Starting phenix.real_space_refine on Sat Jul 26 21:29:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kbz_37088/07_2025/8kbz_37088.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kbz_37088/07_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_37088/07_2025/8kbz_37088.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kbz_37088/07_2025/8kbz_37088.map" model { file = "/net/cci-nas-00/data/ceres_data/8kbz_37088/07_2025/8kbz_37088.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kbz_37088/07_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-5711/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: 9.33, per 1000 atoms: 1.05 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: 2.51 Conformation dependent library (CDL) restraints added in 1.3 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: 0.93 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: 2.55 Time building geometry restraints manager: 2.92 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: 262.770 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 27.530 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.050 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 294.350 ------------------------------------------------------------------------------- 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 : 0.914 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: 0.1951 time to fit residues: 50.8305 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 : 1.017 ------------------------------------------------------------------------------- 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 = 0.152394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.127402 restraints weight = 20085.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.130933 restraints weight = 13283.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.133441 restraints weight = 9718.800| |-----------------------------------------------------------------------------| r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6682 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 46.702 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 4.51251 ( 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 : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 219 MET cc_start: 0.7408 (ttm) cc_final: 0.7197 (ttp) REVERT: C 68 PHE cc_start: 0.8054 (m-80) cc_final: 0.7800 (m-80) REVERT: C 179 THR cc_start: 0.8379 (m) cc_final: 0.8161 (p) REVERT: C 353 ARG cc_start: 0.7084 (ttm-80) cc_final: 0.6869 (ttm110) REVERT: C 383 PHE cc_start: 0.7889 (m-80) cc_final: 0.7688 (m-80) REVERT: C 446 HIS cc_start: 0.7467 (m90) cc_final: 0.7149 (m90) outliers start: 17 outliers final: 11 residues processed: 162 average time/residue: 0.2072 time to fit residues: 46.2009 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 : 1.009 ------------------------------------------------------------------------------- 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: 0.9980 chunk 75 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 119 optimal weight: 0.1980 chunk 128 optimal weight: 3.9990 chunk 19 optimal weight: 0.2980 chunk 56 optimal weight: 0.5980 chunk 100 optimal weight: 0.0010 chunk 61 optimal weight: 5.9990 chunk 66 optimal weight: 0.5980 chunk 112 optimal weight: 0.9980 overall best weight: 0.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4138 r_free = 0.4138 target = 0.148928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.124010 restraints weight = 20474.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.127572 restraints weight = 13363.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.130033 restraints weight = 9706.194| |-----------------------------------------------------------------------------| r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6773 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9049 Z= 0.157 Angle : 0.606 9.827 12501 Z= 0.330 Chirality : 0.042 0.137 1487 Planarity : 0.005 0.048 1699 Dihedral : 4.981 29.713 1481 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.52 % Allowed : 20.26 % Favored : 76.21 % 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: 1.03 (0.23), residues: 1413 helix: 1.70 (0.17), residues: 951 sheet: None (None), residues: 0 loop : -1.54 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 267 HIS 0.010 0.001 HIS A 451 PHE 0.020 0.002 PHE C 383 TYR 0.023 0.002 TYR A 51 ARG 0.005 0.001 ARG B 353 Details of bonding type rmsd hydrogen bonds : bond 0.04227 ( 736) hydrogen bonds : angle 4.26598 ( 2130) covalent geometry : bond 0.00301 ( 9049) covalent geometry : angle 0.60589 (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 169 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 153 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 334 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8138 (mp) REVERT: B 519 CYS cc_start: 0.6983 (t) cc_final: 0.6575 (t) REVERT: C 383 PHE cc_start: 0.7926 (m-80) cc_final: 0.7653 (m-80) outliers start: 16 outliers final: 7 residues processed: 159 average time/residue: 0.2076 time to fit residues: 46.0677 Evaluate side-chains 156 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 