Starting phenix.real_space_refine on Mon Jun 9 06:20:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9itv_60880/06_2025/9itv_60880.cif Found real_map, /net/cci-nas-00/data/ceres_data/9itv_60880/06_2025/9itv_60880.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9itv_60880/06_2025/9itv_60880.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9itv_60880/06_2025/9itv_60880.map" model { file = "/net/cci-nas-00/data/ceres_data/9itv_60880/06_2025/9itv_60880.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9itv_60880/06_2025/9itv_60880.cif" } resolution = 3.97 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 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 33 5.16 5 C 6959 2.51 5 N 1668 2.21 5 O 1759 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 10419 Number of models: 1 Model: "" Number of chains: 16 Chain: "H" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 506 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 69} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "J" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "K" Number of atoms: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 517 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "L" Number of atoms: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 517 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "M" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "N" Number of atoms: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 517 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "O" Number of atoms: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 517 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "P" Number of atoms: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 517 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "Q" Number of atoms: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 517 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "T" Number of atoms: 2064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2064 Classifications: {'peptide': 266} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 250} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "U" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 213 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 2, 'TRANS': 39} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 189 Unresolved non-hydrogen dihedrals: 116 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 75 Chain: "V" Number of atoms: 335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 335 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 2, 'TRANS': 37} Chain: "X" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 234 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 2, 'TRANS': 39} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 61 Chain: "Y" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 388 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "Z" Number of atoms: 2038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2038 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 14, 'TRANS': 246} Chain breaks: 1 Time building chain proxies: 8.18, per 1000 atoms: 0.79 Number of scatterers: 10419 At special positions: 0 Unit cell: (91.14, 126.48, 83.7, 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 33 16.00 O 1759 8.00 N 1668 7.00 C 6959 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS T 135 " - pdb=" SG CYS T 173 " distance=2.38 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: 3.09 Conformation dependent library (CDL) restraints added in 1.6 seconds 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2510 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 1 sheets defined 83.6% alpha, 0.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'H' and resid 3 through 38 removed outlier: 4.445A pdb=" N VAL H 7 " --> pdb=" O GLY H 3 " (cutoff:3.500A) Proline residue: H 20 - end of helix Processing helix chain 'H' and resid 41 through 72 Processing helix chain 'I' and resid 3 through 38 Proline residue: I 20 - end of helix Processing helix chain 'I' and resid 41 through 72 Processing helix chain 'J' and resid 3 through 38 Proline residue: J 20 - end of helix Processing helix chain 'J' and resid 41 through 72 Processing helix chain 'K' and resid 3 through 38 removed outlier: 4.383A pdb=" N GLY K 19 " --> pdb=" O LEU K 15 " (cutoff:3.500A) Proline residue: K 20 - end of helix Processing helix chain 'K' and resid 41 through 72 Processing helix chain 'L' and resid 3 through 15 removed outlier: 3.666A pdb=" N VAL L 7 " --> pdb=" O GLY L 3 " (cutoff:3.500A) Processing helix chain 'L' and resid 18 through 37 removed outlier: 3.865A pdb=" N ARG L 37 " --> pdb=" O GLN L 33 " (cutoff:3.500A) Processing helix chain 'L' and resid 38 through 40 No H-bonds generated for 'chain 'L' and resid 38 through 40' Processing helix chain 'L' and resid 41 through 72 Processing helix chain 'M' and resid 3 through 38 Proline residue: M 20 - end of helix Processing helix chain 'M' and resid 41 through 72 removed outlier: 4.827A pdb=" N THR M 47 " --> pdb=" O ASN M 43 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N TYR M 48 " --> pdb=" O ARG M 44 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LEU M 59 " --> pdb=" O PHE M 55 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA M 60 " --> pdb=" O THR M 56 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 38 removed outlier: 3.735A pdb=" N GLY N 19 " --> pdb=" O LEU N 15 " (cutoff:3.500A) Proline residue: N 20 - end of helix Processing helix chain 'N' and resid 41 through 72 Processing helix chain 'O' and resid 5 through 38 Proline residue: O 20 - end of helix Processing helix chain 'O' and resid 41 through 73 removed outlier: 4.233A pdb=" N LEU O 59 " --> pdb=" O PHE O 55 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA O 60 " --> pdb=" O THR O 56 " (cutoff:3.500A) Processing helix chain 'P' and resid 3 through 38 removed outlier: 3.522A pdb=" N VAL P 7 " --> pdb=" O GLY P 3 " (cutoff:3.500A) Proline residue: P 20 - end of helix removed outlier: 3.635A pdb=" N ARG P 37 " --> pdb=" O GLN P 33 " (cutoff:3.500A) Processing helix chain 'P' and resid 41 through 73 removed outlier: 3.905A pdb=" N THR P 47 " --> pdb=" O ASN P 43 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N TYR P 48 " --> pdb=" O ARG P 44 " (cutoff:3.500A) Processing helix chain 'Q' and resid 3 through 38 removed outlier: 3.741A pdb=" N VAL Q 7 " --> pdb=" O GLY Q 3 " (cutoff:3.500A) Proline residue: Q 20 - end of helix Processing helix chain 'Q' and resid 41 through 72 removed outlier: 4.494A pdb=" N THR Q 47 " --> pdb=" O ASN Q 43 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE Q 55 " --> pdb=" O ILE Q 51 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU Q 59 " --> pdb=" O PHE Q 55 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA Q 60 " --> pdb=" O THR Q 56 " (cutoff:3.500A) Processing helix chain 'T' and resid 49 through 72 removed outlier: 3.586A pdb=" N VAL T 54 " --> pdb=" O ASN T 50 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASN T 72 " --> pdb=" O ALA T 68 " (cutoff:3.500A) Processing helix chain 'T' and resid 79 through 97 Processing helix chain 'T' and resid 106 through 124 removed outlier: 3.593A pdb=" N VAL T 110 " --> pdb=" O ALA T 106 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY T 124 " --> pdb=" O GLY T 120 " (cutoff:3.500A) Processing helix chain 'T' and resid 171 through 178 removed outlier: 4.388A pdb=" N ALA T 175 " --> pdb=" O THR T 172 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N GLN T 176 " --> pdb=" O CYS T 173 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY T 177 " --> pdb=" O ALA T 174 " (cutoff:3.500A) Processing helix chain 'T' and resid 186 through 190 removed outlier: 3.523A pdb=" N ASP T 190 " --> pdb=" O PRO T 187 " (cutoff:3.500A) Processing helix chain 'T' and resid 192 through 212 removed outlier: 3.870A pdb=" N ALA T 212 " --> pdb=" O TRP T 208 " (cutoff:3.500A) Processing helix chain 'T' and resid 216 through 221 Processing helix chain 'T' and resid 227 through 268 removed outlier: 3.554A pdb=" N VAL T 231 " --> pdb=" O ILE T 227 " (cutoff:3.500A) Proline residue: T 243 - end of helix Processing helix chain 'T' and resid 273 through 304 removed outlier: 3.738A pdb=" N PHE T 285 " --> pdb=" O VAL T 281 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA T 292 " --> pdb=" O ALA T 288 " (cutoff:3.500A) Processing helix chain 'U' and resid 9 through 29 Processing helix chain 'U' and resid 30 through 48 Processing helix chain 'V' and resid 7 through 26 Processing helix chain 'V' and resid 30 through 43 Processing helix chain 'X' and resid 7 through 28 Processing helix chain 'X' and resid 30 through 43 Processing helix chain 'Y' and resid 7 through 28 Processing helix chain 'Y' and resid 30 through 47 Processing helix chain 'Z' and resid 17 through 21 removed outlier: 3.729A pdb=" N ALA Z 20 " --> pdb=" O ILE Z 17 " (cutoff:3.500A) Processing helix chain 'Z' and resid 49 through 70 removed outlier: 4.012A pdb=" N VAL Z 54 " --> pdb=" O ASN Z 50 " (cutoff:3.500A) Processing helix chain 'Z' and