Starting phenix.real_space_refine on Fri Nov 15 19:25:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hco_34660/11_2024/8hco_34660_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hco_34660/11_2024/8hco_34660.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hco_34660/11_2024/8hco_34660.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hco_34660/11_2024/8hco_34660.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hco_34660/11_2024/8hco_34660_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hco_34660/11_2024/8hco_34660_neut.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 69 atoms to isotropic. 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 29 5.16 5 C 5966 2.51 5 N 1568 2.21 5 O 1767 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 9330 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2507 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 314} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 387 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 1, 'TRANS': 48} Chain: "C" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 303 Classifications: {'peptide': 37} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 35} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 267 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 3, 'TRANS': 31} Chain: "E" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 295 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 4, 'TRANS': 31} Chain: "G" Number of atoms: 458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 458 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 4, 'TRANS': 56} Chain: "G" Number of atoms: 1333 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 163, 1332 Unusual residues: {'GYS': 1} Classifications: {'peptide': 162, 'undetermined': 1} Link IDs: {'PTRANS': 6, 'TRANS': 155, None: 1} Not linked: pdbres="GYS G 344 " pdbres="VAL G 346 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'GYS:plan-3': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 163, 1332 Unusual residues: {'GYS': 1} Classifications: {'peptide': 162, 'undetermined': 1} Link IDs: {'PTRANS': 6, 'TRANS': 155, None: 1} Not linked: pdbres="GYS G 344 " pdbres="VAL G 346 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'GYS:plan-3': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1361 Chain: "I" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2528 Classifications: {'peptide': 329} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 316} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 387 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 1, 'TRANS': 48} Chain: "K" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 303 Classifications: {'peptide': 37} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 35} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "L" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 267 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 3, 'TRANS': 31} Chain: "M" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 295 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 4, 'TRANS': 31} Time building chain proxies: 6.59, per 1000 atoms: 0.71 Number of scatterers: 9330 At special positions: 0 Unit cell: (98.44, 133.75, 120.91, 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 29 16.00 O 1767 8.00 N 1568 7.00 C 5966 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 additional links: simple=2, symmetry=0 Simple link: pdb=" C GYS G 344 " - pdb=" N VAL G 346 " Simple link: pdb=" C PHE G 342 " - pdb=" N GYS G 344 " Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.60 Conformation dependent library (CDL) restraints added in 1.1 seconds 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2212 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 4 sheets defined 26.0% alpha, 35.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 49 through 56 removed outlier: 4.378A pdb=" N GLN A 53 " --> pdb=" O HIS A 49 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER A 54 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLU A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 72 Processing helix chain 'A' and resid 133 through 135 No H-bonds generated for 'chain 'A' and resid 133 through 135' Processing helix chain 'A' and resid 364 through 372 removed outlier: 3.672A pdb=" N GLN A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 135 Proline residue: B 112 - end of helix Processing helix chain 'C' and resid 14 through 48 Proline residue: C 39 - end of helix Processing helix chain 'D' and resid 30 through 50 Processing helix chain 'D' and resid 51 through 58 removed outlier: 3.588A pdb=" N ASP D 55 " --> pdb=" O SER D 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 42 removed outlier: 3.848A pdb=" N TRP E 32 " --> pdb=" O ALA E 28 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ILE E 33 " --> pdb=" O HIS E 29 " (cutoff:3.500A) Proline residue: E 34 - end of helix Processing helix chain 'E' and resid 49 through 55 Processing helix chain 'G' and resid 334 through 340 removed outlier: 4.840A pdb=" N THR G 340 " --> pdb=" O PRO G 336 " (cutoff:3.500A) Processing helix chain 'I' and resid 364 through 372 removed outlier: 3.651A pdb=" N GLN I 372 " --> pdb=" O LEU I 368 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 135 Proline residue: J 112 - end of helix Processing helix chain 'K' and resid 14 through 48 Proline residue: K 39 - end of helix Processing helix chain 'L' and resid 30 through 50 Processing helix chain 'L' and resid 51 through 58 removed outlier: 3.786A pdb=" N ASP L 55 " --> pdb=" O SER L 51 " (cutoff:3.500A) Processing helix chain 'M' and resid 31 through 43 removed outlier: 3.552A pdb=" N PHE M 35 " --> pdb=" O GLY M 31 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N HIS M 43 " --> pdb=" O LEU M 39 " (cutoff:3.500A) Processing helix chain 'M' and resid 49 through 55 Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 93 removed outlier: 6.067A