C 344 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.141578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.117949 restraints weight = 20549.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.121283 restraints weight = 13396.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.123620 restraints weight = 9673.198| |-----------------------------------------------------------------------------| r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.7361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9049 Z= 0.123 Angle : 0.572 7.454 12501 Z= 0.304 Chirality : 0.042 0.155 1487 Planarity : 0.005 0.073 1699 Dihedral : 4.538 27.651 1481 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.66 % Favored : 94.20 % Rotamer: Outliers : 5.07 % Allowed : 26.21 % Favored : 68.72 % 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: 1.66 (0.23), residues: 1413 helix: 2.19 (0.17), residues: 969 sheet: None (None), residues: 0 loop : -1.49 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP B 267 HIS 0.007 0.001 HIS B 39 PHE 0.047 0.001 PHE C 79 TYR 0.015 0.001 TYR C 364 ARG 0.007 0.001 ARG A 439 Details of bonding type rmsd hydrogen bonds : bond 0.03705 ( 736) hydrogen bonds : angle 4.01887 ( 2130) covalent geometry : bond 0.00240 ( 9049) covalent geometry : angle 0.57210 (12501) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 152 time to evaluate : 0.890 Fit side-chains revert: symmetry clash REVERT: A 284 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.7969 (tp-100) REVERT: B 248 LYS cc_start: 0.8283 (tttm) cc_final: 0.7919 (tptp) REVERT: B 251 PHE cc_start: 0.7244 (m-80) cc_final: 0.6940 (t80) REVERT: B 353 ARG cc_start: 0.8011 (tpp80) cc_final: 0.7585 (tpp80) REVERT: C 38 HIS cc_start: 0.5938 (OUTLIER) cc_final: 0.5571 (p90) REVERT: C 143 TRP cc_start: 0.7560 (t60) cc_final: 0.6837 (t60) REVERT: C 383 PHE cc_start: 0.7942 (m-80) cc_final: 0.7649 (m-80) outliers start: 23 outliers final: 18 residues processed: 161 average time/residue: 0.1786 time to fit residues: 40.6617 Evaluate side-chains 170 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 150 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 TYR Chi-restraints excluded: chain A residue 284 GLN Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 239 GLU Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain B residue 332 TRP Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 464 GLU Chi-restraints excluded: chain B residue 469 PHE Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 114 ASP Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 218 TYR Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 451 HIS Chi-restraints excluded: chain C residue 489 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 17 optimal weight: 0.4980 chunk 0 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 129 optimal weight: 0.9980 chunk 113 optimal weight: 0.2980 chunk 109 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 93 optimal weight: 0.2980 chunk 49 optimal weight: 0.6980 chunk 125 optimal weight: 0.4980 chunk 55 optimal weight: 0.8980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.138998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.115072 restraints weight = 20724.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.118429 restraints weight = 13420.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.120777 restraints weight = 9724.124| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.7638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9049 Z= 0.176 Angle : 0.629 8.521 12501 Z= 0.341 Chirality : 0.044 0.156 1487 Planarity : 0.005 0.075 1699 Dihedral : 4.768 26.774 1481 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.65 % Favored : 93.21 % Rotamer: Outliers : 4.85 % Allowed : 26.87 % Favored : 68.28 % 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: 1.36 (0.23), residues: 1413 helix: 1.97 (0.17), residues: 967 sheet: None (None), residues: 0 loop : -1.61 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 267 HIS 0.006 0.001 HIS B 39 PHE 0.050 0.002 PHE C 79 TYR 0.029 0.002 TYR A 51 ARG 0.005 0.001 ARG A 439 Details of bonding type rmsd hydrogen bonds : bond 0.04178 ( 736) hydrogen bonds : angle 4.28482 ( 2130) covalent geometry : bond 0.00346 ( 9049) covalent geometry : angle 0.62882 (12501) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 152 time to evaluate : 1.007 Fit side-chains REVERT: A 497 ARG cc_start: 0.6690 (mpp80) cc_final: 0.6471 (mtt90) REVERT: B 251 PHE cc_start: 0.7420 (m-80) cc_final: 0.6904 (t80) REVERT: B 255 LEU cc_start: 0.7075 (OUTLIER) cc_final: 0.6836 (tp) REVERT: B 353 ARG cc_start: 0.8048 (tpp80) cc_final: 0.7665 (tpp80) REVERT: C 38 HIS cc_start: 0.6021 (OUTLIER) cc_final: 0.5639 (p90) REVERT: C 143 TRP cc_start: 0.7717 (t60) cc_final: 0.7202 (t60) REVERT: C 383 PHE cc_start: 0.8002 (m-80) cc_final: 0.7704 (m-80) outliers start: 22 outliers final: 17 residues processed: 164 average time/residue: 0.1964 time to fit residues: 46.1218 Evaluate side-chains 169 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 150 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 TYR Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 239 GLU Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 332 TRP Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 464 GLU Chi-restraints excluded: chain B residue 469 PHE Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 114 ASP Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 451 HIS Chi-restraints excluded: chain C residue 489 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 47 optimal weight: 0.1980 chunk 58 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 138 optimal weight: 0.5980 chunk 38 optimal weight: 0.0670 chunk 5 optimal weight: 8.9990 chunk 6 optimal weight: 0.0970 chunk 116 optimal weight: 0.0170 chunk 118 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 overall best weight: 0.1954 ------------------------------------------------------------------------------- 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 = 0.4052 r_free = 0.4052 target = 0.141799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.118168 restraints weight = 20629.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.121550 restraints weight = 13401.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.123936 restraints weight = 9678.933| |-----------------------------------------------------------------------------| r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.7714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9049 Z= 0.121 Angle : 0.585 9.215 12501 Z= 0.309 Chirality : 0.042 0.161 1487 Planarity : 0.005 0.071 1699 Dihedral : 4.539 27.862 1481 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.02 % Favored : 94.90 % Rotamer: Outliers : 3.96 % Allowed : 27.31 % Favored : 68.72 % 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: 1.66 (0.24), residues: 1413 helix: 2.22 (0.17), residues: 968 sheet: None (None), residues: 0 loop : -1.54 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 267 HIS 0.007 0.001 HIS B 39 PHE 0.050 0.001 PHE C 79 TYR 0.029 0.002 TYR A 51 ARG 0.011 0.001 ARG B 356 Details of bonding type rmsd hydrogen bonds : bond 0.03681 ( 736) hydrogen bonds : angle 4.02256 ( 2130) covalent geometry : bond 0.00237 ( 9049) covalent geometry : angle 0.58454 (12501) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3278.33 seconds wall clock time: 57 minutes 53.10 seconds (3473.10 seconds total)