Starting phenix.real_space_refine on Fri Oct 10 20:09:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kbz_37088/10_2025/8kbz_37088.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kbz_37088/10_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 { model { file = "/net/cci-nas-00/data/ceres_data/8kbz_37088/10_2025/8kbz_37088.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kbz_37088/10_2025/8kbz_37088.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8kbz_37088/10_2025/8kbz_37088.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kbz_37088/10_2025/8kbz_37088.map" } resolution = 3.97 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: {'HIS:plan': 6, 'GLU:plan': 22, 'PHE:plan': 22, 'ASN:plan1': 6, 'GLN:plan1': 10, 'TYR:plan': 8, 'ASP:plan': 7, 'ARG:plan': 18, 'TRP:plan': 3} 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: {'GLU:plan': 22, 'ASP:plan': 7, 'ARG:plan': 17, 'ASN:plan1': 9, 'PHE:plan': 22, 'GLN:plan1': 14, 'TYR:plan': 9, 'TRP:plan': 3, 'HIS:plan': 10} 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: {'HIS:plan': 5, 'GLU:plan': 24, 'ASN:plan1': 10, 'ASP:plan': 6, 'PHE:plan': 20, 'GLN:plan1': 17, 'TYR:plan': 5, 'ARG:plan': 22, 'TRP:plan': 3} Unresolved non-hydrogen planarities: 529 Time building chain proxies: 2.12, per 1000 atoms: 0.24 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: 0.96 Conformation dependent library (CDL) restraints added in 429.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.29 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: 1.38 Time building geometry restraints manager: 1.23 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: 20.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.350 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.110 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.001 ARG B 495 TYR 0.017 0.003 TYR C 177 PHE 0.020 0.002 PHE A 368 TRP 0.019 0.003 TRP B 257 HIS 0.008 0.002 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00995 ( 9049) covalent geometry : angle 1.38974 (12501) hydrogen bonds : bond 0.17216 ( 736) hydrogen bonds : angle 7.08406 ( 2130) *********************** 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 : 0.271 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: 0.0877 time to fit residues: 22.9614 Evaluate side-chains 155 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 152 time to evaluate : 0.275 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.3980 chunk 10 optimal weight: 0.0980 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.1980 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.3980 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.2980 overall best weight: 0.2780 ------------------------------------------------------------------------------- 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 ** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.154794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.129472 restraints weight = 20561.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.133136 restraints weight = 13556.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.135706 restraints weight = 9872.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.137549 restraints weight = 7745.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.138832 restraints weight = 6449.408| |-----------------------------------------------------------------------------| r_work (final): 0.4003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6561 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9049 Z= 0.156 Angle : 0.627 9.998 12501 Z= 0.347 Chirality : 0.043 0.170 1487 Planarity : 0.006 0.074 1699 Dihedral : 5.641 47.077 1488 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.18 % Favored : 95.68 % Rotamer: Outliers : 2.42 % Allowed : 19.82 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.22), residues: 1413 helix: 0.97 (0.17), residues: 959 sheet: None (None), residues: 0 loop : -1.80 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 353 TYR 0.018 0.002 TYR A 51 PHE 0.038 0.002 PHE C 383 TRP 0.026 0.002 TRP B 267 HIS 0.015 0.002 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 9049) covalent geometry : angle 0.62742 (12501) hydrogen bonds : bond 0.04536 ( 736) hydrogen bonds : angle 4.42906 ( 2130) *********************** 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 169 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 158 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 68 PHE cc_start: 0.8065 (m-80) cc_final: 0.7847 (m-80) REVERT: C 179 THR cc_start: 0.8379 (m) cc_final: 0.8152 (p) REVERT: C 446 HIS cc_start: 0.7431 (m90) cc_final: 0.7171 (m90) outliers start: 11 outliers final: 8 residues processed: 164 average time/residue: 0.1015 time to fit residues: 22.9038 Evaluate side-chains 161 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 153 time to evaluate : 0.258 ------------------------------------------------------------------------------- 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 292 TRP 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 106 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 86 optimal weight: 0.1980 chunk 56 optimal weight: 0.6980 chunk 87 optimal weight: 0.0770 chunk 85 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 37 optimal weight: 0.0980 chunk 80 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 overall best weight: 0.3538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN A 467 GLN B 216 GLN C 145 HIS C 210 HIS C 342 HIS C 348 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.149710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.124878 restraints weight = 20311.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.128375 restraints weight = 13328.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.130880 restraints weight = 9711.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.132577 restraints weight = 7638.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.133847 restraints weight = 6403.517| |-----------------------------------------------------------------------------| r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6697 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9049 Z= 0.167 Angle : 0.610 9.172 12501 Z= 0.332 Chirality : 0.042 0.154 1487 Planarity : 0.005 0.049 1699 Dihedral : 4.962 29.010 1481 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.95 % Favored : 94.98 % Rotamer: Outliers : 4.85 % Allowed : 19.16 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.23), residues: 1413 helix: 1.73 (0.17), residues: 951 sheet: None (None), residues: 0 loop : -1.54 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 495 TYR 0.022 0.002 TYR A 51 PHE 0.038 0.002 PHE C 383 TRP 0.022 0.002 TRP B 267 HIS 0.018 0.002 HIS B 39 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 9049) covalent geometry : angle 0.60972 (12501) hydrogen bonds : bond 0.04223 ( 736) hydrogen bonds : angle 4.26497 ( 2130) *********************** 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 170 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 351 GLN cc_start: 0.8238 (tp40) cc_final: 0.8029 (tp40) REVERT: B 519 CYS cc_start: 0.7100 (t) cc_final: 0.6641 (t) REVERT: C 243 PHE cc_start: 0.7922 (t80) cc_final: 0.7715 (t80) outliers start: 22 outliers final: 9 residues processed: 158 average time/residue: 0.0899 time to fit residues: 19.8926 Evaluate side-chains 155 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 146 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 223 VAL 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 135 optimal weight: 0.0040 chunk 62 optimal weight: 0.0370 chunk 20 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 49 optimal weight: 0.4980 chunk 23 optimal weight: 0.6980 chunk 122 optimal weight: 0.1980 chunk 7 optimal weight: 0.0670 chunk 10 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.1608 ------------------------------------------------------------------------------- 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 ** B 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 HIS C 181 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.150321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.125808 restraints weight = 20364.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.129300 restraints weight = 13322.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.131768 restraints weight = 9654.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.133477 restraints weight = 7564.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.134727 restraints weight = 6307.491| |-----------------------------------------------------------------------------| r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6660 moved from start: 0.4330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9049 Z= 0.116 Angle : 0.555 7.535 12501 Z= 0.295 Chirality : 0.041 0.146 1487 Planarity : 0.004 0.052 1699 Dihedral : 4.548 26.891 1481 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.82 % Favored : 96.11 % Rotamer: Outliers : 2.86 % Allowed : 22.91 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.61 (0.23), residues: 1413 helix: 2.12 (0.17), residues: 953 sheet: None (None), residues: 0 loop : -1.28 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 337 TYR 0.022 0.001 TYR A 51 PHE 0.034 0.001 PHE C 383 TRP 0.012 0.001 TRP B 267 HIS 0.007 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 9049) covalent geometry : angle 0.55497 (12501) hydrogen bonds : bond 0.03606 ( 736) hydrogen bonds : angle 3.95812 ( 2130) *********************** 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 166 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 153 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 406 HIS cc_start: 0.8349 (m90) cc_final: 0.7949 (m-70) REVERT: B 465 PHE cc_start: 