pdb=" N PHE A 98 " --> pdb=" O PHE A 92 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N CYS A 165 " --> pdb=" O ASN A 184 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N THR A 194 " --> pdb=" O PRO A 185 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU A 255 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU A 275 " --> pdb=" O LEU A 255 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ASP A 319 " --> pdb=" O LYS A 323 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LYS A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 290 through 300 removed outlier: 3.604A pdb=" N VAL G 290 " --> pdb=" O GLY G 313 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY G 313 " --> pdb=" O VAL G 290 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL G 294 " --> pdb=" O GLY G 309 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLY G 309 " --> pdb=" O VAL G 294 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU G 296 " --> pdb=" O VAL G 307 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL G 307 " --> pdb=" O LEU G 296 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLY G 298 " --> pdb=" O PHE G 305 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE G 305 " --> pdb=" O GLY G 298 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG G 308 " --> pdb=" O ILE G 325 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS G 323 " --> pdb=" O GLU G 310 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL G 497 " --> pdb=" O SER G 486 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER G 486 " --> pdb=" O VAL G 497 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR G 478 " --> pdb=" O ALA G 505 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ASN G 427 " --> pdb=" O LYS G 444 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N LYS G 444 " --> pdb=" O ASN G 427 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N TYR G 429 " --> pdb=" O ASN G 442 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE G 439 " --> pdb=" O ASN G 463 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE G 443 " --> pdb=" O HIS G 459 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA G 457 " --> pdb=" O ILE G 445 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N HIS G 447 " --> pdb=" O GLN G 455 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP G 458 " --> pdb=" O SER G 377 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE G 406 " --> pdb=" O THR G 383 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS G 391 " --> pdb=" O VAL G 398 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N ASN G 399 " --> pdb=" O PRO G 291 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N LEU G 293 " --> pdb=" O ASN G 399 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N ILE G 401 " --> pdb=" O LEU G 293 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N GLU G 295 " --> pdb=" O ILE G 401 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N LEU G 403 " --> pdb=" O GLU G 295 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ASP G 297 " --> pdb=" O LEU G 403 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N GLY G 405 " --> pdb=" O ASP G 297 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ASP G 299 " --> pdb=" O GLY G 405 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 85 through 91 removed outlier: 3.773A pdb=" N ALA I 257 " --> pdb=" O THR I 273 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 279 through 281 549 hydrogen bonds defined for protein. 1584 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: 3.08 Time building geometry restraints manager: 2.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1874 1.33 - 1.45: 2305 1.45 - 1.57: 5309 1.57 - 1.69: 1 1.69 - 1.81: 48 Bond restraints: 9537 Sorted by residual: bond pdb=" CB1 GYS G 344 " pdb=" OG1BGYS G 344 " ideal model delta sigma weight residual 1.408 1.611 -0.203 2.00e-02 2.50e+03 1.04e+02 bond pdb=" N VAL G 339 " pdb=" CA VAL G 339 " ideal model delta sigma weight residual 1.461 1.503 -0.042 1.17e-02 7.31e+03 1.26e+01 bond pdb=" N THR G 340 " pdb=" CA THR G 340 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.05e+01 bond pdb=" N MET G 366 " pdb=" CA MET G 366 " ideal model delta sigma weight residual 1.459 1.493 -0.033 1.04e-02 9.25e+03 1.03e+01 bond pdb=" N ASN I 95 " pdb=" CA ASN I 95 " ideal model delta sigma weight residual 1.461 1.490 -0.029 9.20e-03 1.18e+04 9.94e+00 ... (remaining 9532 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 12595 2.55 - 5.10: 295 5.10 - 7.65: 36 7.65 - 10.20: 10 10.20 - 12.75: 2 Bond angle restraints: 12938 Sorted by residual: angle pdb=" N VAL G 339 " pdb=" CA VAL G 339 " pdb=" C VAL G 339 " ideal model delta sigma weight residual 110.42 116.05 -5.63 9.60e-01 1.09e+00 3.44e+01 angle pdb=" C LYS G 436 " pdb=" N ASN G 437 " pdb=" CA ASN G 437 " ideal model delta sigma weight residual 121.54 131.47 -9.93 1.91e+00 2.74e-01 2.70e+01 angle pdb=" N PRO I 96 " pdb=" CA PRO I 96 " pdb=" C PRO I 96 " ideal model delta sigma weight residual 112.47 102.27 10.20 2.06e+00 2.36e-01 2.45e+01 angle pdb=" C ASN A 133 " pdb=" N ASP A 134 " pdb=" CA ASP A 134 " ideal model delta sigma weight residual 121.54 130.26 -8.72 1.91e+00 2.74e-01 2.08e+01 angle pdb=" CA VAL G 339 " pdb=" C VAL G 339 " pdb=" O VAL G 339 " ideal model delta sigma weight residual 121.17 116.63 4.54 1.06e+00 8.90e-01 1.84e+01 ... (remaining 12933 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 5007 17.86 - 35.73: 448 35.73 - 53.59: 124 53.59 - 71.45: 35 71.45 - 89.31: 5 Dihedral angle restraints: 5619 sinusoidal: 2192 harmonic: 3427 Sorted by residual: dihedral pdb=" CA THR G 316 " pdb=" C THR G 316 " pdb=" N ASN G 317 " pdb=" CA ASN G 317 " ideal model delta harmonic sigma weight residual 180.00 155.87 24.13 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA ASN A 95 " pdb=" C ASN A 95 " pdb=" N PRO A 96 " pdb=" CA PRO A 96 " ideal model delta harmonic sigma weight residual 180.00 156.97 23.03 