148 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 183 VAL 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: 0.6980 chunk 87 optimal weight: 0.0870 chunk 131 optimal weight: 0.6980 chunk 119 optimal weight: 0.7980 chunk 128 optimal weight: 3.9990 chunk 135 optimal weight: 0.2980 chunk 76 optimal weight: 0.6980 chunk 84 optimal weight: 0.1980 chunk 79 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 30 optimal weight: 0.4980 overall best weight: 0.3558 ------------------------------------------------------------------------------- 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 ** B 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 HIS C 181 GLN C 342 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.146565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.122158 restraints weight = 20219.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.125644 restraints weight = 13136.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.128038 restraints weight = 9474.030| |-----------------------------------------------------------------------------| r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6831 moved from start: 0.4431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9049 Z= 0.155 Angle : 0.595 7.699 12501 Z= 0.322 Chirality : 0.042 0.153 1487 Planarity : 0.005 0.059 1699 Dihedral : 4.868 28.560 1481 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.96 % Allowed : 22.03 % Favored : 74.01 % 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: 1.29 (0.23), residues: 1413 helix: 1.89 (0.17), residues: 954 sheet: None (None), residues: 0 loop : -1.43 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 267 HIS 0.008 0.001 HIS B 39 PHE 0.037 0.002 PHE C 79 TYR 0.021 0.002 TYR A 51 ARG 0.006 0.001 ARG C 211 Details of bonding type rmsd hydrogen bonds : bond 0.04079 ( 736) hydrogen bonds : angle 4.22292 ( 2130) covalent geometry : bond 0.00296 ( 9049) covalent geometry : angle 0.59475 (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 168 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 406 HIS cc_start: 0.8327 (m90) cc_final: 0.7933 (m-70) REVERT: B 519 CYS cc_start: 0.7099 (t) cc_final: 0.6734 (t) REVERT: C 353 ARG cc_start: 0.7371 (mtm-85) cc_final: 0.7111 (mtm-85) REVERT: C 383 PHE cc_start: 0.7975 (m-80) cc_final: 0.7682 (m-80) outliers start: 18 outliers final: 8 residues processed: 158 average time/residue: 0.1982 time to fit residues: 44.0416 Evaluate side-chains 158 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 150 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 50 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 27 optimal weight: 0.0010 chunk 28 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 136 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 67 optimal weight: 0.2980 chunk 34 optimal weight: 5.9990 chunk 112 optimal weight: 0.9980 overall best weight: 0.5786 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 HIS ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.139742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.115737 restraints weight = 20545.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.119096 restraints weight = 13290.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.121456 restraints weight = 9609.955| |-----------------------------------------------------------------------------| r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.5987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9049 Z= 0.222 Angle : 0.679 8.484 12501 Z= 0.377 Chirality : 0.045 0.163 1487 Planarity : 0.005 0.070 1699 Dihedral : 5.233 27.089 1481 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.79 % Favored : 93.06 % Rotamer: Outliers : 5.29 % Allowed : 20.26 % Favored : 74.45 % 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: 0.88 (0.23), residues: 1413 helix: 1.47 (0.17), residues: 973 sheet: None (None), residues: 0 loop : -1.44 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 452 HIS 0.012 0.002 HIS B 39 PHE 0.025 0.002 PHE A 47 TYR 0.029 0.002 TYR A 164 ARG 0.005 0.001 ARG B 495 Details of bonding type rmsd hydrogen bonds : bond 0.04820 ( 736) hydrogen bonds : angle 4.64660 ( 2130) covalent geometry : bond 0.00430 ( 9049) covalent geometry : angle 0.67949 (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 170 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 146 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 LEU cc_start: 0.6481 (tt) cc_final: 0.6221 (tp) REVERT: B 272 GLU cc_start: 0.7989 (pm20) cc_final: 0.7546 (pm20) REVERT: C 353 ARG cc_start: 0.7474 (mtm-85) cc_final: 0.7228 (mtm-85) REVERT: C 383 PHE cc_start: 0.7931 (m-80) cc_final: 0.7651 (m-80) outliers start: 24 outliers final: 13 residues processed: 160 average time/residue: 0.1834 time to fit residues: 41.6741 Evaluate side-chains 154 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 141 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 319 VAL 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 250 ASN 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 91 ILE Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 114 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 136 optimal weight: 0.2980 chunk 26 optimal weight: 0.8980 chunk 1 optimal weight: 0.2980 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 0.4980 chunk 59 optimal weight: 0.0970 chunk 61 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 90 optimal weight: 0.5980 chunk 93 optimal weight: 0.3980 chunk 60 optimal weight: 0.7980 overall best weight: 0.3178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 GLN C 145 HIS ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.142677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.118635 restraints weight = 20273.