0.7202 (t80) cc_final: 0.6755 (t80) REVERT: B 519 CYS cc_start: 0.6808 (t) cc_final: 0.6398 (t) REVERT: C 353 ARG cc_start: 0.7216 (mtm-85) cc_final: 0.6997 (ttm110) outliers start: 13 outliers final: 7 residues processed: 155 average time/residue: 0.0938 time to fit residues: 19.8327 Evaluate side-chains 156 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 149 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain B residue 220 VAL 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 183 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 114 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 93 optimal weight: 0.4980 chunk 49 optimal weight: 0.5980 chunk 34 optimal weight: 4.9990 chunk 113 optimal weight: 0.4980 chunk 104 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 117 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.139579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.115267 restraints weight = 20524.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.118545 restraints weight = 13383.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.120885 restraints weight = 9755.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.122553 restraints weight = 7698.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.123728 restraints weight = 6466.629| |-----------------------------------------------------------------------------| r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.5758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9049 Z= 0.253 Angle : 0.715 7.767 12501 Z= 0.404 Chirality : 0.046 0.172 1487 Planarity : 0.006 0.056 1699 Dihedral : 5.318 27.747 1481 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.37 % Favored : 93.56 % Rotamer: Outliers : 5.29 % Allowed : 19.38 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.23), residues: 1413 helix: 1.40 (0.17), residues: 976 sheet: None (None), residues: 0 loop : -1.41 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 497 TYR 0.033 0.003 TYR A 164 PHE 0.032 0.003 PHE A 47 TRP 0.016 0.002 TRP B 292 HIS 0.007 0.002 HIS A 39 Details of bonding type rmsd covalent geometry : bond 0.00487 ( 9049) covalent geometry : angle 0.71548 (12501) hydrogen bonds : bond 0.05029 ( 736) hydrogen bonds : angle 4.80770 ( 2130) *********************** 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 177 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 153 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: B 267 TRP cc_start: 0.7588 (p-90) cc_final: 0.7385 (p-90) REVERT: B 465 PHE cc_start: 0.7510 (t80) cc_final: 0.7115 (t80) REVERT: C 68 PHE cc_start: 0.8254 (m-80) cc_final: 0.8049 (m-80) REVERT: C 353 ARG cc_start: 0.7502 (mtm-85) cc_final: 0.7247 (mtm-85) outliers start: 24 outliers final: 12 residues processed: 165 average time/residue: 0.0816 time to fit residues: 19.0881 Evaluate side-chains 163 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 151 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 313 PHE 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 114 ASP Chi-restraints excluded: chain C residue 489 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 64 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 96 optimal weight: 0.5980 chunk 45 optimal weight: 0.0000 chunk 98 optimal weight: 0.8980 chunk 97 optimal weight: 0.5980 chunk 57 optimal weight: 0.6980 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN A 224 ASN ** B 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 GLN B 250 ASN C 145 HIS ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 366 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.140553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.115912 restraints weight = 20639.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.119271 restraints weight = 13506.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.121623 restraints weight = 9840.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.123272 restraints weight = 7774.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.124339 restraints weight = 6548.720| |-----------------------------------------------------------------------------| r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6941 moved from start: 0.6206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9049 Z= 0.187 Angle : 0.619 8.713 12501 Z= 0.342 Chirality : 0.044 0.159 1487 Planarity : 0.005 0.068 1699 Dihedral : 5.010 28.038 1481 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.45 % Favored : 94.41 % Rotamer: Outliers : 4.19 % Allowed : 22.69 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.23), residues: 1413 helix: 1.72 (0.17), residues: 960 sheet: None (None), residues: 0 loop : -1.33 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 337 TYR 0.029 0.002 TYR A 51 PHE 0.036 0.002 PHE C 383 TRP 0.013 0.002 TRP B 257 HIS 0.014 0.001 HIS B 39 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 9049) covalent geometry : angle 0.61889 (12501) hydrogen bonds : bond 0.04303 ( 736) hydrogen bonds : angle 4.40500 ( 2130) *********************** 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 173 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 154 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 247 LEU cc_start: 0.8315 (tp) cc_final: 0.8044 (tt) REVERT: B 267 TRP cc_start: 0.7609 (p-90) cc_final: 0.7298 (p-90) REVERT: B 465 PHE cc_start: 0.7410 (t80) cc_final: 0.6912 (t80) REVERT: C 38 HIS cc_start: 0.6159 (OUTLIER) cc_final: 0.5735 (p90) REVERT: C 342 HIS cc_start: 0.7167 (m90) cc_final: 0.6862 (m90) outliers start: 19 outliers final: 11 residues processed: 163 average time/residue: 0.0841 time to fit residues: 19.5384 Evaluate side-chains 159 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 147 time to evaluate : 0.318 ------------------------------------------------------------------------------- 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 220 VAL Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 342 HIS Chi-restraints excluded: chain B residue 469 PHE Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 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 86 optimal weight: 0.6980 chunk 92 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 22 optimal weight: 0.0980 chunk 75 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 chunk 58 optimal weight: 0.0970 chunk 80 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 90 optimal weight: 0.1980 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN B 55 GLN B 467 GLN C 145 HIS C 344 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.141690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.117526 restraints weight = 20656.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.120829 restraints weight = 13553.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.123144 restraints weight = 9890.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.124798 restraints weight = 7819.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.125961 restraints weight = 6560.295| |-----------------------------------------------------------------------------| r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.6597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9049 Z= 0.149 Angle : 0.595 8.578 12501 Z= 0.322 Chirality : 0.043 0.158 1487 Planarity : 0.005 0.072 1699 Dihedral : 4.721 26.461 1481 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.23 % Favored : 93.63 % Rotamer: Outliers : 4.85 % Allowed : 22.91 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.48 (0.23), residues: 1413 helix: 1.99 (0.17), residues: 962 sheet: None (None), residues: 0 loop : -1.32 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 337 TYR 0.021 0.002 TYR A 51 PHE 0.037 0.002 PHE C 383 TRP 0.014 0.001 TRP C 143 HIS 0.004 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 9049) covalent geometry : angle 0.59505 (12501) hydrogen bonds : bond 0.03935 ( 736) hydrogen bonds : angle 4.17896 ( 2130) *********************** 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 175 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 153 time to evaluate : 0.383 Fit side-chains REVERT: A 299 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8575 (tp) REVERT: B 255 LEU cc_start: 0.6776 (OUTLIER) cc_final: 0.6436 (tp) REVERT: B 267 TRP cc_start: 0.7543 (p-90) cc_final: 0.7277 (p-90) REVERT: B 465 PHE cc_start: 0.7272 (t80) cc_final: 0.6790 (t80) REVERT: C 38 HIS cc_start: 0.6040 (OUTLIER) cc_final: 0.5660 (p90) REVERT: C 143 TRP cc_start: 0.7658 (t60) cc_final: 0.6790 (t60) outliers start: 22 outliers final: 11 residues processed: 164 average time/residue: 0.0902 time to fit residues: 21.2987 Evaluate side-chains 165 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 151 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 TYR Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 299 LEU 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 255 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 218 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 86 optimal weight: 0.0980 chunk 10 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 108 optimal weight: 0.8980 chunk 16 optimal weight: 0.0270 chunk 134 optimal weight: 0.4980 chunk 129 optimal weight: 0.9980 chunk 133 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 123 optimal weight: 0.0980 chunk 114 optimal weight: 0.0570 overall best weight: 0.1556 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.143911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.119673 restraints weight = 20523.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.123145 restraints weight = 13194.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.125568 restraints weight = 9490.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.127279 restraints weight = 7424.