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA ASN A 133 " pdb=" C ASN A 133 " pdb=" N ASP A 134 " pdb=" CA ASP A 134 " ideal model delta harmonic sigma weight residual -180.00 -159.42 -20.58 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 5616 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1081 0.058 - 0.117: 274 0.117 - 0.175: 76 0.175 - 0.233: 14 0.233 - 0.292: 5 Chirality restraints: 1450 Sorted by residual: chirality pdb=" CB ILE I 106 " pdb=" CA ILE I 106 " pdb=" CG1 ILE I 106 " pdb=" CG2 ILE I 106 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CB ILE I 150 " pdb=" CA ILE I 150 " pdb=" CG1 ILE I 150 " pdb=" CG2 ILE I 150 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" CA PHE I 98 " pdb=" N PHE I 98 " pdb=" C PHE I 98 " pdb=" CB PHE I 98 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 1447 not shown) Planarity restraints: 1668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB2 GYS G 344 " -0.013 2.00e-02 2.50e+03 8.89e-02 1.97e+02 pdb=" CG2 GYS G 344 " -0.141 2.00e-02 2.50e+03 pdb=" C1 GYS G 344 " 0.043 2.00e-02 2.50e+03 pdb=" C2 GYS G 344 " 0.065 2.00e-02 2.50e+03 pdb=" CA1 GYS G 344 " -0.024 2.00e-02 2.50e+03 pdb=" CA2 GYS G 344 " 0.088 2.00e-02 2.50e+03 pdb=" CA3 GYS G 344 " -0.186 2.00e-02 2.50e+03 pdb=" N2 GYS G 344 " 0.072 2.00e-02 2.50e+03 pdb=" N3 GYS G 344 " 0.055 2.00e-02 2.50e+03 pdb=" O2 GYS G 344 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR G 337 " 0.024 2.00e-02 2.50e+03 4.88e-02 2.38e+01 pdb=" C THR G 337 " -0.084 2.00e-02 2.50e+03 pdb=" O THR G 337 " 0.031 2.00e-02 2.50e+03 pdb=" N LEU G 338 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB2 GYS G 344 " 0.028 2.00e-02 2.50e+03 2.40e-02 1.15e+01 pdb=" CG2 GYS G 344 " 0.007 2.00e-02 2.50e+03 pdb=" CD1 GYS G 344 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 GYS G 344 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 GYS G 344 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 GYS G 344 " -0.025 2.00e-02 2.50e+03 pdb=" CZ GYS G 344 " -0.023 2.00e-02 2.50e+03 pdb=" OH GYS G 344 " 0.046 2.00e-02 2.50e+03 ... (remaining 1665 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2538 2.81 - 3.33: 7157 3.33 - 3.86: 15881 3.86 - 4.38: 16820 4.38 - 4.90: 30151 Nonbonded interactions: 72547 Sorted by model distance: nonbonded pdb=" OG1 THR G 383 " pdb=" NZ LYS G 385 " model vdw 2.290 3.120 nonbonded pdb=" O ALA B 99 " pdb=" OG1 THR B 103 " model vdw 2.363 3.040 nonbonded pdb=" O ALA J 99 " pdb=" OG1 THR J 103 " model vdw 2.365 3.040 nonbonded pdb=" OG SER A 238 " pdb=" O TRP A 243 " model vdw 2.367 3.040 nonbonded pdb=" O GLN C 20 " pdb=" OG1 THR C 24 " model vdw 2.380 3.040 ... (remaining 72542 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' selection = (chain 'I' and (resid 49 through 282 or resid 291 through 382)) } ncs_group { reference = chain 'B' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'L' } ncs_group { reference = chain 'E' selection = chain 'M' } 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=0.00 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: 1.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.060 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6545 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 : 0.007 0.203 9537 Z= 0.425 Angle : 0.965 12.753 12938 Z= 0.561 Chirality : 0.060 0.292 1450 Planarity : 0.008 0.089 1667 Dihedral : 15.439 89.313 3405 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 10.99 % Allowed : 13.76 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.21), residues: 1166 helix: -2.53 (0.18), residues: 308 sheet: -0.53 (0.22), residues: 479 loop : -1.83 (0.27), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 42 HIS 0.004 0.001 HIS M 29 PHE 0.028 0.003 PHE G 342 TYR 0.014 0.002 TYR M 30 ARG 0.003 0.000 ARG A 315 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 383 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8022 (ttm-80) cc_final: 0.7142 (ttm-80) REVERT: A 69 GLU cc_start: 0.8313 (mp0) cc_final: 0.7725 (mp0) REVERT: A 120 PHE cc_start: 0.8599 (t80) cc_final: 0.8358 (t80) REVERT: A 132 ASP cc_start: 0.8517 (m-30) cc_final: 0.8210 (m-30) REVERT: A 169 GLN cc_start: 0.7818 (mt0) cc_final: 0.7413 (mt0) REVERT: A 183 LEU cc_start: 0.8856 (tp) cc_final: 0.8499 (tp) REVERT: A 184 ASN cc_start: 0.8548 (m-40) cc_final: 0.8153 (m110) REVERT: A 203 GLN cc_start: 0.7945 (tt0) cc_final: 0.7105 (tt0) REVERT: A 235 ARG cc_start: 0.8632 (ttt180) cc_final: 0.8132 (ttt180) REVERT: A 240 LYS cc_start: 0.8096 (ptpt) cc_final: 0.7798 (ttpt) REVERT: A 249 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8694 (mp) REVERT: A 250 GLN cc_start: 0.7998 (mm110) cc_final: 0.7696 (tp40) REVERT: A 314 TYR cc_start: 0.8950 (t80) cc_final: 0.8205 (t80) REVERT: A 336 LEU cc_start: 0.8848 (tp) cc_final: 0.8575 (tt) REVERT: A 349 ASN cc_start: 0.8280 (m110) cc_final: 0.7971 (t0) REVERT: A 369 MET cc_start: 0.7713 (mmm) cc_final: 0.7375 (mmm) REVERT: B 122 GLN cc_start: 0.8078 (tt0) cc_final: 0.7865 (tp40) REVERT: D 54 MET cc_start: 0.8329 (tpt) cc_final: 0.7844 (tpp) REVERT: D 56 MET cc_start: 0.6597 (mtt) cc_final: 0.6152 (mtt) REVERT: E 49 ASN cc_start: 0.8443 (p0) cc_final: 0.7802 (p0) REVERT: E 52 ASN cc_start: 0.8864 (t0) cc_final: 0.8425 (t0) REVERT: G 300 VAL cc_start: 0.5146 (OUTLIER) cc_final: 0.4757 (m) REVERT: G 338 LEU cc_start: -0.1170 (OUTLIER) cc_final: -0.1798 (mp) REVERT: G 397 LEU cc_start: -0.0330 (OUTLIER) cc_final: -0.0620 (tm) REVERT: G 398 VAL cc_start: 0.2215 (t) cc_final: 0.1997 (t) REVERT: G 447 HIS cc_start: 0.3455 (OUTLIER) cc_final: 0.1646 (m-70) REVERT: I 74 VAL cc_start: 0.9295 (t) cc_final: 0.8932 (m) REVERT: I 75 PHE cc_start: 0.8939 (m-80) cc_final: 0.8566 (m-80) REVERT: I 79 TYR cc_start: 0.8508 (m-80) cc_final: 0.8013 (m-10) REVERT: I 94 MET cc_start: 0.6299 (tpt) cc_final: 0.5888 (tmm) REVERT: I 120 PHE cc_start: 0.8463 (t80) cc_final: 0.8010 (t80) REVERT: I 140 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.8099 (ttp-110) REVERT: I 143 TYR cc_start: 0.8661 (t80) cc_final: 0.7905 (t80) REVERT: I 179 ASN cc_start: 0.7816 (t0) cc_final: 0.7509 (t0) REVERT: I 181 LYS cc_start: 0.9231 (ptpp) cc_final: 0.8871 (ptmt) REVERT: I 183 LEU cc_start: 0.8940 (tp) cc_final: 0.8588 (tp) REVERT: I 184 ASN cc_start: 0.9088 (m-40) cc_final: 0.8708 (m-40) REVERT: I 187 PHE cc_start: 0.7021 (m-80) cc_final: 0.5501 (p90) REVERT: I 198 VAL cc_start: 0.9238 (OUTLIER) cc_final: 0.8806 (t) REVERT: I 211 LEU cc_start: 0.9050 (tp) cc_final: 0.8835 (mm) REVERT: I 227 ASP cc_start: 0.8182 (m-30) cc_final: 0.7500 (t0) REVERT: I 297 VAL cc_start: 0.9067 (OUTLIER) cc_final: 0.8857 (p) REVERT: I 310 ARG cc_start: 0.8120 (ptp90) cc_final: 0.7360 (ptm-80) REVERT: I 324 VAL cc_start: 0.9259 (t) cc_final: 0.9018 (p) REVERT: I 359 PHE cc_start: 0.8440 (t80) cc_final: 0.8126 (t80) REVERT: I 375 ASP cc_start: 0.7520 (t0) cc_final: 0.6698 (t0) REVERT: J 89 ARG cc_start: 0.5330 (tpt90) cc_final: 0.3900 (mtt90) REVERT: K 18 GLN cc_start: 0.8250 (tt0) cc_final: 0.7930 (pt0) REVERT: K 22 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7383 (mt-10) REVERT: K 30 TYR cc_start: 0.6043 (m-10) cc_final: 0.5832 (t80) REVERT: L 55 ASP cc_start: 0.7731 (OUTLIER) cc_final: 0.7474 (m-30) REVERT: L 56 MET cc_start: 0.6355 (mtt) cc_final: 0.5766 (mtp) REVERT: M 32 TRP cc_start: 0.8257 (t-100) cc_final: 0.7847 (t-100) REVERT: M 35 PHE cc_start: 0.8328 (t80) cc_final: 0.7812 (t80) REVERT: M 49 ASN cc_start: 0.8231 (p0) cc_final: 0.7538 (p0) outliers start: 111 outliers final: 29 residues processed: 443 average time/residue: 0.2029 time to fit residues: 125.7359 Evaluate side-chains 314 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 276 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.3980 chunk 86 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 58 optimal weight: 0.1980 chunk 46 optimal weight: 5.9990 chunk 89 optimal weight: 0.0270 chunk 34 optimal weight: 0.8980 chunk 54 optimal weight: 0.3980 chunk 66 optimal weight: 10.0000 chunk 103 optimal weight: 0.9980 overall best weight: 0.3838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 317 ASN I 67 ASN I 89 ASN ** I 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 ASN M 52 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6538 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9537 Z= 0.182 Angle : 0.637 6.929 12938 Z= 0.327 Chirality : 0.044 0.180 1450 Planarity : 0.005 0.052 1667 Dihedral : 4.783 40.599 1252 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.10 % Allowed : 3.37 % Favored : 96.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.23), residues: 1166 helix: 0.01 (0.26), residues: 300 sheet: -0.52 (0.22), residues: 494 loop : -1.37 (0.28), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 243 HIS 0.005 0.001 HIS G 355 PHE 0.013 0.001 PHE I 359 TYR 0.014 0.001 TYR G 478 ARG 0.005 0.001 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 346 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 111 LEU cc_start: 0.9644 (mm) cc_final: 0.9366 (mm) REVERT: A 169 GLN cc_start: 0.7863 (mt0) cc_final: 0.7362 (mt0) REVERT: A 219 ARG cc_start: 0.8235 (tpp80) cc_final: 0.7634 (tpp80) REVERT: A 240 LYS cc_start: 0.7993 (ptpt) cc_final: 0.7691 (ttpt) REVERT: A 244 ILE cc_start: 0.9313 (pt) cc_final: 0.8933 (pt) REVERT: A 259 LEU cc_start: 0.9308 (tp) cc_final: 0.8955 (tp) REVERT: A 298 GLU cc_start: 0.8737 (tp30) cc_final: 0.8510 (tp30) REVERT: A 314 TYR cc_start: 0.8791 (t80) cc_final: 0.8168 (t80) REVERT: A 336 LEU cc_start: 0.8710 (tp) cc_final: 0.8407 (tt) REVERT: A 349 ASN cc_start: 0.8503 (m110) cc_final: 0.8128 (t0) REVERT: A 369 MET cc_start: 0.7901 (mmm) cc_final: 0.7573 (mmm) REVERT: B 122 GLN cc_start: 0.8145 (tt0) cc_final: 0.7928 (tp40) REVERT: C 20 GLN cc_start: 0.8094 (OUTLIER) cc_final: 0.7244 (tp-100) REVERT: C 23 LYS cc_start: 0.8936 (mttt) cc_final: 0.8525 (mppt) REVERT: C 24 THR cc_start: 0.9350 (m) cc_final: 0.8616 (m) REVERT: E 49 ASN cc_start: 0.8408 (p0) cc_final: 0.7790 (p0) REVERT: I 94 MET cc_start: 0.6552 (tpt) cc_final: 0.6189 (tmm) REVERT: I 150 ILE cc_start: 0.9289 (tp) cc_final: 0.9001 (mt) REVERT: I 159 ASP cc_start: 0.6989 (t70) cc_final: 0.6776 (t70) REVERT: I 179 ASN cc_start: 0.8339 (t0) cc_final: 0.8024 (t0) REVERT: I 181 LYS cc_start: 0.9196 (ptpp) cc_final: 0.8805 (ptmt) REVERT: I 227 ASP cc_start: 0.8471 (m-30) cc_final: 0.7977 (t0) REVERT: I 234 THR cc_start: 0.9121 (m) cc_final: 0.8842 (p) REVERT: I 310 ARG cc_start: 0.8021 (ptp90) cc_final: 0.7389 (ptm-80) REVERT: I 359 PHE cc_start: 0.8567 (t80) cc_final: 0.8224 (t80) REVERT: J 89 ARG cc_start: 0.5491 (tpt90) cc_final: 0.3887 (mtt90) REVERT: J 121 GLN cc_start: 0.7563 (mm110) cc_final: 0.7037 (mt0) REVERT: K 22 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7471 (mt-10) outliers start: 1 outliers final: 0 residues processed: 346 average time/residue: 0.1912 time to fit residues: 94.6567 Evaluate side-chains 280 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 279 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 103 optimal weight: 0.4980 chunk 112 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 102 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN D 38 ASN M 29 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6638 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9537 Z= 0.269 Angle : 0.633 7.596 12938 Z= 0.331 Chirality : 0.044 0.184 1450 Planarity : 0.004 0.038 1667 Dihedral : 4.710 34.422 1252 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.10 % Allowed : 4.26 % Favored : 95.