resid 79 through 99 removed outlier: 3.796A pdb=" N VAL Z 83 " --> pdb=" O GLY Z 79 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE Z 87 " --> pdb=" O VAL Z 83 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU Z 88 " --> pdb=" O MET Z 84 " (cutoff:3.500A) Processing helix chain 'Z' and resid 102 through 125 Proline residue: Z 108 - end of helix removed outlier: 3.945A pdb=" N VAL Z 117 " --> pdb=" O ILE Z 113 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LEU Z 125 " --> pdb=" O ASN Z 121 " (cutoff:3.500A) Processing helix chain 'Z' and resid 172 through 176 Processing helix chain 'Z' and resid 190 through 214 removed outlier: 3.531A pdb=" N THR Z 194 " --> pdb=" O ASP Z 190 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA Z 212 " --> pdb=" O TRP Z 208 " (cutoff:3.500A) Processing helix chain 'Z' and resid 214 through 220 removed outlier: 3.899A pdb=" N LEU Z 218 " --> pdb=" O GLY Z 214 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS Z 219 " --> pdb=" O PRO Z 215 " (cutoff:3.500A) Processing helix chain 'Z' and resid 221 through 225 removed outlier: 3.701A pdb=" N ASN Z 225 " --> pdb=" O PHE Z 222 " (cutoff:3.500A) Processing helix chain 'Z' and resid 230 through 268 removed outlier: 3.521A pdb=" N ILE Z 234 " --> pdb=" O PHE Z 230 " (cutoff:3.500A) Proline residue: Z 243 - end of helix removed outlier: 3.668A pdb=" N LEU Z 250 " --> pdb=" O LEU Z 246 " (cutoff:3.500A) Processing helix chain 'Z' and resid 273 through 304 removed outlier: 3.688A pdb=" N PHE Z 285 " --> pdb=" O VAL Z 281 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Z' and resid 133 through 135 920 hydrogen bonds defined for protein. 2739 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: 3.13 Time building geometry restraints manager: 3.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3285 1.34 - 1.46: 2351 1.46 - 1.58: 4922 1.58 - 1.70: 0 1.70 - 1.81: 62 Bond restraints: 10620 Sorted by residual: bond pdb=" N ILE J 70 " pdb=" CA ILE J 70 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.19e-02 7.06e+03 8.73e+00 bond pdb=" N ILE I 70 " pdb=" CA ILE I 70 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.17e-02 7.31e+03 8.33e+00 bond pdb=" N VAL T 303 " pdb=" CA VAL T 303 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.34e-02 5.57e+03 7.70e+00 bond pdb=" N CYS T 173 " pdb=" CA CYS T 173 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.32e-02 5.74e+03 5.95e+00 bond pdb=" N TYR T 296 " pdb=" CA TYR T 296 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.58e+00 ... (remaining 10615 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 14068 1.52 - 3.03: 325 3.03 - 4.55: 41 4.55 - 6.06: 16 6.06 - 7.58: 4 Bond angle restraints: 14454 Sorted by residual: angle pdb=" C ASP Z 171 " pdb=" CA ASP Z 171 " pdb=" CB ASP Z 171 " ideal model delta sigma weight residual 116.34 110.31 6.03 1.40e+00 5.10e-01 1.85e+01 angle pdb=" N ILE N 41 " pdb=" CA ILE N 41 " pdb=" C ILE N 41 " ideal model delta sigma weight residual 111.91 108.59 3.32 8.90e-01 1.26e+00 1.39e+01 angle pdb=" C CYS T 173 " pdb=" CA CYS T 173 " pdb=" CB CYS T 173 " ideal model delta sigma weight residual 110.37 104.84 5.53 1.78e+00 3.16e-01 9.64e+00 angle pdb=" N ILE J 41 " pdb=" CA ILE J 41 " pdb=" CB ILE J 41 " ideal model delta sigma weight residual 112.39 108.99 3.40 1.17e+00 7.31e-01 8.43e+00 angle pdb=" C LEU V 10 " pdb=" N PHE V 11 " pdb=" CA PHE V 11 " ideal model delta sigma weight residual 121.14 116.07 5.07 1.75e+00 3.27e-01 8.41e+00 ... (remaining 14449 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 5306 17.78 - 35.56: 600 35.56 - 53.35: 127 53.35 - 71.13: 20 71.13 - 88.91: 14 Dihedral angle restraints: 6067 sinusoidal: 2125 harmonic: 3942 Sorted by residual: dihedral pdb=" CB CYS T 135 " pdb=" SG CYS T 135 " pdb=" SG CYS T 173 " pdb=" CB CYS T 173 " ideal model delta sinusoidal sigma weight residual -86.00 -6.70 -79.30 1 1.00e+01 1.00e-02 7.82e+01 dihedral pdb=" CA LEU T 272 " pdb=" C LEU T 272 " pdb=" N PRO T 273 " pdb=" CA PRO T 273 " ideal model delta harmonic sigma weight residual -180.00 -162.60 -17.40 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA ASN Z 121 " pdb=" CB ASN Z 121 " pdb=" CG ASN Z 121 " pdb=" OD1 ASN Z 121 " ideal model delta sinusoidal sigma weight residual -90.00 -161.98 71.98 2 2.00e+01 2.50e-03 1.09e+01 ... (remaining 6064 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1346 0.044 - 0.087: 347 0.087 - 0.131: 77 0.131 - 0.174: 6 0.174 - 0.218: 4 Chirality restraints: 1780 Sorted by residual: chirality pdb=" CA ILE I 70 " pdb=" N ILE I 70 " pdb=" C ILE I 70 " pdb=" CB ILE I 70 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CB ILE H 41 " pdb=" CA ILE H 41 " pdb=" CG1 ILE H 41 " pdb=" CG2 ILE H 41 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA ILE J 70 " pdb=" N ILE J 70 " pdb=" C ILE J 70 " pdb=" CB ILE J 70 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 1777 not shown) Planarity restraints: 1819 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY Q 19 " 0.037 5.00e-02 4.00e+02 5.69e-02 5.17e+00 pdb=" N PRO Q 20 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO Q 20 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO Q 20 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY H 19 " 0.033 5.00e-02 4.00e+02 5.07e-02 4.11e+00 pdb=" N PRO H 20 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO H 20 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO H 20 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY J 19 " 0.033 5.00e-02 4.00e+02 4.98e-02 3.97e+00 pdb=" N PRO J 20 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO J 20 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO J 20 " 0.028 5.00e-02 4.00e+02 ... (remaining 1816 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2796 2.80 - 3.33: 11306 3.33 - 3.85: 18364 3.85 - 4.38: 19603 4.38 - 4.90: 34673 Nonbonded interactions: 86742 Sorted by model distance: nonbonded pdb=" OD1 ASN O 43 " pdb=" N ARG O 44 " model vdw 2.277 3.120 nonbonded pdb=" O ILE Y 6 " pdb=" OG1 THR Z 172 " model vdw 2.292 3.040 nonbonded pdb=" O ASN T 99 " pdb=" OH TYR T 296 " model vdw 2.298 3.040 nonbonded pdb=" O ARG Z 249 " pdb=" ND2 ASN Z 253 " model vdw 2.321 3.120 nonbonded pdb=" O SER T 131 " pdb=" N ASN U 7 " model vdw 2.337 3.120 ... (remaining 86737 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 'H' selection = (chain 'I' and ((resid 1 through 2 and (name N or name CA or name C or name O or \ name CB )) or resid 3 through 72)) selection = (chain 'J' and ((resid 1 through 2 and (name N or name CA or name C or name O or \ name CB )) or resid 3 through 72)) selection = (chain 'K' and ((resid 1 through 2 and (name N or name CA or name C or name O or \ name CB )) or resid 3 through 72)) selection = (chain 'L' and ((resid 1 through 2 and (name N or name CA or name C or name O or \ name CB )) or resid 3 through 72)) selection = (chain 'M' and ((resid 1 through 2 and (name N or name CA or name C or name O or \ name CB )) or resid 3 through 72)) selection = (chain 'N' and ((resid 1 through 2 and (name N or name CA or name C or name O or \ name CB )) or resid 3 through 72)) selection = (chain 'O' and ((resid 1 through 2 and (name N or name CA or name C or name O or \ name CB )) or resid 3 through 72)) selection = (chain 'P' and ((resid 1 through 2 and (name N or name CA or name C or name O or \ name CB )) or resid 3 through 72)) selection = (chain 'Q' and ((resid 1 through 2 and (name N or name CA or name C or name O or \ name CB )) or resid 3 through 72)) } ncs_group { reference = (chain 'T' and (resid 19 through 136 or resid 169 through 304)) selection = (chain 'Z' and resid 19 through 304) } ncs_group { reference = (chain 'U' and resid 7 through 44) selection = (chain 'V' and (resid 7 or (resid 8 through 44 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'X' and (resid 7 or (resid 8 through 44 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'Y' and (resid 7 or (resid 8 through 44 and (name N or name CA or name C \ or name 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: 4.