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.122017 restraints weight = 13179.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.124350 restraints weight = 9540.477| |-----------------------------------------------------------------------------| r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.6247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9049 Z= 0.140 Angle : 0.583 9.664 12501 Z= 0.314 Chirality : 0.042 0.169 1487 Planarity : 0.004 0.066 1699 Dihedral : 4.757 26.889 1481 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.24 % Favored : 94.62 % Rotamer: Outliers : 3.96 % Allowed : 24.01 % 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: 1.54 (0.23), residues: 1413 helix: 2.06 (0.17), residues: 956 sheet: None (None), residues: 0 loop : -1.28 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 267 HIS 0.014 0.001 HIS B 39 PHE 0.024 0.001 PHE C 79 TYR 0.021 0.002 TYR C 364 ARG 0.006 0.001 ARG C 353 Details of bonding type rmsd hydrogen bonds : bond 0.03922 ( 736) hydrogen bonds : angle 4.12604 ( 2130) covalent geometry : bond 0.00269 ( 9049) covalent geometry : angle 0.58267 (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 164 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 272 GLU cc_start: 0.7959 (pm20) cc_final: 0.7643 (pm20) REVERT: C 251 PHE cc_start: 0.7635 (m-10) cc_final: 0.7411 (m-10) REVERT: C 342 HIS cc_start: 0.7015 (m90) cc_final: 0.6667 (m90) REVERT: C 353 ARG cc_start: 0.7333 (mtm-85) cc_final: 0.7118 (mtm-85) REVERT: C 383 PHE cc_start: 0.7992 (m-80) cc_final: 0.7672 (m-80) outliers start: 18 outliers final: 11 residues processed: 155 average time/residue: 0.1959 time to fit residues: 42.7040 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 : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 356 ARG 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 40 optimal weight: 0.5980 chunk 120 optimal weight: 0.7980 chunk 80 optimal weight: 0.6980 chunk 100 optimal weight: 0.0010 chunk 55 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 91 optimal weight: 0.0170 chunk 3 optimal weight: 0.4980 chunk 107 optimal weight: 0.6980 chunk 88 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 overall best weight: 0.3424 ------------------------------------------------------------------------------- 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 A 348 HIS B 250 ASN B 342 HIS B 467 GLN C 145 HIS C 344 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.141611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.117221 restraints weight = 20319.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.120718 restraints weight = 13017.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.123150 restraints weight = 9338.134| |-----------------------------------------------------------------------------| r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.6592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9049 Z= 0.147 Angle : 0.591 7.889 12501 Z= 0.318 Chirality : 0.043 0.146 1487 Planarity : 0.005 0.068 1699 Dihedral : 4.661 25.459 1481 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.09 % Favored : 93.77 % Rotamer: Outliers : 4.19 % Allowed : 23.79 % 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: 1.53 (0.23), residues: 1413 helix: 2.03 (0.17), residues: 968 sheet: None (None), residues: 0 loop : -1.35 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 267 HIS 0.006 0.001 HIS B 39 PHE 0.022 0.001 PHE C 79 TYR 0.018 0.002 TYR C 364 ARG 0.009 0.001 ARG A 439 Details of bonding type rmsd hydrogen bonds : bond 0.03935 ( 736) hydrogen bonds : angle 4.10435 ( 2130) covalent geometry : bond 0.00287 ( 9049) covalent geometry : angle 0.59125 (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 177 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 158 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 272 GLU cc_start: 0.8064 (pm20) cc_final: 0.7711 (pm20) REVERT: C 38 HIS cc_start: 0.6185 (OUTLIER) cc_final: 0.5767 (p90) REVERT: C 251 PHE cc_start: 0.7623 (m-10) cc_final: 0.7387 (m-10) REVERT: C 353 ARG cc_start: 0.7375 (mtm-85) cc_final: 0.7156 (mtm-85) REVERT: C 383 PHE cc_start: 0.8004 (m-80) cc_final: 0.7673 (m-80) outliers start: 19 outliers final: 14 residues processed: 165 average time/residue: 0.1891 time to fit residues: 43.7509 Evaluate side-chains 168 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 153 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 TYR Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain B residue 230 LEU 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 461 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 49 optimal weight: 0.3980 chunk 121 optimal weight: 0.9980 chunk 79 optimal weight: 0.0970 chunk 85 optimal weight: 0.0670 chunk 10 optimal weight: 0.5980 chunk 64 optimal weight: 0.0470 chunk 119 optimal weight: 0.5980 chunk 137 optimal weight: 0.6980 chunk 140 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 overall best weight: 0.2414 ------------------------------------------------------------------------------- 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 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.143180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.119151 restraints weight = 20599.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.122561 restraints weight = 13308.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.124925 restraints weight = 9603.278| |-----------------------------------------------------------------------------| r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 0.6790 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= 0.124 Angle : 0.572 9.265 12501 Z= 0.304 Chirality : 0.042 0.149 1487 Planarity : 0.004 0.067 1699 Dihedral : 4.539 27.096 1481 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.10 % Favored : 94.76 % Rotamer: Outliers : 4.19 % Allowed : 25.99 % 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: 1.80 (0.23), residues: 1413 helix: 2.26 (0.17), residues: 962 sheet: None (None), residues: 0 loop : -1.27 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP C 143 HIS 0.005 0.001 HIS A 451 PHE 0.022 0.001 PHE C 79 TYR 0.022 0.001 TYR C 364 ARG 0.009 0.001 ARG A 337 Details of bonding type rmsd hydrogen bonds : bond 0.03704 ( 736) hydrogen bonds : angle 3.94904 ( 2130) covalent geometry : bond 0.00241 ( 9049) covalent geometry : angle 0.57194 (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: 19 poor density : 156 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 247 LEU cc_start: 0.8185 (tt) cc_final: 0.7844 (tp) REVERT: B 255 LEU cc_start: 0.6850 (OUTLIER) cc_final: 0.6476 (tp) REVERT: B 272 GLU cc_start: 0.8111 (pm20) cc_final: 0.7851 (pm20) REVERT: B 353 ARG cc_start: 0.8064 (tpp80) cc_final: 0.7451 (tpp80) REVERT: C 38 HIS cc_start: 0.6106 (OUTLIER) cc_final: 0.5694 (p90) REVERT: C 251 PHE cc_start: 0.7581 (m-10) cc_final: 0.7336 (m-10) REVERT: C 346 LEU cc_start: 0.7804 (mp) cc_final: 0.7566 (mt) REVERT: C 383 PHE cc_start: 0.7987 (m-80) cc_final: 0.7689 (m-80) outliers start: 19 outliers final: 16 residues processed: 164 average time/residue: 0.1867 time to fit residues: 43.2534 Evaluate side-chains 169 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 151 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 TYR Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 332 TRP 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 143 TRP Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 218 TYR Chi-restraints excluded: chain C residue 451 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 55 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 chunk 114 optimal weight: 0.3980 chunk 71 optimal weight: 0.9980 chunk 136 optimal weight: 0.7980 chunk 139 optimal weight: 0.9980 chunk 108 optimal weight: 0.8980 chunk 69 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 37 optimal weight: 0.0980 chunk 77 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN C 145 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.139215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.115210 restraints weight = 20556.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.118494 restraints weight = 13357.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.120780 restraints weight = 9700.712| |-----------------------------------------------------------------------------| r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.7211 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= 0.195 Angle : 0.638 9.922 12501 Z= 0.351 Chirality : 0.044 0.170 1487 Planarity : 0.005 0.072 1699 Dihedral : 4.848 25.319 1481 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.37 % Favored : 93.49 % Rotamer: Outliers : 3.96 % Allowed : 26.65 % Favored : 69.38 % 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: 1.31 (0.23), residues: 1413 helix: 1.89 (0.17), residues: 961 sheet: None (None), residues: 0 loop : -1.45 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP C 143 HIS 0.012 0.001 HIS C 342 PHE 0.021 0.002 PHE C 79 TYR 0.024 0.002 TYR A 51 ARG 0.017 0.001 ARG C 353 Details of bonding type rmsd hydrogen bonds : bond 0.04341 ( 736) hydrogen bonds : angle 4.33462 ( 2130) covalent geometry : bond 0.00380 ( 9049) covalent geometry : angle 0.63792 (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 174 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 156 time to evaluate : 0.936 Fit side-chains revert: symmetry clash REVERT: A 439 ARG cc_start: 0.7239 (mtm-85) cc_final: 0.7001 (mtm-85) REVERT: B 255 LEU cc_start: 0.6989 (OUTLIER) cc_final: 0.6697 (tp) REVERT: B 272 GLU cc_start: 0.8102 (pm20) cc_final: 