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.24), residues: 1166 helix: 0.99 (0.28), residues: 299 sheet: -0.57 (0.23), residues: 497 loop : -0.82 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 243 HIS 0.008 0.001 HIS A 102 PHE 0.023 0.002 PHE A 359 TYR 0.025 0.002 TYR A 307 ARG 0.005 0.001 ARG A 315 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 320 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 LEU cc_start: 0.9620 (mm) cc_final: 0.9289 (mm) REVERT: A 130 ASN cc_start: 0.8214 (t0) cc_final: 0.7829 (t0) REVERT: A 152 LYS cc_start: 0.9218 (mttt) cc_final: 0.8531 (mmtp) REVERT: A 156 GLN cc_start: 0.8453 (tp40) cc_final: 0.7990 (tp40) REVERT: A 169 GLN cc_start: 0.7943 (mt0) cc_final: 0.7440 (mt0) REVERT: A 219 ARG cc_start: 0.8431 (tpp80) cc_final: 0.7584 (mmm160) REVERT: A 240 LYS cc_start: 0.8084 (ptpt) cc_final: 0.7779 (ttpt) REVERT: A 259 LEU cc_start: 0.9386 (tp) cc_final: 0.9066 (tp) REVERT: A 343 GLU cc_start: 0.8033 (tt0) cc_final: 0.7774 (tt0) REVERT: A 349 ASN cc_start: 0.8549 (m110) cc_final: 0.8168 (t0) REVERT: A 357 LEU cc_start: 0.9412 (pt) cc_final: 0.9194 (pt) REVERT: A 369 MET cc_start: 0.8113 (mmm) cc_final: 0.7809 (mmm) REVERT: C 23 LYS cc_start: 0.8973 (mttt) cc_final: 0.8727 (mttm) REVERT: C 40 MET cc_start: 0.8881 (mpp) cc_final: 0.8535 (mpp) REVERT: E 49 ASN cc_start: 0.8434 (p0) cc_final: 0.7861 (p0) REVERT: G 496 MET cc_start: 0.0356 (mpp) cc_final: -0.0404 (mtp) REVERT: I 120 PHE cc_start: 0.8682 (t80) cc_final: 0.8305 (t80) REVERT: I 130 ASN cc_start: 0.8251 (t0) cc_final: 0.8047 (t0) REVERT: I 132 ASP cc_start: 0.7883 (m-30) cc_final: 0.7650 (m-30) REVERT: I 155 LEU cc_start: 0.9088 (mt) cc_final: 0.8876 (mt) REVERT: I 176 PHE cc_start: 0.8567 (p90) cc_final: 0.8305 (p90) REVERT: I 179 ASN cc_start: 0.8394 (t0) cc_final: 0.7751 (t0) REVERT: I 181 LYS cc_start: 0.9149 (ptpp) cc_final: 0.8814 (ptmt) REVERT: I 203 GLN cc_start: 0.7733 (tt0) cc_final: 0.6978 (tp40) REVERT: I 227 ASP cc_start: 0.8520 (m-30) cc_final: 0.7985 (t0) REVERT: I 310 ARG cc_start: 0.8154 (ptp90) cc_final: 0.7500 (ptm-80) REVERT: I 343 GLU cc_start: 0.7401 (tt0) cc_final: 0.6768 (tt0) REVERT: I 359 PHE cc_start: 0.8522 (t80) cc_final: 0.7953 (t80) REVERT: J 89 ARG cc_start: 0.5695 (tpt90) cc_final: 0.4057 (mtt90) REVERT: J 121 GLN cc_start: 0.7601 (mm110) cc_final: 0.7165 (mt0) REVERT: K 22 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7439 (mt-10) REVERT: M 52 ASN cc_start: 0.8654 (m-40) cc_final: 0.8276 (p0) outliers start: 1 outliers final: 0 residues processed: 320 average time/residue: 0.2000 time to fit residues: 90.7341 Evaluate side-chains 260 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 53 optimal weight: 0.5980 chunk 11 optimal weight: 0.0270 chunk 49 optimal weight: 20.0000 chunk 69 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 overall best weight: 1.3244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6662 moved from start: 0.3852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9537 Z= 0.263 Angle : 0.622 7.039 12938 Z= 0.323 Chirality : 0.044 0.194 1450 Planarity : 0.004 0.037 1667 Dihedral : 4.720 35.304 1252 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.25), residues: 1166 helix: 1.40 (0.29), residues: 298 sheet: -0.47 (0.23), residues: 509 loop : -0.53 (0.35), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 243 HIS 0.006 0.001 HIS A 102 PHE 0.023 0.002 PHE A 120 TYR 0.016 0.002 TYR A 307 ARG 0.004 0.001 ARG I 140 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 309 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 LYS cc_start: 0.9342 (mttt) cc_final: 0.8226 (mttp) REVERT: A 156 GLN cc_start: 0.8476 (tp40) cc_final: 0.8033 (tp40) REVERT: A 169 GLN cc_start: 0.7968 (mt0) cc_final: 0.7427 (mt0) REVERT: A 219 ARG cc_start: 0.8442 (tpp80) cc_final: 0.7501 (tpp80) REVERT: A 240 LYS cc_start: 0.8115 (ptpt) cc_final: 0.7785 (ttpt) REVERT: A 259 LEU cc_start: 0.9389 (tp) cc_final: 0.9083 (tp) REVERT: A 349 ASN cc_start: 0.8578 (m110) cc_final: 0.8181 (t0) REVERT: A 369 MET cc_start: 0.8124 (mmm) cc_final: 0.7754 (mmm) REVERT: B 126 MET cc_start: 0.7881 (tmm) cc_final: 0.7675 (tmm) REVERT: C 23 LYS cc_start: 0.8971 (mttt) cc_final: 0.8766 (mttm) REVERT: C 40 MET cc_start: 0.8823 (mpp) cc_final: 0.8487 (mpp) REVERT: D 50 GLN cc_start: 0.8397 (mm110) cc_final: 0.8174 (mm110) REVERT: E 49 ASN cc_start: 0.8407 (p0) cc_final: 0.7857 (p0) REVERT: G 366 MET cc_start: 0.0426 (tpt) cc_final: -0.0627 (mtt) REVERT: G 496 MET cc_start: 0.0164 (mpp) cc_final: -0.0747 (mtp) REVERT: I 120 PHE cc_start: 0.8716 (t80) cc_final: 0.8232 (t80) REVERT: I 130 ASN cc_start: 0.8305 (t0) cc_final: 0.8049 (t0) REVERT: I 132 ASP cc_start: 0.8017 (m-30) cc_final: 0.7723 (m-30) REVERT: I 179 ASN cc_start: 0.8303 (t0) cc_final: 0.7885 (t0) REVERT: I 181 LYS cc_start: 0.9103 (ptpp) cc_final: 0.8797 (ptmt) REVERT: I 208 GLN cc_start: 0.7616 (mm110) cc_final: 0.7171 (mm-40) REVERT: I 310 ARG cc_start: 0.8275 (ptp90) cc_final: 0.7615 (ptm-80) REVERT: I 341 CYS cc_start: 0.8247 (p) cc_final: 0.8029 (p) REVERT: I 359 PHE cc_start: 0.8508 (t80) cc_final: 0.7853 (t80) REVERT: J 87 PHE cc_start: 0.4016 (t80) cc_final: 0.3776 (t80) REVERT: J 89 ARG cc_start: 0.5650 (tpt90) cc_final: 0.4103 (mtt90) REVERT: J 121 GLN cc_start: 0.7714 (mm110) cc_final: 0.7199 (mt0) REVERT: K 22 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7777 (tp30) REVERT: M 52 ASN cc_start: 0.8683 (m-40) cc_final: 0.8212 (p0) outliers start: 0 outliers final: 0 residues processed: 309 average time/residue: 0.1994 time to fit residues: 86.8665 Evaluate side-chains 268 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 0.7980 chunk 62 optimal weight: 7.9990 chunk 1 optimal weight: 0.6980 chunk 82 optimal weight: 5.9990 chunk 45 optimal weight: 0.5980 chunk 94 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 56 optimal weight: 9.9990 chunk 98 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 38 ASN ** L 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6666 moved from start: 0.4140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9537 Z= 0.252 Angle : 0.636 8.601 12938 Z= 0.326 Chirality : 0.044 0.195 1450 Planarity : 0.004 0.038 1667 Dihedral : 4.679 31.565 1252 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.25), residues: 1166 helix: 1.38 (0.29), residues: 305 sheet: -0.35 (0.23), residues: 506 loop : -0.45 (0.36), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 243 HIS 0.006 0.001 HIS A 102 PHE 0.020 0.001 PHE B 130 TYR 0.030 0.002 TYR A 307 ARG 0.004 0.000 ARG I 140 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 320 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ASN cc_start: 0.8372 (t0) cc_final: 0.7920 (t0) REVERT: A 152 LYS cc_start: 0.9206 (mttt) cc_final: 0.8805 (mttp) REVERT: A 169 GLN cc_start: 0.7944 (mt0) cc_final: 0.7478 (mt0) REVERT: A 219 ARG cc_start: 0.8410 (tpp80) cc_final: 0.7860 (tpp80) REVERT: A 240 LYS cc_start: 0.8131 (ptpt) cc_final: 0.7790 (ttpt) REVERT: A 259 LEU cc_start: 0.9373 (tp) cc_final: 0.9058 (tp) REVERT: A 314 TYR cc_start: 0.8818 (t80) cc_final: 0.8146 (t80) REVERT: A 323 LYS cc_start: 0.8662 (ttpt) cc_final: 0.8426 (ttpt) REVERT: A 343 GLU cc_start: 0.7989 (tt0) cc_final: 0.7742 (tt0) REVERT: A 349 ASN cc_start: 0.8644 (m110) cc_final: 0.8164 (t0) REVERT: A 369 MET cc_start: 0.8154 (mmm) cc_final: 0.7771 (mmm) REVERT: C 40 MET cc_start: 0.8829 (mpp) cc_final: 0.8490 (mpp) REVERT: E 49 ASN cc_start: 0.8384 (p0) cc_final: 0.7832 (p0) REVERT: G 496 MET cc_start: -0.0062 (mpp) cc_final: -0.0993 (mtp) REVERT: I 120 PHE cc_start: 0.8744 (t80) cc_final: 0.8515 (t80) REVERT: I 130 ASN cc_start: 0.8224 (t0) cc_final: 0.8002 (t0) REVERT: I 132 ASP cc_start: 0.8056 (m-30) cc_final: 0.7731 (m-30) REVERT: I 134 ASP cc_start: 0.7964 (t70) cc_final: 0.7687 (t70) REVERT: I 179 ASN cc_start: 0.8333 (t0) cc_final: 0.7869 (t0) REVERT: I 181 LYS cc_start: 0.9030 (ptpp) cc_final: 0.8670 (ptmt) REVERT: I 227 ASP cc_start: 0.8367 (m-30) cc_final: 0.8025 (t0) REVERT: I 261 ARG cc_start: 0.7989 (tmt-80) cc_final: 0.7786 (tpt-90) REVERT: I 310 ARG cc_start: 0.8346 (ptp90) cc_final: 0.7711 (ptm-80) REVERT: I 341 CYS cc_start: 0.8302 (p) cc_final: 0.8078 (p) REVERT: J 89 ARG cc_start: 0.5892 (tpt90) cc_final: 0.4314 (mtt90) REVERT: J 121 GLN cc_start: 0.7746 (mm110) cc_final: 0.7269 (mt0) REVERT: K 22 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7851 (tp30) REVERT: M 52 ASN cc_start: 0.8743 (m-40) cc_final: 0.8181 (p0) outliers start: 0 outliers final: 0 residues processed: 320 average time/residue: 0.1916 time to fit residues: 87.4172 Evaluate side-chains 273 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 0.9990 chunk 99 optimal weight: 0.0970 chunk 21 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 51 optimal weight: 0.3980 chunk 9 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 57 optimal weight: 20.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 ASN I 294 GLN ** L 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6654 moved from start: 0.4356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9537 Z= 0.234 Angle : 0.631 7.574 12938 Z= 0.325 Chirality : 0.044 0.186 1450 Planarity : 0.004 0.042 1667 Dihedral : 4.653 29.221 1252 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.20 % Allowed : 1.78 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.25), residues: 1166 helix: 1.41 (0.29), residues: 305 sheet: -0.27 (0.23), residues: 504 loop : -0.37 (0.36), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 243 HIS 0.005 0.001 HIS A 102 PHE 0.029 0.002 PHE E 35 TYR 0.026 0.002 TYR A 307 ARG 0.003 0.000 ARG I 140 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 317 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ASN cc_start: 0.8370 (t0) cc_final: 0.7914 (t0) REVERT: A 152 LYS cc_start: 0.9096 (mttt) cc_final: 0.8503 (mttp) REVERT: A 156 GLN cc_start: 0.8475 (tp40) cc_final: 0.8274 (tp40) REVERT: A 169 GLN cc_start: 0.7973 (mt0) cc_final: 0.7485 (mt0) REVERT: A 179 ASN cc_start: 0.8953 (t0) cc_final: 0.8554 (t0) REVERT: A 219 ARG cc_start: 0.8395 (tpp80) cc_final: 0.7103 (tpp80) REVERT: A 240 LYS cc_start: 0.8149 (ptpt) cc_final: 0.7808 (ttpt) REVERT: A 259 LEU cc_start: 0.9391 (tp) cc_final: 0.9076 (tp) REVERT: A 323 LYS cc_start: 0.8637 (ttpt) cc_final: 0.8338 (ttpt) REVERT: A 349 ASN cc_start: 0.8523 (m110) cc_final: 0.8158 (t0) REVERT: A 369 MET cc_start: 0.8141 (mmm) cc_final: 0.7779 (mmm) REVERT: C 40 MET cc_start: 0.8860 (mpp) cc_final: 0.8493 (mpp) REVERT: E 49 ASN cc_start: 0.8302 (p0) cc_final: 0.7789 (p0) REVERT: G 496 MET cc_start: -0.0064 (mpp) cc_final: -0.1121 (mtp) REVERT: I 72 ARG cc_start: 0.7313 (ttm110) cc_final: 0.6933 (ttm110) REVERT: I 120 PHE cc_start: 0.8795 (t80) cc_final: 0.8500 (t80) REVERT: I 132 ASP cc_start: 0.7898 (m-30) cc_final: 0.7603 (m-30) REVERT: I 169 GLN cc_start: 0.7790 (tt0) cc_final: 0.7500 (tp40) REVERT: I 179 ASN cc_start: 0.8213 (t0) cc_final: 0.7883 (t0) REVERT: I 181 LYS cc_start: 0.9062 (ptpp) cc_final: 0.8665 (ptmt) REVERT: I 208 GLN cc_start: 0.7632 (mm110) cc_final: 0.7195 (mm-40) REVERT: I 227 ASP cc_start: 0.8489 (m-30) cc_final: 0.8082 (t0) REVERT: I 310 ARG cc_start: 0.8351 (ptp90) cc_final: 0.7694 (ptm-80) REVERT: I 359 PHE cc_start: 0.8059 (t80) cc_final: 0.7763 (t80) REVERT: I 360 GLU cc_start: 0.8100 (tp30) cc_final: 0.7817 (tp30) REVERT: J 89 ARG cc_start: 0.5647 (tpt90) cc_final: 0.4262 (mtt90) REVERT: J 121 GLN cc_start: 0.7720 (mm110) cc_final: 0.7172 (mt0) REVERT: K 22 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7867 (tp30) REVERT: M 52 ASN cc_start: 0.8719 (m-40) cc_final: 0.8125 (p0) outliers start: 2 outliers final: 0 residues processed: 318 average time/residue: 0.2002 time to fit residues: 93.3186 Evaluate side-chains 269 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 0.5980 chunk 12 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 80 optimal weight: 5.9990 chunk 92 optimal weight: 0.4980 chunk 61 optimal weight: 0.0370 chunk 109 optimal weight: 0.6980 chunk 68 optimal weight: 10.0000 chunk 66 optimal weight: 8.9990 chunk 50 optimal weight: 6.9990 chunk 67 optimal weight: 6.