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 29.000 Find NCS groups from input model: 0.570 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: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 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 : 0.004 0.349 10621 Z= 0.237 Angle : 0.741 55.897 14456 Z= 0.415 Chirality : 0.041 0.218 1780 Planarity : 0.005 0.057 1819 Dihedral : 15.894 88.908 3554 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.10 % Allowed : 25.59 % Favored : 74.31 % 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: 2.12 (0.23), residues: 1388 helix: 1.98 (0.15), residues: 1140 sheet: None (None), residues: 0 loop : -1.35 (0.43), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP Z 122 HIS 0.001 0.000 HIS Z 31 PHE 0.025 0.001 PHE T 230 TYR 0.011 0.001 TYR T 296 ARG 0.007 0.000 ARG H 37 Details of bonding type rmsd hydrogen bonds : bond 0.10350 ( 920) hydrogen bonds : angle 3.95877 ( 2739) SS BOND : bond 0.34946 ( 1) SS BOND : angle 39.54072 ( 2) covalent geometry : bond 0.00280 (10620) covalent geometry : angle 0.57750 (14454) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 507 time to evaluate : 1.003 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 18 ILE cc_start: 0.8571 (mt) cc_final: 0.8287 (mt) REVERT: H 29 SER cc_start: 0.9769 (t) cc_final: 0.9506 (p) REVERT: H 44 ARG cc_start: 0.8600 (mtp85) cc_final: 0.8277 (mtp85) REVERT: H 48 TYR cc_start: 0.8860 (m-80) cc_final: 0.8574 (m-80) REVERT: H 49 MET cc_start: 0.9404 (tmm) cc_final: 0.9013 (ppp) REVERT: H 50 PHE cc_start: 0.9412 (m-80) cc_final: 0.9093 (m-80) REVERT: H 66 ILE cc_start: 0.9429 (tt) cc_final: 0.9199 (tt) REVERT: I 28 VAL cc_start: 0.9677 (t) cc_final: 0.9350 (m) REVERT: I 33 GLN cc_start: 0.9279 (mt0) cc_final: 0.8771 (mm-40) REVERT: I 37 ARG cc_start: 0.9160 (mtt90) cc_final: 0.8815 (mpp80) REVERT: I 48 TYR cc_start: 0.9293 (m-80) cc_final: 0.8525 (m-80) REVERT: I 49 MET cc_start: 0.9563 (ttp) cc_final: 0.9033 (ppp) REVERT: I 51 ILE cc_start: 0.9123 (mt) cc_final: 0.8457 (mm) REVERT: I 53 ILE cc_start: 0.9548 (mt) cc_final: 0.9334 (mt) REVERT: I 55 PHE cc_start: 0.9419 (m-10) cc_final: 0.9026 (m-80) REVERT: I 62 PHE cc_start: 0.9312 (m-10) cc_final: 0.8949 (m-10) REVERT: J 49 MET cc_start: 0.9537 (ttt) cc_final: 0.9047 (ppp) REVERT: J 57 GLU cc_start: 0.9684 (mm-30) cc_final: 0.9400 (mm-30) REVERT: K 11 LEU cc_start: 0.9310 (mt) cc_final: 0.9084 (tp) REVERT: K 20 PRO cc_start: 0.9246 (Cg_exo) cc_final: 0.9015 (Cg_endo) REVERT: K 28 VAL cc_start: 0.9417 (t) cc_final: 0.9100 (p) REVERT: K 43 ASN cc_start: 0.9272 (m-40) cc_final: 0.8838 (p0) REVERT: K 57 GLU cc_start: 0.9590 (tp30) cc_final: 0.9284 (pt0) REVERT: K 59 LEU cc_start: 0.9117 (mt) cc_final: 0.8577 (mm) REVERT: K 66 ILE cc_start: 0.9196 (tt) cc_final: 0.8970 (mm) REVERT: L 11 LEU cc_start: 0.9482 (mt) cc_final: 0.9128 (tt) REVERT: L 15 LEU cc_start: 0.9151 (mt) cc_final: 0.8534 (tp) REVERT: L 24 ILE cc_start: 0.9533 (mt) cc_final: 0.9246 (mt) REVERT: L 26 ILE cc_start: 0.9622 (mt) cc_final: 0.9275 (tt) REVERT: L 48 TYR cc_start: 0.8814 (m-80) cc_final: 0.7954 (m-80) REVERT: L 51 ILE cc_start: 0.9015 (mt) cc_final: 0.8600 (mt) REVERT: L 55 PHE cc_start: 0.9133 (m-80) cc_final: 0.8519 (m-80) REVERT: L 66 ILE cc_start: 0.9454 (mm) cc_final: 0.9136 (mm) REVERT: M 1 MET cc_start: 0.7137 (mmm) cc_final: 0.6810 (mmt) REVERT: M 4 LEU cc_start: 0.9397 (tp) cc_final: 0.9080 (tp) REVERT: M 20 PRO cc_start: 0.9205 (Cg_exo) cc_final: 0.8960 (Cg_endo) REVERT: M 68 PHE cc_start: 0.8276 (m-10) cc_final: 0.7930 (m-80) REVERT: O 1 MET cc_start: 0.6269 (tpp) cc_final: 0.5834 (tpp) REVERT: O 50 PHE cc_start: 0.9326 (m-10) cc_final: 0.8999 (m-80) REVERT: O 51 ILE cc_start: 0.8802 (mm) cc_final: 0.8398 (tp) REVERT: O 57 GLU cc_start: 0.9273 (tp30) cc_final: 0.9017 (mm-30) REVERT: O 59 LEU cc_start: 0.9567 (mt) cc_final: 0.9267 (mt) REVERT: O 62 PHE cc_start: 0.9194 (m-10) cc_final: 0.8753 (m-80) REVERT: P 1 MET cc_start: 0.6030 (mtt) cc_final: 0.5425 (ptp) REVERT: P 11 LEU cc_start: 0.9437 (mt) cc_final: 0.8987 (mm) REVERT: P 18 ILE cc_start: 0.8423 (mt) cc_final: 0.8178 (mt) REVERT: P 33 GLN cc_start: 0.9252 (mt0) cc_final: 0.8898 (mm-40) REVERT: P 38 ASN cc_start: 0.8877 (t0) cc_final: 0.7687 (t0) REVERT: P 41 ILE cc_start: 0.9464 (tp) cc_final: 0.8837 (tt) REVERT: P 48 TYR cc_start: 0.9282 (m-80) cc_final: 0.8723 (m-80) REVERT: P 49 MET cc_start: 0.9547 (ttt) cc_final: 0.9153 (ppp) REVERT: P 57 GLU cc_start: 0.9387 (mm-30) cc_final: 0.8974 (tm-30) REVERT: P 66 ILE cc_start: 0.9599 (mm) cc_final: 0.9328 (tp) REVERT: Q 26 ILE cc_start: 0.9636 (mt) cc_final: 0.9365 (tp) REVERT: Q 33 GLN cc_start: 0.9162 (mt0) cc_final: 0.8951 (mm-40) REVERT: Q 38 ASN cc_start: 0.9334 (t0) cc_final: 0.8667 (t0) REVERT: Q 48 TYR cc_start: 0.8945 (m-10) cc_final: 0.8208 (m-80) REVERT: Q 49 MET cc_start: 0.9290 (tmm) cc_final: 0.8788 (tmm) REVERT: Q 64 LEU cc_start: 0.9342 (tp) cc_final: 0.8896 (tp) REVERT: Q 66 ILE cc_start: 0.9674 (mm) cc_final: 0.9466 (mm) REVERT: T 78 ARG cc_start: 0.8825 (ptt180) cc_final: 0.8448 (tpt170) REVERT: T 102 TYR cc_start: 0.8130 (m-80) cc_final: 0.7637 (m-80) REVERT: T 119 PHE cc_start: 0.2930 (m-80) cc_final: 0.2337 (m-80) REVERT: T 239 GLU cc_start: 0.9212 (tp30) cc_final: 0.8966 (mm-30) REVERT: T 246 LEU cc_start: 0.9804 (mt) cc_final: 0.9254 (pp) REVERT: T 249 ARG cc_start: 0.9546 (ttp-110) cc_final: 0.9163 (mtm110) REVERT: T 296 TYR cc_start: 0.9064 (t80) cc_final: 0.7874 (t80) REVERT: V 16 ILE cc_start: 0.9410 (mt) cc_final: 0.9147 (tp) REVERT: V 24 ILE cc_start: 0.9434 (tt) cc_final: 0.9166 (tp) REVERT: V 25 LEU cc_start: 0.9361 (mt) cc_final: 0.9144 (mt) REVERT: V 34 MET cc_start: 0.9244 (tpp) cc_final: 0.8901 (mmm) REVERT: V 38 ASN cc_start: 0.9300 (m-40) cc_final: 0.8869 (m-40) REVERT: Y 17 ASN cc_start: 0.9198 (m110) cc_final: 0.8304 (t0) REVERT: Y 46 GLU cc_start: 0.8986 (mt-10) cc_final: 0.8490 (mt-10) REVERT: Z 102 TYR cc_start: 0.8852 (m-80) cc_final: 0.8590 (m-80) REVERT: Z 185 ARG cc_start: 0.8655 (ttt90) cc_final: 0.8095 (ttp-110) REVERT: Z 190 ASP cc_start: 0.8990 (t0) cc_final: 0.8435 (p0) REVERT: Z 260 LEU cc_start: 0.9744 (tp) cc_final: 0.9347 (tp) REVERT: Z 264 MET cc_start: 0.9490 (mmm) cc_final: 0.9278 (mmp) REVERT: Z 290 ILE cc_start: 0.9673 (mm) cc_final: 0.9465 (mt) outliers start: 1 outliers final: 1 residues processed: 508 average time/residue: 0.1941 time to fit residues: 142.8629 Evaluate side-chains 399 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 398 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 136 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 0.6980 chunk 104 optimal weight: 0.2980 chunk 58 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 70 optimal weight: 9.9990 chunk 55 optimal weight: 2.9990 chunk 108 optimal weight: 0.0670 chunk 41 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 80 optimal weight: 0.5980 chunk 125 optimal weight: 0.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 74 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.090819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.069520 restraints weight = 43761.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.071204 restraints weight = 31002.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.072366 restraints weight = 23928.471| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10621 Z= 0.169 Angle : 0.722 12.290 14456 Z= 0.361 Chirality : 0.046 0.280 1780 Planarity : 0.005 0.053 1819 Dihedral : 3.997 37.788 1478 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 20.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.45 % Allowed : 27.47 % Favored : 68.08 % 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: 1.42 (0.22), residues: 1388 helix: 1.54 (0.15), residues: 1124 sheet: None (None), residues: 0 loop : -1.63 (0.40), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP T 208 HIS 0.002 0.001 HIS Z 136 PHE 0.048 0.002 PHE H 55 TYR 0.018 0.002 TYR M 48 ARG 0.007 0.000 ARG Z 249 Details of bonding type rmsd hydrogen bonds : bond 0.04871 ( 920) hydrogen bonds : angle 4.02101 ( 2739) SS BOND : bond 0.00108 ( 1) SS BOND : angle 6.06324 ( 2) covalent geometry : bond 0.00385 (10620) covalent geometry : angle 0.71898 (14454) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 420 time to evaluate : 1.147 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 18 ILE cc_start: 0.8585 (mt) cc_final: 0.8385 (mt) REVERT: H 29 SER cc_start: 0.9781 (t) cc_final: 0.9505 (p) REVERT: H 44 ARG cc_start: 0.8649 (mtp85) cc_final: 0.8076 (mtp85) REVERT: H 48 TYR cc_start: 0.8955 (m-80) cc_final: 0.8349 (m-80) REVERT: H 49 MET cc_start: 0.9468 (OUTLIER) cc_final: 0.9001 (ppp) REVERT: H 50 PHE cc_start: 0.9326 (m-80) cc_final: 0.9092 (m-80) REVERT: H 51 ILE cc_start: 0.9499 (OUTLIER) cc_final: 0.9282 (pt) REVERT: H 55 PHE cc_start: 0.9492 (m-80) cc_final: 0.9138 (m-80) REVERT: H 59 LEU cc_start: 0.9356 (mt) cc_final: 0.8731 (mm) REVERT: H 62 PHE cc_start: 0.9346 (m-80) cc_final: 0.8970 (m-80) REVERT: H 70 ILE cc_start: 0.8325 (mm) cc_final: 0.8085 (mm) REVERT: I 33 GLN cc_start: 0.9309 (mt0) cc_final: 0.8847 (mm-40) REVERT: I 37 ARG cc_start: 0.9162 (mtt90) cc_final: 0.8808 (mpp80) REVERT: I 41 ILE cc_start: 0.8753 (tp) cc_final: 0.8538 (tp) REVERT: I 48 TYR cc_start: 0.9283 (m-80) cc_final: 0.8541 (m-80) REVERT: I 49 MET cc_start: 0.9554 (ttp) cc_final: 0.9240 (ppp) REVERT: I 51 ILE cc_start: 0.9093 (mt) cc_final: 0.8405 (mm) REVERT: I 55 PHE cc_start: 0.9411 (m-10) cc_final: 0.8900 (m-80) REVERT: I 57 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8170 (tp30) REVERT: J 28 VAL cc_start: 0.9743 (t) cc_final: 0.9516 (m) REVERT: J 49 MET cc_start: 0.9450 (ttt) cc_final: 0.9133 (ppp) REVERT: J 57 GLU cc_start: 0.9756 (mm-30) cc_final: 0.9106 (pt0) REVERT: K 43 ASN cc_start: 0.9118 (m-40) cc_final: 0.8908 (p0) REVERT: K 57 GLU cc_start: 0.9615 (tp30) cc_final: 0.9311 (pt0) REVERT: K 59 LEU cc_start: 0.9056 (mt) cc_final: 0.8780 (mm) REVERT: K 62 PHE cc_start: 0.8553 (m-10) cc_final: 0.8254 (m-10) REVERT: K 66 ILE cc_start: 0.9130 (tt) cc_final: 0.8895 (mm) REVERT: L 11 LEU cc_start: 0.9570 (mt) cc_final: 0.9307 (tp) REVERT: L 13 VAL cc_start: 0.9590 (t) cc_final: 0.9386 (m) REVERT: L 15 LEU cc_start: 0.9197 (mt) cc_final: 0.8670 (tp) REVERT: L 57 GLU cc_start: 0.9440 (mm-30) cc_final: 0.9146 (pt0) REVERT: L 66 ILE cc_start: 0.9394 (mm) cc_final: 0.9098 (mm) REVERT: M 20 PRO cc_start: 0.9235 (Cg_exo) cc_final: 0.8730 (Cg_endo) REVERT: M 29 SER cc_start: 0.9630 (t) cc_final: 0.9157 (p) REVERT: M 66 ILE cc_start: 0.9300 (mm) cc_final: 0.9063 (mm) REVERT: M 68 PHE cc_start: 0.8264 (m-10) cc_final: 0.7885 (m-80) REVERT: O 11 LEU cc_start: 0.9528 (tt) cc_final: 0.9324 (tp) REVERT: O 50 PHE cc_start: 0.9219 (m-10) cc_final: 0.8942 (m-80) REVERT: O 51 ILE cc_start: 0.8774 (mm) cc_final: 0.8452 (tp) REVERT: O 62 PHE cc_start: 0.9162 (m-10) cc_final: 0.8705 (m-80) REVERT: P 1 MET cc_start: 0.6206 (mtt) cc_final: 0.5266 (tpp) REVERT: P 18 ILE cc_start: 0.8570 (mt) cc_final: 0.8160 (mt) REVERT: P 38 ASN cc_start: 0.8800 (t0) cc_final: 0.7861 (t0) REVERT: P 41 ILE cc_start: 0.9415 (tp) cc_final: 0.8944 (tt) REVERT: P 48 TYR cc_start: 0.9253 (m-80) cc_final: 0.8695 (m-80) REVERT: P 49 MET cc_start: 0.9592 (ttt) cc_final: 0.9181 (tmm) REVERT: P 66 ILE cc_start: 0.9609 (mm) cc_final: 0.9403 (tp) REVERT: Q 26 ILE cc_start: 0.9649 (mt) cc_final: 0.9364 (tp) REVERT: Q 38 ASN cc_start: 0.9304 (t0) cc_final: 0.8632 (t0) REVERT: Q 41 ILE cc_start: 0.8805 (tp) cc_final: 0.8164 (tp) REVERT: Q 48 TYR cc_start: 0.8851 (m-10) cc_final: 0.8146 (m-80) REVERT: Q 49 MET cc_start: 0.9386 (tmm) cc_final: 0.9052 (tmm) REVERT: Q 64 LEU cc_start: 0.9321 (tp) cc_final: 0.9060 (tt) REVERT: T 78 ARG cc_start: 0.8804 (ptt180) cc_final: 0.8441 (tpt170) REVERT: T 102 TYR cc_start: 0.8012 (m-80) cc_final: 0.7400 (m-80) REVERT: T 119 PHE cc_start: 0.2817 (m-80) cc_final: 0.2576 (m-80) REVERT: T 250 LEU cc_start: 0.9351 (tp) cc_final: 0.9097 (tp) REVERT: T 291 PHE cc_start: 0.9398 (OUTLIER) cc_final: 0.9145 (m-80) REVERT: T 296 TYR cc_start: 0.8997 (t80) cc_final: 0.7700 (t80) REVERT: Y 11 PHE cc_start: 0.8963 (t80) cc_final: 0.8744 (m-80) REVERT: Z 89 GLU cc_start: 0.8406 (tp30) cc_final: 0.8160 (tp30) REVERT: Z 185 ARG cc_start: 0.8616 (ttt90) cc_final: 0.8063 (ttp-170) outliers start: 45 outliers final: 19 residues processed: 441 average time/residue: 0.1865 time to fit residues: 120.4271 Evaluate side-chains 412 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 390 time to evaluate : 1.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 49 MET Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain I residue 61 ILE Chi-restraints excluded: chain J residue 47 THR Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 47 THR Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain O residue 6 LEU Chi-restraints excluded: chain P residue 56 THR Chi-restraints excluded: chain T residue 240 LEU Chi-restraints excluded: chain T residue 253 ASN Chi-restraints excluded: chain T residue 291 PHE Chi-restraints excluded: chain V residue 11 PHE Chi-restraints excluded: chain V residue 28 LEU Chi-restraints excluded: chain Y residue 24 ILE Chi-restraints excluded: chain Z residue 48 ILE Chi-restraints excluded: chain Z residue 53 VAL Chi-restraints excluded: chain Z residue 109 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 112 optimal weight: 20.0000 chunk 1 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 73 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 83 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 chunk 40 optimal weight: 0.8980 chunk 90 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 14 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.087790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.066586 restraints weight = 46480.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.068148 restraints weight = 32518.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.069260 restraints weight = 25096.123| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 10621 Z= 0.226 Angle : 0.742 9.994 14456 Z= 0.379 Chirality : 0.047 0.270 1780 Planarity : 0.005 0.049 1819 Dihedral : 3.900 19.282 1476 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 23.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 6.52 % Allowed : 29.35 % Favored : 64.13 % 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: 1.01 (0.22), residues: 1388 helix: 1.22 (0.15), residues: 1122 sheet: None (None), residues: 0 loop : -1.57 (0.41), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP T 208 HIS 0.002 0.001 HIS T 136 PHE 0.042 0.002 PHE T 282 TYR 0.019 0.002 TYR K 48 ARG 0.008 0.000 ARG Z 249 Details of bonding type rmsd hydrogen bonds : bond 0.04935 ( 920) hydrogen bonds : angle 4.21118 ( 2739) SS BOND : bond 0.01293 ( 1) SS BOND : angle 4.17334 ( 2) covalent geometry : bond 0.00516 (10620) covalent geometry : angle 0.74033 (14454) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 393 time to evaluate : 1.055 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: 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: H 29 SER cc_start: 0.9758 (t) cc_final: 0.9493 (p) REVERT: H 44 ARG cc_start: 0.8619 (mtp85) cc_final: 0.8260 (mmm-85) REVERT: H 48 TYR cc_start: 0.8871 (m-80) cc_final: 0.8392 (m-80) REVERT: H 49 MET cc_start: 0.9411 (OUTLIER) cc_final: 0.9071 (ppp) REVERT: H 51 ILE cc_start: 0.9518 (mt) cc_final: 0.9284 (pt) REVERT: H 59 LEU cc_start: 0.9383 (mt) cc_final: 0.8831 (mm) REVERT: H 62 PHE cc_start: 0.9441 (m-80) cc_final: 0.9084 (m-80) REVERT: H 70 ILE cc_start: 0.8463 (mm) cc_final: 0.8233 (mm) REVERT: I 33 GLN cc_start: 0.9322 (mt0) cc_final: 0.8855 (mm-40) REVERT: I 37 ARG cc_start: 0.9182 (mtt90) cc_final: 0.8916 (mpp80) REVERT: I 49 MET cc_start: 0.9515 (ttp) cc_final: 0.9219 (ppp) REVERT: I 51 ILE cc_start: 0.9137 (mt) cc_final: 0.8400 (mm) REVERT: I 55 PHE cc_start: 0.9434 (m-10) cc_final: 0.8884 (m-80) REVERT: J 49 MET cc_start: 0.9561 (ttt) cc_final: 0.9144 (tmm) REVERT: J 57 GLU cc_start: 0.9759 (mm-30) cc_final: 0.9494 (mm-30) REVERT: K 57 GLU cc_start: 0.9582 (tp30) cc_final: 0.9321 (pt0) REVERT: K 59 LEU cc_start: 0.9187 (mt) cc_final: 0.8813 (mm) REVERT: K 62 PHE cc_start: 0.8640 (m-10) cc_final: 0.8297 (m-10) REVERT: K 66 ILE cc_start: 0.9228 (tt) cc_final: 0.9023 (mm) REVERT: L 11 LEU cc_start: 0.9590 (mt) cc_final: 0.9365 (tt) REVERT: L 13 VAL cc_start: 0.9600 (t) cc_final: 0.9386 (m) REVERT: L 66 ILE cc_start: 0.9522 (mm) cc_final: 0.9238 (mm) REVERT: M 66 ILE cc_start: 0.9381 (mm) cc_final: 0.9144 (mm) REVERT: M 68 PHE cc_start: 0.8299 (m-10) cc_final: 0.7886 (m-80) REVERT: N 41 ILE cc_start: 0.8696 (tp) cc_final: 0.8240 (pt) REVERT: N 48 TYR cc_start: 0.9007 (m-10) cc_final: 0.8344 (m-80) REVERT: O 50 PHE cc_start: 0.9279 (m-10) cc_final: 0.8985 (m-80) REVERT: O 51 ILE cc_start: 0.8709 (mm) cc_final: 0.8441 (tp) REVERT: O 62 PHE cc_start: 0.9250 (m-10) cc_final: 0.8786 (m-80) REVERT: P 1 MET cc_start: 0.6213 (mtt) cc_final: 0.5115 (tpp) REVERT: P 38 ASN cc_start: 0.8917 (t0) cc_final: 0.8003 (t0) REVERT: P 41 ILE cc_start: 0.9464 (tp) cc_final: 0.9040 (tt) REVERT: P 48 TYR cc_start: 0.9255 (m-80) cc_final: 0.8733 (m-80) REVERT: P 49 MET cc_start: 0.9644 (ttt) cc_final: 0.9264 (tmm) REVERT: Q 26 ILE cc_start: 0.9722 (mt) cc_final: 0.9394 (tp) REVERT: Q 38 ASN cc_start: 0.9309 (t0) cc_final: 0.8798 (t0) REVERT: Q 48 TYR cc_start: 0.8907 (m-10) cc_final: 0.8238 (m-80) REVERT: Q 49 MET cc_start: 0.9417 (tmm) cc_final: 0.9016 (tmm) REVERT: Q 64 LEU cc_start: 0.9318 (tp) cc_final: 0.8959 (tp) REVERT: T 102 TYR cc_start: 0.8109 (m-80) cc_final: 0.7505 (m-80) REVERT: T 235 GLU cc_start: 0.9559 (tp30) cc_final: 0.9159 (mt-10) REVERT: T 250 LEU cc_start: 0.9350 (tp) cc_final: 0.9139 (tp) REVERT: T 291 PHE cc_start: 0.9430 (OUTLIER) cc_final: 0.9191 (m-80) REVERT: T 296 TYR cc_start: 0.9019 (t80) cc_final: 0.7901 (t80) REVERT: V 34 MET cc_start: 0.9189 (mmm) cc_final: 0.8820 (mmm) REVERT: V 38 ASN cc_start: 0.9164 (m-40) cc_final: 0.8894 (m110) REVERT: Y 36 LEU cc_start: 0.9321 (pp) cc_final: 0.8943 (mm) REVERT: Y 42 ARG cc_start: 0.8982 (mmp80) cc_final: 0.8568 (mmp80) REVERT: Z 132 ILE cc_start: 0.8368 (mm) cc_final: 0.7936 (mt) REVERT: Z 185 ARG cc_start: 0.8825 (ttt90) cc_final: 0.8311 (ttp-110) outliers start: 66 outliers final: 39 residues processed: 423 average time/residue: 0.2107 time to fit residues: 132.2574 Evaluate side-chains 412 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 371 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 49 MET Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 27 ILE Chi-restraints excluded: chain J residue 47 THR Chi-restraints excluded: chain K residue 27 ILE Chi-restraints excluded: chain L residue 7 VAL Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 47 THR Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain N residue 61 ILE Chi-restraints excluded: chain O residue 6 LEU Chi-restraints excluded: chain O residue 18 ILE Chi-restraints excluded: chain P residue 28 VAL Chi-restraints excluded: chain P residue 56 THR Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 65 VAL Chi-restraints excluded: chain T residue 253 ASN Chi-restraints excluded: chain T residue 274 LEU Chi-restraints excluded: chain T residue 291 PHE Chi-restraints excluded: chain V residue 11 PHE Chi-restraints excluded: chain V residue 28 LEU Chi-restraints excluded: chain Y residue 6 ILE Chi-restraints excluded: chain Y residue 21 LEU Chi-restraints excluded: chain Y residue 24 ILE Chi-restraints excluded: chain Y residue 33 VAL Chi-restraints excluded: chain Z residue 48 ILE Chi-restraints excluded: chain Z residue 53 VAL Chi-restraints excluded: chain Z residue 109 LEU Chi-restraints excluded: chain Z residue 200 ILE Chi-restraints excluded: chain Z residue 250 LEU Chi-restraints excluded: chain Z residue 271 LEU Chi-restraints excluded: chain Z residue 289 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 47 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 79 optimal weight: 20.0000 chunk 49 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 121 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 300 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 = 0.3853 r_free = 0.3853 target = 0.089144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.067281 restraints weight = 46003.