0.7816 (pm20) REVERT: B 353 ARG cc_start: 0.8092 (tpp80) cc_final: 0.7539 (tpp80) REVERT: C 38 HIS cc_start: 0.6068 (OUTLIER) cc_final: 0.5671 (p90) REVERT: C 383 PHE cc_start: 0.7951 (m-80) cc_final: 0.7660 (m-80) outliers start: 18 outliers final: 13 residues processed: 167 average time/residue: 0.1915 time to fit residues: 44.7798 Evaluate side-chains 167 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 152 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 332 TRP 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 451 HIS 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: 0.6980 chunk 129 optimal weight: 0.7980 chunk 113 optimal weight: 0.2980 chunk 109 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 93 optimal weight: 0.4980 chunk 49 optimal weight: 0.4980 chunk 125 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 GLN C 145 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.139515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.115491 restraints weight = 20603.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.118856 restraints weight = 13359.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.121180 restraints weight = 9674.268| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.7467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9049 Z= 0.182 Angle : 0.634 8.133 12501 Z= 0.345 Chirality : 0.044 0.167 1487 Planarity : 0.005 0.077 1699 Dihedral : 4.896 29.717 1481 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.16 % Favored : 93.70 % Rotamer: Outliers : 4.85 % Allowed : 27.75 % Favored : 67.40 % 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: 1.32 (0.23), residues: 1413 helix: 1.89 (0.17), residues: 956 sheet: None (None), residues: 0 loop : -1.38 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP C 143 HIS 0.005 0.001 HIS C 342 PHE 0.049 0.002 PHE C 79 TYR 0.036 0.002 TYR A 51 ARG 0.006 0.001 ARG B 353 Details of bonding type rmsd hydrogen bonds : bond 0.04239 ( 736) hydrogen bonds : angle 4.30159 ( 2130) covalent geometry : bond 0.00358 ( 9049) covalent geometry : angle 0.63356 (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 : 1.032 Fit side-chains REVERT: A 247 LEU cc_start: 0.6891 (tt) cc_final: 0.6585 (tp) REVERT: A 439 ARG cc_start: 0.7236 (mtm-85) cc_final: 0.7027 (mtm-85) REVERT: B 255 LEU cc_start: 0.7013 (OUTLIER) cc_final: 0.6717 (tp) REVERT: B 272 GLU cc_start: 0.8098 (pm20) cc_final: 0.7833 (pm20) REVERT: B 353 ARG cc_start: 0.8100 (tpp80) cc_final: 0.7582 (tpp80) REVERT: C 38 HIS cc_start: 0.6054 (OUTLIER) cc_final: 0.5645 (p90) REVERT: C 353 ARG cc_start: 0.7312 (mtm-85) cc_final: 0.7044 (ttp-110) REVERT: C 383 PHE cc_start: 0.7972 (m-80) cc_final: 0.7693 (m-80) outliers start: 22 outliers final: 18 residues processed: 162 average time/residue: 0.1936 time to fit residues: 44.4399 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 : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 TYR Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 332 TRP Chi-restraints excluded: chain B residue 453 GLN 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 143 TRP 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 461 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 47 optimal weight: 0.0670 chunk 58 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 138 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 5 optimal weight: 8.9990 chunk 6 optimal weight: 0.2980 chunk 116 optimal weight: 0.0570 chunk 118 optimal weight: 0.6980 chunk 22 optimal weight: 0.0060 overall best weight: 0.2252 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 145 HIS ** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 342 HIS ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.141981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.118162 restraints weight = 20472.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.121521 restraints weight = 13307.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.123838 restraints weight = 9631.978| |-----------------------------------------------------------------------------| r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6942 moved from start: 0.7558 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= 0.125 Angle : 0.596 9.560 12501 Z= 0.312 Chirality : 0.042 0.166 1487 Planarity : 0.005 0.072 1699 Dihedral : 4.587 27.539 1481 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.23 % Favored : 93.63 % Rotamer: Outliers : 3.52 % Allowed : 29.07 % Favored : 67.40 % 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: 1.65 (0.24), residues: 1413 helix: 2.15 (0.17), residues: 969 sheet: None (None), residues: 0 loop : -1.41 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP C 143 HIS 0.005 0.001 HIS B 39 PHE 0.051 0.001 PHE C 79 TYR 0.034 0.002 TYR A 51 ARG 0.013 0.001 ARG A 497 Details of bonding type rmsd hydrogen bonds : bond 0.03749 ( 736) hydrogen bonds : angle 4.02743 ( 2130) covalent geometry : bond 0.00243 ( 9049) covalent geometry : angle 0.59552 (12501) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3623.03 seconds wall clock time: 63 minutes 25.50 seconds (3805.50 seconds total)