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.128469 restraints weight = 6197.088| |-----------------------------------------------------------------------------| r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6853 moved from start: 0.6744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9049 Z= 0.116 Angle : 0.568 9.152 12501 Z= 0.300 Chirality : 0.042 0.151 1487 Planarity : 0.005 0.068 1699 Dihedral : 4.508 27.010 1481 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.02 % Favored : 94.83 % Rotamer: Outliers : 2.20 % Allowed : 27.09 % Favored : 70.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.75 (0.23), residues: 1413 helix: 2.24 (0.17), residues: 960 sheet: None (None), residues: 0 loop : -1.32 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 337 TYR 0.034 0.002 TYR A 51 PHE 0.038 0.001 PHE C 383 TRP 0.013 0.001 TRP A 267 HIS 0.006 0.001 HIS B 39 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 9049) covalent geometry : angle 0.56810 (12501) hydrogen bonds : bond 0.03562 ( 736) hydrogen bonds : angle 3.94387 ( 2130) *********************** 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 163 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 153 time to evaluate : 0.362 Fit side-chains REVERT: B 267 TRP cc_start: 0.7502 (p-90) cc_final: 0.7177 (p-90) REVERT: B 465 PHE cc_start: 0.7194 (t80) cc_final: 0.6670 (t80) REVERT: C 143 TRP cc_start: 0.7547 (t60) cc_final: 0.6658 (t60) outliers start: 10 outliers final: 10 residues processed: 158 average time/residue: 0.0880 time to fit residues: 19.7777 Evaluate side-chains 158 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 148 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 TYR 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 60 THR Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 218 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 88 optimal weight: 0.0770 chunk 133 optimal weight: 0.8980 chunk 92 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 chunk 63 optimal weight: 0.5980 chunk 125 optimal weight: 0.2980 chunk 84 optimal weight: 0.5980 chunk 115 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 342 HIS C 145 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.140514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.116652 restraints weight = 20513.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.119956 restraints weight = 13305.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.122251 restraints weight = 9651.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.123854 restraints weight = 7608.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.124989 restraints weight = 6395.235| |-----------------------------------------------------------------------------| r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 moved from start: 0.7071 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= 0.169 Angle : 0.614 8.149 12501 Z= 0.336 Chirality : 0.043 0.153 1487 Planarity : 0.005 0.074 1699 Dihedral : 4.696 25.720 1481 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.37 % Favored : 93.49 % Rotamer: Outliers : 3.52 % Allowed : 26.65 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.45 (0.23), residues: 1413 helix: 1.99 (0.17), residues: 970 sheet: None (None), residues: 0 loop : -1.45 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 439 TYR 0.032 0.002 TYR A 51 PHE 0.044 0.002 PHE C 79 TRP 0.013 0.001 TRP C 143 HIS 0.005 0.001 HIS B 39 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 9049) covalent geometry : angle 0.61428 (12501) hydrogen bonds : bond 0.04065 ( 736) hydrogen bonds : angle 4.22022 ( 2130) *********************** 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 176 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 160 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: B 255 LEU cc_start: 0.6912 (OUTLIER) cc_final: 0.6620 (tp) REVERT: B 267 TRP cc_start: 0.7590 (p-90) cc_final: 0.7341 (p-90) REVERT: B 465 PHE cc_start: 0.7287 (t80) cc_final: 0.6811 (t80) REVERT: C 38 HIS cc_start: 0.5828 (OUTLIER) cc_final: 0.5456 (p90) REVERT: C 143 TRP cc_start: 0.7685 (t60) cc_final: 0.6937 (t60) outliers start: 16 outliers final: 14 residues processed: 168 average time/residue: 0.0875 time to fit residues: 20.9837 Evaluate side-chains 173 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 157 time to evaluate : 0.374 ------------------------------------------------------------------------------- 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 315 SER 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 183 VAL Chi-restraints excluded: chain C residue 264 LEU 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 83 optimal weight: 0.9990 chunk 138 optimal weight: 0.0970 chunk 43 optimal weight: 0.0670 chunk 30 optimal weight: 0.9980 chunk 5 optimal weight: 6.9990 chunk 132 optimal weight: 0.0030 chunk 50 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 65 optimal weight: 0.0050 chunk 69 optimal weight: 0.0980 chunk 103 optimal weight: 0.9990 overall best weight: 0.0540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN A 224 ASN C 210 HIS C 344 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.145355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.121055 restraints weight = 20543.