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.068932 restraints weight = 32334.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.070111 restraints weight = 24876.797| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10621 Z= 0.175 Angle : 0.761 13.826 14456 Z= 0.376 Chirality : 0.047 0.313 1780 Planarity : 0.004 0.051 1819 Dihedral : 3.981 17.097 1476 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 22.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 4.05 % Allowed : 32.61 % Favored : 63.34 % 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: 0.84 (0.22), residues: 1388 helix: 1.08 (0.15), residues: 1123 sheet: None (None), residues: 0 loop : -1.56 (0.41), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Z 208 HIS 0.002 0.001 HIS Z 31 PHE 0.045 0.002 PHE T 282 TYR 0.020 0.001 TYR M 48 ARG 0.010 0.000 ARG Z 249 Details of bonding type rmsd hydrogen bonds : bond 0.05014 ( 920) hydrogen bonds : angle 4.14150 ( 2739) SS BOND : bond 0.00241 ( 1) SS BOND : angle 3.24689 ( 2) covalent geometry : bond 0.00410 (10620) covalent geometry : angle 0.76048 (14454) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 413 time to evaluate : 1.221 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 15 LEU cc_start: 0.8955 (mt) cc_final: 0.8722 (mp) REVERT: H 29 SER cc_start: 0.9744 (t) cc_final: 0.9494 (p) REVERT: H 44 ARG cc_start: 0.8554 (mtp85) cc_final: 0.8160 (mmm-85) REVERT: H 48 TYR cc_start: 0.8827 (m-80) cc_final: 0.8386 (m-80) REVERT: H 49 MET cc_start: 0.9394 (OUTLIER) cc_final: 0.8924 (ppp) REVERT: H 59 LEU cc_start: 0.9372 (mt) cc_final: 0.8803 (mm) REVERT: H 62 PHE cc_start: 0.9399 (m-80) cc_final: 0.9086 (m-80) REVERT: H 70 ILE cc_start: 0.8426 (mm) cc_final: 0.8212 (mm) REVERT: I 33 GLN cc_start: 0.9297 (mt0) cc_final: 0.8919 (mm-40) REVERT: I 37 ARG cc_start: 0.9142 (mtt90) cc_final: 0.8806 (mpp80) REVERT: I 48 TYR cc_start: 0.9321 (m-80) cc_final: 0.8682 (m-80) REVERT: I 49 MET cc_start: 0.9542 (ttp) cc_final: 0.9254 (ppp) REVERT: I 51 ILE cc_start: 0.9104 (mt) cc_final: 0.8313 (mm) REVERT: I 55 PHE cc_start: 0.9453 (m-10) cc_final: 0.8873 (m-80) REVERT: J 49 MET cc_start: 0.9552 (ttt) cc_final: 0.9207 (tmm) REVERT: J 57 GLU cc_start: 0.9748 (mm-30) cc_final: 0.9483 (mm-30) REVERT: K 57 GLU cc_start: 0.9570 (tp30) cc_final: 0.9310 (pt0) REVERT: K 59 LEU cc_start: 0.9193 (mt) cc_final: 0.8766 (mt) REVERT: K 62 PHE cc_start: 0.8649 (m-10) cc_final: 0.8304 (m-10) REVERT: K 66 ILE cc_start: 0.9243 (tt) cc_final: 0.9033 (mm) REVERT: L 15 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8588 (tp) REVERT: L 66 ILE cc_start: 0.9514 (mm) cc_final: 0.9243 (mm) REVERT: M 29 SER cc_start: 0.9608 (t) cc_final: 0.8956 (m) REVERT: M 41 ILE cc_start: 0.8983 (tp) cc_final: 0.8772 (tp) REVERT: M 66 ILE cc_start: 0.9368 (mm) cc_final: 0.9104 (mm) REVERT: M 68 PHE cc_start: 0.8224 (m-10) cc_final: 0.7848 (m-80) REVERT: N 26 ILE cc_start: 0.9376 (OUTLIER) cc_final: 0.9093 (tp) REVERT: N 40 GLU cc_start: 0.8523 (mp0) cc_final: 0.8195 (mp0) REVERT: N 48 TYR cc_start: 0.8987 (m-10) cc_final: 0.8318 (m-80) REVERT: N 64 LEU cc_start: 0.9336 (tp) cc_final: 0.9114 (tt) REVERT: O 1 MET cc_start: 0.6936 (tpp) cc_final: 0.6536 (tpt) REVERT: O 38 ASN cc_start: 0.8675 (t0) cc_final: 0.8426 (t0) REVERT: O 50 PHE cc_start: 0.9233 (m-10) cc_final: 0.8973 (m-80) REVERT: O 51 ILE cc_start: 0.8751 (mm) cc_final: 0.8476 (tp) REVERT: O 62 PHE cc_start: 0.9238 (m-10) cc_final: 0.8766 (m-80) REVERT: P 1 MET cc_start: 0.6176 (mtt) cc_final: 0.5767 (ptp) REVERT: P 38 ASN cc_start: 0.8935 (t0) cc_final: 0.7974 (t0) REVERT: P 41 ILE cc_start: 0.9443 (tp) cc_final: 0.8987 (tt) REVERT: P 48 TYR cc_start: 0.9190 (m-80) cc_final: 0.8688 (m-80) REVERT: P 49 MET cc_start: 0.9667 (ttt) cc_final: 0.9279 (tmm) REVERT: P 51 ILE cc_start: 0.9494 (mm) cc_final: 0.9031 (tt) REVERT: Q 1 MET cc_start: 0.4311 (mmt) cc_final: 0.3991 (mmt) REVERT: Q 26 ILE cc_start: 0.9697 (mt) cc_final: 0.9364 (tp) REVERT: Q 33 GLN cc_start: 0.9114 (mm-40) cc_final: 0.8875 (mm110) REVERT: Q 38 ASN cc_start: 0.9247 (t0) cc_final: 0.8723 (t0) REVERT: Q 48 TYR cc_start: 0.8867 (m-10) cc_final: 0.8226 (m-80) REVERT: Q 49 MET cc_start: 0.9427 (tmm) cc_final: 0.9130 (ppp) REVERT: Q 64 LEU cc_start: 0.9279 (tp) cc_final: 0.8836 (tp) REVERT: T 102 TYR cc_start: 0.8063 (m-80) cc_final: 0.7510 (m-80) REVERT: T 235 GLU cc_start: 0.9563 (tp30) cc_final: 0.9204 (tm-30) REVERT: T 296 TYR cc_start: 0.8926 (t80) cc_final: 0.8012 (t80) REVERT: Y 20 LEU cc_start: 0.9439 (mm) cc_final: 0.9087 (tp) REVERT: Y 36 LEU cc_start: 0.9307 (pp) cc_final: 0.8854 (mm) REVERT: Y 42 ARG cc_start: 0.9047 (mmp80) cc_final: 0.8204 (mmp80) REVERT: Y 45 GLU cc_start: 0.7526 (pp20) cc_final: 0.5529 (pp20) REVERT: Z 185 ARG cc_start: 0.8788 (ttt90) cc_final: 0.8260 (ttp-110) REVERT: Z 190 ASP cc_start: 0.8566 (t70) cc_final: 0.8069 (p0) REVERT: Z 235 GLU cc_start: 0.9612 (mm-30) cc_final: 0.8875 (pt0) REVERT: Z 239 GLU cc_start: 0.9444 (mm-30) cc_final: 0.9208 (mm-30) outliers start: 41 outliers final: 24 residues processed: 428 average time/residue: 0.1802 time to fit residues: 113.4252 Evaluate side-chains 414 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 387 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 49 MET Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 27 ILE Chi-restraints excluded: chain J residue 47 THR Chi-restraints excluded: chain L residue 15 LEU Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 47 THR Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain O residue 6 LEU Chi-restraints excluded: chain O residue 18 ILE Chi-restraints excluded: chain P residue 56 THR Chi-restraints excluded: chain Q residue 32 VAL Chi-restraints excluded: chain T residue 114 PHE Chi-restraints excluded: chain T residue 240 LEU Chi-restraints excluded: chain T residue 253 ASN Chi-restraints excluded: chain T residue 274 LEU Chi-restraints excluded: chain V residue 11 PHE Chi-restraints excluded: chain Y residue 24 ILE Chi-restraints excluded: chain Y residue 33 VAL Chi-restraints excluded: chain Z residue 48 ILE Chi-restraints excluded: chain Z residue 109 LEU Chi-restraints excluded: chain Z residue 250 LEU Chi-restraints excluded: chain Z residue 289 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 66 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 127 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 74 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 134 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 287 GLN ** T 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.089024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.067456 restraints weight = 45489.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.069047 restraints weight = 32263.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.070192 restraints weight = 24901.875| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10621 Z= 0.174 Angle : 0.786 13.590 14456 Z= 0.384 Chirality : 0.047 0.320 1780 Planarity : 0.005 0.051 1819 Dihedral : 4.006 17.228 1476 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 22.