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6604 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9537 Z= 0.185 Angle : 0.630 7.210 12938 Z= 0.318 Chirality : 0.044 0.181 1450 Planarity : 0.004 0.040 1667 Dihedral : 4.433 23.884 1252 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.26), residues: 1166 helix: 1.57 (0.29), residues: 307 sheet: -0.20 (0.23), residues: 503 loop : -0.30 (0.36), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 243 HIS 0.003 0.001 HIS A 102 PHE 0.017 0.001 PHE A 201 TYR 0.022 0.001 TYR A 314 ARG 0.004 0.000 ARG A 85 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 314 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.7744 (ttm-80) cc_final: 0.7471 (ttm-80) REVERT: A 64 GLU cc_start: 0.8470 (mt-10) cc_final: 0.8207 (mp0) REVERT: A 79 TYR cc_start: 0.8231 (m-80) cc_final: 0.7961 (m-10) REVERT: A 130 ASN cc_start: 0.8260 (t0) cc_final: 0.7970 (t0) REVERT: A 169 GLN cc_start: 0.7905 (mt0) cc_final: 0.7476 (mt0) REVERT: A 219 ARG cc_start: 0.8371 (tpp80) cc_final: 0.7576 (tpp80) REVERT: A 240 LYS cc_start: 0.8082 (ptpt) cc_final: 0.7719 (ttpt) REVERT: A 323 LYS cc_start: 0.8510 (ttpt) cc_final: 0.8290 (ttpt) REVERT: A 349 ASN cc_start: 0.8604 (m110) cc_final: 0.8190 (t0) REVERT: A 369 MET cc_start: 0.8076 (mmm) cc_final: 0.7732 (mmm) REVERT: C 40 MET cc_start: 0.8841 (mpp) cc_final: 0.8528 (mpp) REVERT: E 49 ASN cc_start: 0.8253 (p0) cc_final: 0.7743 (p0) REVERT: G 496 MET cc_start: -0.0225 (mpp) cc_final: -0.1569 (mtp) REVERT: I 72 ARG cc_start: 0.7241 (ttm110) cc_final: 0.6834 (ttm110) REVERT: I 120 PHE cc_start: 0.8786 (t80) cc_final: 0.8540 (t80) REVERT: I 150 ILE cc_start: 0.9313 (mp) cc_final: 0.9014 (mp) REVERT: I 169 GLN cc_start: 0.7855 (tt0) cc_final: 0.7648 (tp40) REVERT: I 171 TYR cc_start: 0.8328 (t80) cc_final: 0.8061 (t80) REVERT: I 179 ASN cc_start: 0.8249 (t0) cc_final: 0.7956 (t0) REVERT: I 181 LYS cc_start: 0.9102 (ptpp) cc_final: 0.8650 (ptmt) REVERT: I 227 ASP cc_start: 0.8318 (m-30) cc_final: 0.8101 (t0) REVERT: I 310 ARG cc_start: 0.8280 (ptp90) cc_final: 0.7582 (ptm-80) REVERT: I 359 PHE cc_start: 0.7962 (t80) cc_final: 0.7587 (t80) REVERT: J 121 GLN cc_start: 0.7717 (mm110) cc_final: 0.7028 (mt0) REVERT: K 22 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7874 (tp30) REVERT: M 52 ASN cc_start: 0.8726 (m-40) cc_final: 0.8168 (p0) outliers start: 0 outliers final: 0 residues processed: 314 average time/residue: 0.1940 time to fit residues: 86.8712 Evaluate side-chains 275 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 3.9990 chunk 65 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 69 optimal weight: 0.0870 chunk 74 optimal weight: 0.9990 chunk 54 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 ASN K 17 HIS ** L 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6616 moved from start: 0.4625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9537 Z= 0.209 Angle : 0.648 8.638 12938 Z= 0.328 Chirality : 0.044 0.181 1450 Planarity : 0.004 0.039 1667 Dihedral : 4.427 22.192 1252 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.26), residues: 1166 helix: 1.73 (0.29), residues: 298 sheet: -0.23 (0.24), residues: 503 loop : -0.27 (0.35), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP I 243 HIS 0.004 0.001 HIS A 102 PHE 0.024 0.001 PHE B 130 TYR 0.023 0.001 TYR I 236 ARG 0.003 0.000 ARG A 85 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 310 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.7739 (ttm-80) cc_final: 0.7378 (ttm-80) REVERT: A 130 ASN cc_start: 0.8321 (t0) cc_final: 0.7964 (t0) REVERT: A 169 GLN cc_start: 0.7944 (mt0) cc_final: 0.7552 (mt0) REVERT: A 219 ARG cc_start: 0.8391 (tpp80) cc_final: 0.7132 (tpp80) REVERT: A 240 LYS cc_start: 0.8112 (ptpt) cc_final: 0.7762 (ttpt) REVERT: A 261 ARG cc_start: 0.8530 (tpt-90) cc_final: 0.8147 (ttt90) REVERT: A 323 LYS cc_start: 0.8558 (ttpt) cc_final: 0.8356 (ttpt) REVERT: A 349 ASN cc_start: 0.8573 (m110) cc_final: 0.8233 (t0) REVERT: A 369 MET cc_start: 0.8133 (mmm) cc_final: 0.7799 (mmm) REVERT: B 120 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7977 (mm-30) REVERT: C 40 MET cc_start: 0.8860 (mpp) cc_final: 0.8414 (mpp) REVERT: E 46 ASN cc_start: 0.8608 (p0) cc_final: 0.8380 (p0) REVERT: E 49 ASN cc_start: 0.8259 (p0) cc_final: 0.7738 (p0) REVERT: G 496 MET cc_start: -0.0284 (mpp) cc_final: -0.1590 (mtp) REVERT: I 72 ARG cc_start: 0.7307 (ttm110) cc_final: 0.6910 (ttm110) REVERT: I 181 LYS cc_start: 0.9108 (ptpp) cc_final: 0.8776 (ptmt) REVERT: I 310 ARG cc_start: 0.8440 (ptp90) cc_final: 0.7647 (ptm-80) REVERT: I 359 PHE cc_start: 0.7963 (t80) cc_final: 0.7636 (t80) REVERT: J 121 GLN cc_start: 0.7676 (mm110) cc_final: 0.7169 (mt0) REVERT: J 125 GLU cc_start: 0.7311 (mt-10) cc_final: 0.7020 (mt-10) REVERT: K 22 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7876 (tp30) REVERT: M 52 ASN cc_start: 0.8756 (m-40) cc_final: 0.8166 (p0) outliers start: 0 outliers final: 0 residues processed: 310 average time/residue: 0.1954 time to fit residues: 86.4829 Evaluate side-chains 266 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 105 optimal weight: 0.7980 chunk 61 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 92 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 66 optimal weight: 0.2980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6609 moved from start: 0.4736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9537 Z= 0.199 Angle : 0.645 8.511 12938 Z= 0.326 Chirality : 0.044 0.188 1450 Planarity : 0.004 0.039 1667 Dihedral : 4.377 22.081 1252 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.10 % Allowed : 0.40 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.26), residues: 1166 helix: 1.77 (0.30), residues: 298 sheet: -0.25 (0.24), residues: 504 loop : -0.23 (0.36), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP I 243 HIS 0.004 0.001 HIS A 102 PHE 0.023 0.001 PHE A 120 TYR 0.010 0.001 TYR A 314 ARG 0.003 0.000 ARG A 85 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 310 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 TYR cc_start: 0.8242 (m-80) cc_final: 