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.124619 restraints weight = 13194.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.126990 restraints weight = 9464.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.128796 restraints weight = 7424.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.130072 restraints weight = 6173.871| |-----------------------------------------------------------------------------| r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6828 moved from start: 0.7122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9049 Z= 0.117 Angle : 0.585 10.229 12501 Z= 0.304 Chirality : 0.042 0.146 1487 Planarity : 0.004 0.071 1699 Dihedral : 4.399 27.137 1481 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.74 % Favored : 95.12 % Rotamer: Outliers : 2.86 % Allowed : 28.19 % Favored : 68.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.78 (0.23), residues: 1413 helix: 2.31 (0.17), residues: 961 sheet: None (None), residues: 0 loop : -1.45 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 337 TYR 0.034 0.002 TYR A 51 PHE 0.046 0.001 PHE C 79 TRP 0.016 0.001 TRP A 267 HIS 0.006 0.001 HIS B 39 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 9049) covalent geometry : angle 0.58527 (12501) hydrogen bonds : bond 0.03403 ( 736) hydrogen bonds : angle 3.89903 ( 2130) ********************** 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 170 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 157 time to evaluate : 0.350 Fit side-chains REVERT: A 210 HIS cc_start: 0.6563 (m90) cc_final: 0.6351 (m90) REVERT: B 267 TRP cc_start: 0.7490 (p-90) cc_final: 0.7236 (p-90) REVERT: B 334 LEU cc_start: 0.8399 (mp) cc_final: 0.8166 (tt) REVERT: B 342 HIS cc_start: 0.8166 (t70) cc_final: 0.7801 (t70) REVERT: B 453 GLN cc_start: 0.7777 (pt0) cc_final: 0.7575 (pm20) REVERT: C 143 TRP cc_start: 0.7449 (t60) cc_final: 0.6637 (t60) REVERT: C 353 ARG cc_start: 0.7251 (mtm-85) cc_final: 0.6833 (mmm-85) outliers start: 13 outliers final: 11 residues processed: 163 average time/residue: 0.0848 time to fit residues: 19.9329 Evaluate side-chains 163 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 152 time to evaluate : 0.346 ------------------------------------------------------------------------------- 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 374 THR Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 332 TRP 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 218 TYR Chi-restraints excluded: chain C residue 264 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 0.2980 chunk 18 optimal weight: 0.0000 chunk 31 optimal weight: 0.1980 chunk 115 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 117 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 90 optimal weight: 0.4980 chunk 44 optimal weight: 0.8980 chunk 66 optimal weight: 0.0670 chunk 116 optimal weight: 0.6980 overall best weight: 0.2122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 145 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.143697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.119539 restraints weight = 20364.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.122924 restraints weight = 13343.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.125184 restraints weight = 9710.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.126872 restraints weight = 7705.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.127902 restraints weight = 6491.448| |-----------------------------------------------------------------------------| r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 moved from start: 0.7278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9049 Z= 0.121 Angle : 0.589 10.843 12501 Z= 0.308 Chirality : 0.042 0.162 1487 Planarity : 0.005 0.064 1699 Dihedral : 4.310 25.065 1481 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.80 % Favored : 94.06 % Rotamer: Outliers : 1.98 % Allowed : 28.85 % Favored : 69.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.81 (0.23), residues: 1413 helix: 2.30 (0.17), residues: 968 sheet: None (None), residues: 0 loop : -1.39 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 497 TYR 0.032 0.001 TYR A 51 PHE 0.049 0.002 PHE C 79 TRP 0.016 0.001 TRP A 267 HIS 0.005 0.001 HIS B 39 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 9049) covalent geometry : angle 0.58943 (12501) hydrogen bonds : bond 0.03502 ( 736) hydrogen bonds : angle 3.90967 ( 2130) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1870.51 seconds wall clock time: 32 minutes 54.72 seconds (1974.72 seconds total)