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.15 % Allowed : 34.58 % Favored : 61.26 % 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: 0.68 (0.22), residues: 1388 helix: 0.96 (0.15), residues: 1125 sheet: None (None), residues: 0 loop : -1.59 (0.42), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP T 208 HIS 0.001 0.000 HIS Z 31 PHE 0.052 0.002 PHE H 55 TYR 0.028 0.001 TYR K 48 ARG 0.011 0.000 ARG Z 249 Details of bonding type rmsd hydrogen bonds : bond 0.04995 ( 920) hydrogen bonds : angle 4.19510 ( 2739) SS BOND : bond 0.00177 ( 1) SS BOND : angle 2.82408 ( 2) covalent geometry : bond 0.00404 (10620) covalent geometry : angle 0.78534 (14454) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 398 time to evaluate : 1.157 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 29 SER cc_start: 0.9739 (t) cc_final: 0.9464 (p) REVERT: H 44 ARG cc_start: 0.8572 (mtp85) cc_final: 0.8149 (mmm-85) REVERT: H 48 TYR cc_start: 0.8914 (m-80) cc_final: 0.8392 (m-80) REVERT: H 49 MET cc_start: 0.9379 (OUTLIER) cc_final: 0.8868 (ppp) REVERT: H 57 GLU cc_start: 0.9358 (mt-10) cc_final: 0.9127 (mt-10) REVERT: H 59 LEU cc_start: 0.9353 (mt) cc_final: 0.8821 (mm) REVERT: H 62 PHE cc_start: 0.9413 (m-80) cc_final: 0.9093 (m-80) REVERT: I 33 GLN cc_start: 0.9302 (mt0) cc_final: 0.8739 (mm-40) REVERT: I 37 ARG cc_start: 0.9149 (mtt90) cc_final: 0.8897 (mtt90) REVERT: I 48 TYR cc_start: 0.9321 (m-80) cc_final: 0.8727 (m-80) REVERT: I 49 MET cc_start: 0.9519 (ttp) cc_final: 0.9226 (ppp) REVERT: I 55 PHE cc_start: 0.9408 (m-10) cc_final: 0.8849 (m-80) REVERT: I 62 PHE cc_start: 0.9240 (m-10) cc_final: 0.9027 (m-10) REVERT: J 49 MET cc_start: 0.9590 (ttt) cc_final: 0.9235 (tmm) REVERT: J 57 GLU cc_start: 0.9760 (mm-30) cc_final: 0.9484 (mm-30) REVERT: K 43 ASN cc_start: 0.9191 (m-40) cc_final: 0.8885 (p0) REVERT: K 50 PHE cc_start: 0.9104 (OUTLIER) cc_final: 0.8804 (m-80) REVERT: K 57 GLU cc_start: 0.9638 (tp30) cc_final: 0.9323 (pt0) REVERT: K 59 LEU cc_start: 0.9141 (mt) cc_final: 0.8596 (mm) REVERT: K 62 PHE cc_start: 0.8685 (m-10) cc_final: 0.8315 (m-10) REVERT: L 15 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8672 (tp) REVERT: L 50 PHE cc_start: 0.8841 (m-80) cc_final: 0.8626 (m-80) REVERT: L 66 ILE cc_start: 0.9508 (mm) cc_final: 0.9189 (mm) REVERT: M 29 SER cc_start: 0.9584 (t) cc_final: 0.8917 (m) REVERT: M 66 ILE cc_start: 0.9378 (mm) cc_final: 0.9159 (mm) REVERT: M 68 PHE cc_start: 0.8184 (m-10) cc_final: 0.7780 (m-80) REVERT: N 26 ILE cc_start: 0.9303 (OUTLIER) cc_final: 0.9041 (tp) REVERT: O 1 MET cc_start: 0.6794 (tpp) cc_final: 0.6566 (tpt) REVERT: O 50 PHE cc_start: 0.9264 (m-10) cc_final: 0.8910 (m-80) REVERT: O 51 ILE cc_start: 0.8731 (mm) cc_final: 0.8461 (tp) REVERT: O 62 PHE cc_start: 0.9240 (m-10) cc_final: 0.8758 (m-80) REVERT: P 1 MET cc_start: 0.6169 (mtt) cc_final: 0.5768 (ptp) REVERT: P 38 ASN cc_start: 0.8958 (t0) cc_final: 0.8050 (t0) REVERT: P 41 ILE cc_start: 0.9432 (tp) cc_final: 0.8966 (tt) REVERT: P 48 TYR cc_start: 0.9160 (m-80) cc_final: 0.8675 (m-80) REVERT: P 49 MET cc_start: 0.9699 (ttt) cc_final: 0.9326 (tmm) REVERT: P 51 ILE cc_start: 0.9507 (mm) cc_final: 0.9098 (tt) REVERT: Q 26 ILE cc_start: 0.9683 (mt) cc_final: 0.9321 (tp) REVERT: Q 33 GLN cc_start: 0.9183 (mm-40) cc_final: 0.8923 (mm110) REVERT: Q 38 ASN cc_start: 0.9243 (t0) cc_final: 0.8710 (t0) REVERT: Q 48 TYR cc_start: 0.8801 (m-10) cc_final: 0.8200 (m-80) REVERT: Q 49 MET cc_start: 0.9412 (tmm) cc_final: 0.9100 (ppp) REVERT: Q 64 LEU cc_start: 0.9315 (tp) cc_final: 0.8942 (tp) REVERT: T 84 MET cc_start: 0.6339 (mtt) cc_final: 0.5802 (ptp) REVERT: T 102 TYR cc_start: 0.8060 (m-80) cc_final: 0.7544 (m-80) REVERT: T 185 ARG cc_start: 0.6754 (ttt-90) cc_final: 0.6083 (ptm-80) REVERT: T 235 GLU cc_start: 0.9584 (tp30) cc_final: 0.9251 (tm-30) REVERT: T 264 MET cc_start: 0.7223 (ptp) cc_final: 0.7019 (ptp) REVERT: T 296 TYR cc_start: 0.8844 (t80) cc_final: 0.7963 (t80) REVERT: Y 18 PHE cc_start: 0.9091 (t80) cc_final: 0.8747 (t80) REVERT: Y 20 LEU cc_start: 0.9414 (mm) cc_final: 0.9068 (tp) REVERT: Y 36 LEU cc_start: 0.9324 (pp) cc_final: 0.8817 (mm) REVERT: Y 42 ARG cc_start: 0.8936 (mmp80) cc_final: 0.8261 (mmp80) REVERT: Y 45 GLU cc_start: 0.6959 (pp20) cc_final: 0.6478 (pp20) REVERT: Z 185 ARG cc_start: 0.8770 (ttt90) cc_final: 0.8273 (ttp-110) REVERT: Z 190 ASP cc_start: 0.8541 (t70) cc_final: 0.8065 (p0) outliers start: 42 outliers final: 28 residues processed: 417 average time/residue: 0.2123 time to fit residues: 132.0246 Evaluate side-chains 405 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 373 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 49 MET Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 27 ILE Chi-restraints excluded: chain K residue 50 PHE Chi-restraints excluded: chain L residue 15 LEU Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 47 THR Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain O residue 6 LEU Chi-restraints excluded: chain O residue 18 ILE Chi-restraints excluded: chain P residue 28 VAL Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 56 THR Chi-restraints excluded: chain Q residue 32 VAL Chi-restraints excluded: chain T residue 240 LEU Chi-restraints excluded: chain T residue 253 ASN Chi-restraints excluded: chain T residue 274 LEU Chi-restraints excluded: chain V residue 6 ILE Chi-restraints excluded: chain V residue 11 PHE Chi-restraints excluded: chain Y residue 24 ILE Chi-restraints excluded: chain Y residue 33 VAL Chi-restraints excluded: chain Z residue 48 ILE Chi-restraints excluded: chain Z residue 109 LEU Chi-restraints excluded: chain Z residue 250 LEU Chi-restraints excluded: chain Z residue 260 LEU Chi-restraints excluded: chain Z residue 289 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 30 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 81 optimal weight: 8.9990 chunk 88 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 192 ASN T 287 GLN ** T 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.088593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.067450 restraints weight = 45288.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.069112 restraints weight = 32217.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.070275 restraints weight = 24768.512| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.4285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10621 Z= 0.177 Angle : 0.784 13.117 14456 Z= 0.387 Chirality : 0.049 0.319 1780 Planarity : 0.005 0.054 1819 Dihedral : 4.006 21.323 1476 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 23.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.05 % Allowed : 37.45 % Favored : 58.50 % 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: 0.63 (0.22), residues: 1388 helix: 0.93 (0.15), residues: 1118 sheet: None (None), residues: 0 loop : -1.56 (0.41), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP T 208 HIS 0.002 0.000 HIS Z 31 PHE 0.051 0.002 PHE T 282 TYR 0.025 0.001 TYR K 48 ARG 0.010 0.000 ARG Z 249 Details of bonding type rmsd hydrogen bonds : bond 0.04983 ( 920) hydrogen bonds : angle 4.22813 ( 2739) SS BOND : bond 0.00137 ( 1) SS BOND : angle 2.52435 ( 2) covalent geometry : bond 0.00417 (10620) covalent geometry : angle 0.78397 (14454) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 395 time to evaluate : 1.151 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 29 SER cc_start: 0.9766 (t) cc_final: 0.9495 (p) REVERT: H 44 ARG cc_start: 0.8575 (mtp85) cc_final: 0.8165 (mmm-85) REVERT: H 48 TYR cc_start: 0.8955 (m-80) cc_final: 0.8380 (m-80) REVERT: H 49 MET cc_start: 0.9359 (OUTLIER) cc_final: 0.8901 (ppp) REVERT: H 57 GLU cc_start: 0.9321 (mt-10) cc_final: 0.9078 (mt-10) REVERT: H 59 LEU cc_start: 0.9318 (mt) cc_final: 0.8791 (mm) REVERT: H 62 PHE cc_start: 0.9381 (m-80) cc_final: 0.9087 (m-80) REVERT: I 33 GLN cc_start: 0.9298 (mt0) cc_final: 0.8814 (mm-40) REVERT: I 37 ARG cc_start: 0.9121 (mtt90) cc_final: 0.8757 (mpp80) REVERT: I 48 TYR cc_start: 0.9284 (m-80) cc_final: 0.8693 (m-80) REVERT: I 49 MET cc_start: 0.9498 (ttp) cc_final: 0.9243 (ppp) REVERT: I 51 ILE cc_start: 0.9140 (mt) cc_final: 0.8489 (mm) REVERT: I 55 PHE cc_start: 0.9386 (m-10) cc_final: 0.8853 (m-80) REVERT: I 62 PHE cc_start: 0.9260 (m-10) cc_final: 0.8978 (m-10) REVERT: J 49 MET cc_start: 0.9597 (ttt) cc_final: 0.9252 (tmm) REVERT: K 43 ASN cc_start: 0.9191 (m-40) cc_final: 0.8890 (p0) REVERT: K 48 TYR cc_start: 0.9548 (m-80) cc_final: 0.9337 (m-80) REVERT: K 50 PHE cc_start: 0.9141 (OUTLIER) cc_final: 0.8754 (m-80) REVERT: K 57 GLU cc_start: 0.9639 (tp30) cc_final: 0.9314 (pt0) REVERT: L 15 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8605 (tp) REVERT: L 50 PHE cc_start: 0.8806 (m-80) cc_final: 0.8551 (m-80) REVERT: L 66 ILE cc_start: 0.9461 (mm) cc_final: 0.9096 (mm) REVERT: M 29 SER cc_start: 0.9579 (t) cc_final: 0.8934 (m) REVERT: M 66 ILE cc_start: 0.9350 (mm) cc_final: 0.9125 (mm) REVERT: M 68 PHE cc_start: 0.8227 (m-10) cc_final: 0.7796 (m-80) REVERT: N 48 TYR cc_start: 0.8973 (m-10) cc_final: 0.8409 (m-80) REVERT: O 50 PHE cc_start: 0.9241 (m-10) cc_final: 0.8878 (m-80) REVERT: O 62 PHE cc_start: 0.9231 (m-10) cc_final: 0.8736 (m-80) REVERT: P 1 MET cc_start: 0.6008 (mtt) cc_final: 0.5064 (tpp) REVERT: P 38 ASN cc_start: 0.8976 (t0) cc_final: 0.8087 (t0) REVERT: P 41 ILE cc_start: 0.9441 (tp) cc_final: 0.8952 (tt) REVERT: P 48 TYR cc_start: 0.9146 (m-80) cc_final: 0.8670 (m-80) REVERT: P 49 MET cc_start: 0.9700 (ttt) cc_final: 0.9355 (tmm) REVERT: P 51 ILE cc_start: 0.9547 (mm) cc_final: 0.9134 (tt) REVERT: Q 26 ILE cc_start: 0.9686 (mt) cc_final: 0.9353 (tp) REVERT: Q 33 GLN cc_start: 0.9209 (mm-40) cc_final: 0.8914 (mm110) REVERT: Q 38 ASN cc_start: 0.9202 (t0) cc_final: 0.8684 (t0) REVERT: Q 48 TYR cc_start: 0.8815 (m-10) cc_final: 0.8228 (m-80) REVERT: Q 49 MET cc_start: 0.9379 (tmm) cc_final: 0.8869 (tmm) REVERT: Q 64 LEU cc_start: 0.9267 (tp) cc_final: 0.9060 (tp) REVERT: T 92 TYR cc_start: 0.7713 (OUTLIER) cc_final: 0.7159 (m-80) REVERT: T 102 TYR cc_start: 0.8007 (m-80) cc_final: 0.7520 (m-80) REVERT: T 235 GLU cc_start: 0.9568 (tp30) cc_final: 0.9247 (tm-30) REVERT: T 296 TYR cc_start: 0.8784 (t80) cc_final: 0.7957 (t80) REVERT: Y 18 PHE cc_start: 0.9140 (t80) cc_final: 0.8811 (t80) REVERT: Y 36 LEU cc_start: 0.9321 (pp) cc_final: 0.8825 (mm) REVERT: Y 42 ARG cc_start: 0.8970 (mmp80) cc_final: 0.8283 (mmp80) REVERT: Y 45 GLU cc_start: 0.7237 (pp20) cc_final: 0.6696 (pp20) REVERT: Z 190 ASP cc_start: 0.8593 (t70) cc_final: 0.8081 (p0) outliers start: 41 outliers final: 28 residues processed: 412 average time/residue: 0.2175 time to fit residues: 133.4343 Evaluate side-chains 408 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 376 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 18 ILE Chi-restraints excluded: chain H residue 49 MET Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 27 ILE Chi-restraints excluded: chain K residue 50 PHE Chi-restraints excluded: chain L residue 15 LEU Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 47 THR Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain O residue 6 LEU Chi-restraints excluded: chain P residue 56 THR Chi-restraints excluded: chain Q residue 6 LEU Chi-restraints excluded: chain Q residue 32 VAL Chi-restraints excluded: chain T residue 92 TYR Chi-restraints excluded: chain T residue 240 LEU Chi-restraints excluded: chain T residue 253 ASN Chi-restraints excluded: chain T residue 274 LEU Chi-restraints excluded: chain V residue 6 ILE Chi-restraints excluded: chain V residue 11 PHE Chi-restraints excluded: chain Y residue 24 ILE Chi-restraints excluded: chain Y residue 33 VAL Chi-restraints excluded: chain Z residue 48 ILE Chi-restraints excluded: chain Z residue 109 LEU Chi-restraints excluded: chain Z residue 250 LEU Chi-restraints excluded: chain Z residue 260 LEU Chi-restraints excluded: chain Z residue 289 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 123 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 113 optimal weight: 6.9990 chunk 5 optimal weight: 0.7980 chunk 132 optimal weight: 0.4980 chunk 50 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 114 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 287 GLN ** T 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.088629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.067474 restraints weight = 45990.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.069175 restraints weight = 32568.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.070395 restraints weight = 24830.811| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.4480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 10621 Z= 0.175 Angle : 0.811 14.492 14456 Z= 0.398 Chirality : 0.049 0.314 1780 Planarity : 0.005 0.054 1819 Dihedral : 4.036 23.426 1476 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 23.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 4.05 % Allowed : 38.34 % Favored : 57.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.22), residues: 1388 helix: 0.90 (0.15), residues: 1119 sheet: None (None), residues: 0 loop : -1.63 (0.40), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP T 208 HIS 0.002 0.001 HIS Z 136 PHE 0.060 0.001 PHE P 62 TYR 0.025 0.001 TYR K 48 ARG 0.012 0.000 ARG Z 249 Details of bonding type rmsd hydrogen bonds : bond 0.04978 ( 920) hydrogen bonds : angle 4.27379 ( 2739) SS BOND : bond 0.00122 ( 1) SS BOND : angle 2.28290 ( 2) covalent geometry : bond 0.00410 (10620) covalent geometry : angle 0.81028 (14454) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 392 time to evaluate : 1.688 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 29 SER cc_start: 0.9774 (t) cc_final: 0.9368 (p) REVERT: H 33 GLN cc_start: 0.9387 (mt0) cc_final: 0.8859 (mm-40) REVERT: H 37 ARG cc_start: 0.9070 (mtt90) cc_final: 0.8743 (mtt90) REVERT: H 44 ARG cc_start: 0.8651 (mtp85) cc_final: 0.8223 (mmm-85) REVERT: H 48 TYR cc_start: 0.9027 (m-80) cc_final: 0.8346 (m-80) REVERT: H 49 MET cc_start: 0.9389 (OUTLIER) cc_final: 0.8925 (ppp) REVERT: H 57 GLU cc_start: 0.9313 (mt-10) cc_final: 0.9074 (mt-10) REVERT: H 59 LEU cc_start: 0.9293 (mt) cc_final: 0.8786 (mm) REVERT: H 62 PHE cc_start: 0.9403 (m-80) cc_final: 0.9115 (m-80) REVERT: I 33 GLN cc_start: 0.9319 (mt0) cc_final: 0.8784 (mm-40) REVERT: I 37 ARG cc_start: 0.9139 (mtt90) cc_final: 0.8744 (mpp80) REVERT: I 48 TYR cc_start: 0.9314 (m-80) cc_final: 0.8723 (m-80) REVERT: I 49 MET cc_start: 0.9523 (ttp) cc_final: 0.9277 (ppp) REVERT: I 51 ILE cc_start: 0.9141 (mt) cc_final: 0.8515 (mm) REVERT: I 55 PHE cc_start: 0.9372 (m-10) cc_final: 0.8862 (m-80) REVERT: I 62 PHE cc_start: 0.9313 (m-10) cc_final: 0.9042 (m-10) REVERT: J 49 MET cc_start: 0.9631 (ttt) cc_final: 0.9273 (tmm) REVERT: K 43 ASN cc_start: 0.9227 (m-40) cc_final: 0.8908 (p0) REVERT: K 50 PHE cc_start: 0.9105 (OUTLIER) cc_final: 0.8752 (m-80) REVERT: K 57 GLU cc_start: 0.9630 (tp30) cc_final: 0.9277 (pt0) REVERT: L 1 MET cc_start: 0.5876 (mmt) cc_final: 0.5437 (mmp) REVERT: L 11 LEU cc_start: 0.9397 (tt) cc_final: 0.9180 (tt) REVERT: L 15 LEU cc_start: 0.9167 (mm) cc_final: 0.8730 (tp) REVERT: L 50 PHE cc_start: 0.8766 (m-80) cc_final: 0.8516 (m-80) REVERT: L 57 GLU cc_start: 0.9488 (mm-30) cc_final: 0.9287 (mm-30) REVERT: L 66 ILE cc_start: 0.9501 (mm) cc_final: 0.9178 (mm) REVERT: M 4 LEU cc_start: 0.9464 (OUTLIER) cc_final: 0.9068 (tp) REVERT: M 29 SER cc_start: 0.9569 (t) cc_final: 0.8895 (m) REVERT: M 68 PHE cc_start: 0.8240 (m-10) cc_final: 0.7791 (m-80) REVERT: O 1 MET cc_start: 0.7181 (tpp) cc_final: 0.6870 (tpt) REVERT: O 50 PHE cc_start: 0.9256 (m-10) cc_final: 0.8753 (m-80) REVERT: O 51 ILE cc_start: 0.8722 (mm) cc_final: 0.8400 (tp) REVERT: O 62 PHE cc_start: 0.9235 (m-10) cc_final: 0.8873 (m-10) REVERT: P 1 MET cc_start: 0.6194 (mtt) cc_final: 0.5753 (ptp) REVERT: P 38 ASN cc_start: 0.9004 (t0) cc_final: 0.8085 (t0) REVERT: P 41 ILE cc_start: 0.9494 (tp) cc_final: 0.8968 (tt) REVERT: P 48 TYR cc_start: 0.9176 (m-80) cc_final: 0.8656 (m-80) REVERT: P 49 MET cc_start: 0.9712 (ttt) cc_final: 0.9349 (tmm) REVERT: P 51 ILE cc_start: 0.9553 (mm) cc_final: 0.9123 (tt) REVERT: P 55 PHE cc_start: 0.9667 (m-80) cc_final: 0.9393 (m-80) REVERT: P 57 GLU cc_start: 0.9409 (mm-30) cc_final: 0.8889 (pt0) REVERT: Q 26 ILE cc_start: 0.9661 (mt) cc_final: 0.9314 (tp) REVERT: Q 33 GLN cc_start: 0.9309 (mm-40) cc_final: 0.8931 (mm110) REVERT: Q 38 ASN cc_start: 0.9247 (t0) cc_final: 0.8684 (t0) REVERT: Q 48 TYR cc_start: 0.8874 (m-10) cc_final: 0.8212 (m-80) REVERT: Q 49 MET cc_start: 0.9375 (tmm) cc_final: 0.8900 (tmm) REVERT: T 84 MET cc_start: 0.6417 (mtt) cc_final: 0.5918 (ptp) REVERT: T 92 TYR cc_start: 0.7722 (OUTLIER) cc_final: 0.7218 (m-80) REVERT: T 102 TYR cc_start: 0.8056 (m-80) cc_final: 0.7569 (m-80) REVERT: T 235 GLU cc_start: 0.9570 (tp30) cc_final: 0.9251 (tm-30) REVERT: T 296 TYR cc_start: 0.8810 (t80) cc_final: 0.8141 (t80) REVERT: V 35 ASN cc_start: 0.9300 (m-40) cc_final: 0.8950 (p0) REVERT: Y 18 PHE cc_start: 0.9183 (t80) cc_final: 0.8875 (t80) REVERT: Y 20 LEU cc_start: 0.9444 (mm) cc_final: 0.9122 (tp) REVERT: Y 36 LEU cc_start: 0.9361 (pp) cc_final: 0.8872 (mm) REVERT: Y 42 ARG cc_start: 0.8966 (mmp80) cc_final: 0.8326 (mmp80) REVERT: Y 45 GLU cc_start: 0.7288 (pp20) cc_final: 0.6803 (pp20) REVERT: Z 190 ASP cc_start: 0.8602 (t70) cc_final: 0.8035 (p0) REVERT: Z 264 MET cc_start: 0.9490 (mmm) cc_final: 0.9258 (mmm) outliers start: 41 outliers final: 32 residues processed: 411 average time/residue: 0.1837 time to fit residues: 111.5785 Evaluate side-chains 406 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 370 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 18 ILE Chi-restraints excluded: chain H residue 49 MET Chi-restraints excluded: chain I residue 50 PHE Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 27 ILE Chi-restraints excluded: chain K residue 50 PHE Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 47 THR Chi-restraints excluded: chain M residue 50 PHE Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain O residue 6 LEU Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain Q residue 6 LEU Chi-restraints excluded: chain Q residue 32 VAL Chi-restraints excluded: chain T residue 92 TYR Chi-restraints excluded: chain T residue 114 PHE Chi-restraints excluded: chain T residue 240 LEU Chi-restraints excluded: chain T residue 253 ASN Chi-restraints excluded: chain T residue 274 LEU Chi-restraints excluded: chain V residue 6 ILE Chi-restraints excluded: chain V residue 11 PHE Chi-restraints excluded: chain Y residue 24 ILE Chi-restraints excluded: chain Y residue 33 VAL Chi-restraints excluded: chain Z residue 32 VAL Chi-restraints excluded: chain Z residue 48 ILE Chi-restraints excluded: chain Z residue 109 LEU Chi-restraints excluded: chain Z residue 250 LEU Chi-restraints excluded: chain Z residue 260 LEU Chi-restraints excluded: chain Z residue 289 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 124 optimal weight: 9.9990 chunk 137 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 72 optimal weight: 0.0370 chunk 19 optimal weight: 0.8980 chunk 118 optimal weight: 0.2980 chunk 117 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 121 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 287 GLN ** T 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.089371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.068142 restraints weight = 45488.