0.8019 (m-10) REVERT: A 130 ASN cc_start: 0.8296 (t0) cc_final: 0.7923 (t0) REVERT: A 152 LYS cc_start: 0.9024 (mttt) cc_final: 0.8414 (mttm) REVERT: A 169 GLN cc_start: 0.7840 (mt0) cc_final: 0.7478 (mt0) REVERT: A 219 ARG cc_start: 0.8397 (tpp80) cc_final: 0.7553 (tpp80) REVERT: A 240 LYS cc_start: 0.8150 (ptpt) cc_final: 0.7807 (ttpt) REVERT: A 261 ARG cc_start: 0.8498 (tpt-90) cc_final: 0.8129 (ttt90) REVERT: A 349 ASN cc_start: 0.8591 (m110) cc_final: 0.8228 (t0) REVERT: A 369 MET cc_start: 0.8147 (mmm) cc_final: 0.7852 (mmm) REVERT: B 120 GLU cc_start: 0.8256 (mm-30) cc_final: 0.8038 (mm-30) REVERT: C 19 GLU cc_start: 0.9159 (pt0) cc_final: 0.8936 (pt0) REVERT: C 40 MET cc_start: 0.8861 (mpp) cc_final: 0.8490 (mpp) REVERT: E 49 ASN cc_start: 0.8194 (p0) cc_final: 0.7663 (p0) REVERT: G 496 MET cc_start: -0.0190 (mpp) cc_final: -0.1532 (mtp) REVERT: I 72 ARG cc_start: 0.7407 (ttm110) cc_final: 0.6733 (mtm-85) REVERT: I 179 ASN cc_start: 0.8411 (t0) cc_final: 0.8128 (t0) REVERT: I 310 ARG cc_start: 0.8383 (ptp90) cc_final: 0.7523 (ptm-80) REVERT: J 120 GLU cc_start: 0.7508 (tp30) cc_final: 0.7290 (tp30) REVERT: J 121 GLN cc_start: 0.7641 (mm110) cc_final: 0.7035 (mt0) REVERT: K 22 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7896 (tp30) REVERT: M 52 ASN cc_start: 0.8747 (m-40) cc_final: 0.8111 (p0) outliers start: 1 outliers final: 0 residues processed: 311 average time/residue: 0.1960 time to fit residues: 86.5036 Evaluate side-chains 277 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 277 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 30.0000 chunk 75 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 ASN ** L 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 29 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6653 moved from start: 0.4849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9537 Z= 0.257 Angle : 0.676 8.871 12938 Z= 0.346 Chirality : 0.045 0.183 1450 Planarity : 0.004 0.038 1667 Dihedral : 4.529 23.268 1252 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.26), residues: 1166 helix: 1.49 (0.29), residues: 307 sheet: -0.30 (0.24), residues: 505 loop : -0.23 (0.36), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP I 243 HIS 0.005 0.001 HIS A 102 PHE 0.024 0.002 PHE I 120 TYR 0.012 0.001 TYR A 314 ARG 0.007 0.001 ARG A 85 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 310 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ARG cc_start: 0.8049 (ttt90) cc_final: 0.7603 (ttt90) REVERT: A 130 ASN cc_start: 0.8401 (t0) cc_final: 0.7814 (t0) REVERT: A 156 GLN cc_start: 0.7745 (tp40) cc_final: 0.7488 (tp40) REVERT: A 167 LEU cc_start: 0.9329 (tt) cc_final: 0.9127 (tt) REVERT: A 169 GLN cc_start: 0.7944 (mt0) cc_final: 0.7604 (mt0) REVERT: A 219 ARG cc_start: 0.8382 (tpp80) cc_final: 0.7070 (tpp80) REVERT: A 240 LYS cc_start: 0.8192 (ptpt) cc_final: 0.7860 (ttpt) REVERT: A 261 ARG cc_start: 0.8663 (tpt-90) cc_final: 0.8111 (ttt90) REVERT: A 323 LYS cc_start: 0.8711 (ttpt) cc_final: 0.8478 (ttpt) REVERT: A 349 ASN cc_start: 0.8591 (m110) cc_final: 0.8269 (t0) REVERT: A 369 MET cc_start: 0.8164 (mmm) cc_final: 0.7834 (mmm) REVERT: C 19 GLU cc_start: 0.9076 (pt0) cc_final: 0.8817 (pt0) REVERT: C 23 LYS cc_start: 0.8866 (mttt) cc_final: 0.8152 (mttp) REVERT: C 40 MET cc_start: 0.8891 (mpp) cc_final: 0.8596 (mpp) REVERT: D 56 MET cc_start: 0.7399 (ttm) cc_final: 0.7069 (ttm) REVERT: E 46 ASN cc_start: 0.8513 (p0) cc_final: 0.8142 (p0) REVERT: E 48 PRO cc_start: 0.8714 (Cg_endo) cc_final: 0.8405 (Cg_exo) REVERT: E 49 ASN cc_start: 0.8216 (p0) cc_final: 0.7623 (p0) REVERT: G 356 MET cc_start: 0.2424 (pmm) cc_final: 0.2161 (ptt) REVERT: G 496 MET cc_start: -0.0127 (mpp) cc_final: -0.1435 (mtp) REVERT: I 72 ARG cc_start: 0.7535 (ttm110) cc_final: 0.7013 (ttm110) REVERT: I 117 SER cc_start: 0.8565 (t) cc_final: 0.8362 (t) REVERT: I 130 ASN cc_start: 0.8303 (t0) cc_final: 0.8017 (t0) REVERT: I 183 LEU cc_start: 0.9279 (mp) cc_final: 0.9067 (mt) REVERT: I 310 ARG cc_start: 0.8369 (ptp90) cc_final: 0.7697 (ptm-80) REVERT: I 359 PHE cc_start: 0.8050 (t80) cc_final: 0.7707 (t80) REVERT: J 89 ARG cc_start: 0.5514 (tpt90) cc_final: 0.4175 (mtt90) REVERT: J 120 GLU cc_start: 0.7558 (tp30) cc_final: 0.7283 (tp30) REVERT: J 121 GLN cc_start: 0.7608 (mm110) cc_final: 0.7094 (mt0) REVERT: K 22 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7901 (tp30) REVERT: M 52 ASN cc_start: 0.8782 (m-40) cc_final: 0.8117 (p0) outliers start: 0 outliers final: 0 residues processed: 310 average time/residue: 0.1969 time to fit residues: 86.3383 Evaluate side-chains 263 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 93 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.166537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.125553 restraints weight = 16673.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.124084 restraints weight = 10814.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.125301 restraints weight = 8507.441| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3543 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3543 r_free = 0.3543 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3542 r_free = 0.3542 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| r_final: 0.3542 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.4897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9537 Z= 0.228 Angle : 0.681 9.226 12938 Z= 0.346 Chirality : 0.045 0.184 1450 Planarity : 0.004 0.050 1667 Dihedral : 4.505 23.171 1252 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.26), residues: 1166 helix: 1.51 (0.30), residues: 307 sheet: -0.28 (0.24), residues: 504 loop : -0.23 (0.36), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP I 243 HIS 0.005 0.001 HIS M 29 PHE 0.023 0.001 PHE A 120 TYR 0.011 0.001 TYR A 314 ARG 0.007 0.001 ARG A 85 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2506.42 seconds wall clock time: 46 minutes 6.18 seconds (2766.18 seconds total)