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.069717 restraints weight = 32329.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.071017 restraints weight = 24975.228| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.4635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 10621 Z= 0.177 Angle : 0.851 14.201 14456 Z= 0.411 Chirality : 0.050 0.324 1780 Planarity : 0.005 0.055 1819 Dihedral : 4.077 25.287 1476 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 23.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 4.15 % Allowed : 40.12 % Favored : 55.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.22), residues: 1388 helix: 0.90 (0.15), residues: 1126 sheet: None (None), residues: 0 loop : -1.79 (0.41), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP T 208 HIS 0.001 0.000 HIS Z 31 PHE 0.061 0.002 PHE T 282 TYR 0.015 0.001 TYR M 48 ARG 0.012 0.000 ARG Z 249 Details of bonding type rmsd hydrogen bonds : bond 0.05002 ( 920) hydrogen bonds : angle 4.30074 ( 2739) SS BOND : bond 0.00128 ( 1) SS BOND : angle 2.13925 ( 2) covalent geometry : bond 0.00421 (10620) covalent geometry : angle 0.85079 (14454) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 387 time to evaluate : 1.709 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 29 SER cc_start: 0.9777 (t) cc_final: 0.9356 (p) REVERT: H 33 GLN cc_start: 0.9360 (mt0) cc_final: 0.9015 (mm-40) REVERT: H 44 ARG cc_start: 0.8622 (mtp85) cc_final: 0.8200 (mmm-85) REVERT: H 48 TYR cc_start: 0.9061 (m-80) cc_final: 0.8333 (m-80) REVERT: H 49 MET cc_start: 0.9364 (OUTLIER) cc_final: 0.8916 (ppp) REVERT: H 57 GLU cc_start: 0.9283 (mt-10) cc_final: 0.9040 (mt-10) REVERT: H 59 LEU cc_start: 0.9268 (mt) cc_final: 0.8775 (mm) REVERT: H 62 PHE cc_start: 0.9370 (m-80) cc_final: 0.9101 (m-80) REVERT: I 33 GLN cc_start: 0.9309 (mt0) cc_final: 0.8819 (mm-40) REVERT: I 37 ARG cc_start: 0.9122 (mtt90) cc_final: 0.8732 (mpp80) REVERT: I 48 TYR cc_start: 0.9301 (m-80) cc_final: 0.8725 (m-80) REVERT: I 49 MET cc_start: 0.9511 (ttp) cc_final: 0.9266 (ppp) REVERT: I 51 ILE cc_start: 0.9127 (mt) cc_final: 0.8522 (mm) REVERT: I 55 PHE cc_start: 0.9369 (m-10) cc_final: 0.8864 (m-80) REVERT: I 62 PHE cc_start: 0.9275 (m-10) cc_final: 0.9034 (m-10) REVERT: J 49 MET cc_start: 0.9610 (ttt) cc_final: 0.9272 (tmm) REVERT: K 43 ASN cc_start: 0.9214 (m-40) cc_final: 0.8889 (p0) REVERT: K 50 PHE cc_start: 0.9122 (OUTLIER) cc_final: 0.8768 (m-10) REVERT: K 57 GLU cc_start: 0.9610 (tp30) cc_final: 0.9258 (pt0) REVERT: L 15 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8541 (tp) REVERT: L 50 PHE cc_start: 0.8730 (m-80) cc_final: 0.8480 (m-80) REVERT: L 66 ILE cc_start: 0.9488 (mm) cc_final: 0.9149 (mm) REVERT: M 29 SER cc_start: 0.9569 (t) cc_final: 0.8891 (m) REVERT: M 68 PHE cc_start: 0.8180 (m-10) cc_final: 0.7708 (m-80) REVERT: O 1 MET cc_start: 0.6748 (tpp) cc_final: 0.6021 (tpp) REVERT: O 50 PHE cc_start: 0.9204 (m-10) cc_final: 0.8710 (m-80) REVERT: O 51 ILE cc_start: 0.8703 (mm) cc_final: 0.8385 (tp) REVERT: P 1 MET cc_start: 0.6222 (mtt) cc_final: 0.5812 (ptp) REVERT: P 38 ASN cc_start: 0.8983 (t0) cc_final: 0.8086 (t0) REVERT: P 41 ILE cc_start: 0.9472 (tp) cc_final: 0.8941 (tt) REVERT: P 48 TYR cc_start: 0.9154 (m-80) cc_final: 0.8644 (m-80) REVERT: P 49 MET cc_start: 0.9709 (ttt) cc_final: 0.9332 (tmm) REVERT: P 62 PHE cc_start: 0.9197 (t80) cc_final: 0.8887 (t80) REVERT: Q 26 ILE cc_start: 0.9638 (mt) cc_final: 0.9275 (tp) REVERT: Q 33 GLN cc_start: 0.9305 (mm-40) cc_final: 0.8949 (mm110) REVERT: Q 38 ASN cc_start: 0.9236 (t0) cc_final: 0.8680 (t0) REVERT: Q 48 TYR cc_start: 0.8831 (m-10) cc_final: 0.8192 (m-80) REVERT: Q 49 MET cc_start: 0.9360 (tmm) cc_final: 0.8919 (tmm) REVERT: T 84 MET cc_start: 0.6273 (mtt) cc_final: 0.5844 (ptp) REVERT: T 92 TYR cc_start: 0.7670 (OUTLIER) cc_final: 0.7164 (m-80) REVERT: T 102 TYR cc_start: 0.8023 (m-80) cc_final: 0.7556 (m-80) REVERT: T 235 GLU cc_start: 0.9548 (tp30) cc_final: 0.9229 (tm-30) REVERT: T 296 TYR cc_start: 0.8850 (t80) cc_final: 0.8201 (t80) REVERT: V 35 ASN cc_start: 0.9281 (m-40) cc_final: 0.8904 (p0) REVERT: Y 18 PHE cc_start: 0.9178 (t80) cc_final: 0.8920 (t80) REVERT: Y 20 LEU cc_start: 0.9439 (mm) cc_final: 0.9106 (tp) REVERT: Y 45 GLU cc_start: 0.7354 (pp20) cc_final: 0.6600 (pp20) REVERT: Z 84 MET cc_start: 0.8932 (tmm) cc_final: 0.8709 (tmm) REVERT: Z 190 ASP cc_start: 0.8590 (t70) cc_final: 0.8044 (p0) REVERT: Z 264 MET cc_start: 0.9491 (mmm) cc_final: 0.9219 (mmm) outliers start: 42 outliers final: 31 residues processed: 405 average time/residue: 0.2062 time to fit residues: 124.0042 Evaluate side-chains 406 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 371 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 18 ILE Chi-restraints excluded: chain H residue 49 MET Chi-restraints excluded: chain I residue 35 ILE Chi-restraints excluded: chain I residue 50 PHE Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 27 ILE Chi-restraints excluded: chain K residue 50 PHE Chi-restraints excluded: chain L residue 15 LEU Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 47 THR Chi-restraints excluded: chain M residue 50 PHE Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain O residue 6 LEU Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain Q residue 32 VAL Chi-restraints excluded: chain T residue 92 TYR Chi-restraints excluded: chain T residue 114 PHE Chi-restraints excluded: chain T residue 240 LEU Chi-restraints excluded: chain T residue 250 LEU Chi-restraints excluded: chain T residue 253 ASN Chi-restraints excluded: chain T residue 274 LEU Chi-restraints excluded: chain V residue 6 ILE Chi-restraints excluded: chain V residue 11 PHE Chi-restraints excluded: chain Y residue 24 ILE Chi-restraints excluded: chain Y residue 33 VAL Chi-restraints excluded: chain Z residue 32 VAL Chi-restraints excluded: chain Z residue 48 ILE Chi-restraints excluded: chain Z residue 250 LEU Chi-restraints excluded: chain Z residue 260 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 87 optimal weight: 2.9990 chunk 124 optimal weight: 10.0000 chunk 100 optimal weight: 0.0040 chunk 67 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 121 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 72 optimal weight: 0.0010 chunk 35 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 overall best weight: 0.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 300 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 = 0.3856 r_free = 0.3856 target = 0.089029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.067933 restraints weight = 45715.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.069570 restraints weight = 32767.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.070526 restraints weight = 25447.080| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.4813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 10621 Z= 0.183 Angle : 0.893 15.487 14456 Z= 0.429 Chirality : 0.051 0.366 1780 Planarity : 0.005 0.056 1819 Dihedral : 4.083 23.647 1476 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 24.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.56 % Allowed : 41.40 % Favored : 55.04 % 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: 0.41 (0.22), residues: 1388 helix: 0.78 (0.15), residues: 1128 sheet: None (None), residues: 0 loop : -1.75 (0.41), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP T 208 HIS 0.001 0.000 HIS Z 31 PHE 0.060 0.002 PHE T 282 TYR 0.019 0.001 TYR K 48 ARG 0.013 0.000 ARG Z 249 Details of bonding type rmsd hydrogen bonds : bond 0.05047 ( 920) hydrogen bonds : angle 4.37963 ( 2739) SS BOND : bond 0.00105 ( 1) SS BOND : angle 2.02657 ( 2) covalent geometry : bond 0.00436 (10620) covalent geometry : angle 0.89275 (14454) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 382 time to evaluate : 1.168 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 29 SER cc_start: 0.9755 (t) cc_final: 0.9319 (p) REVERT: H 33 GLN cc_start: 0.9366 (mt0) cc_final: 0.8990 (mm-40) REVERT: H 44 ARG cc_start: 0.8601 (mtp85) cc_final: 0.8226 (mmm-85) REVERT: H 48 TYR cc_start: 0.9025 (m-80) cc_final: 0.8331 (m-80) REVERT: H 49 MET cc_start: 0.9363 (OUTLIER) cc_final: 0.9043 (ppp) REVERT: H 57 GLU cc_start: 0.9253 (mt-10) cc_final: 0.9014 (mt-10) REVERT: H 59 LEU cc_start: 0.9256 (mt) cc_final: 0.8751 (mm) REVERT: H 62 PHE cc_start: 0.9360 (m-80) cc_final: 0.9110 (m-80) REVERT: I 33 GLN cc_start: 0.9281 (mt0) cc_final: 0.8801 (mm-40) REVERT: I 37 ARG cc_start: 0.9111 (mtt90) cc_final: 0.8742 (mpp80) REVERT: I 48 TYR cc_start: 0.9283 (m-80) cc_final: 0.8708 (m-80) REVERT: I 49 MET cc_start: 0.9502 (ttp) cc_final: 0.9248 (ppp) REVERT: I 51 ILE cc_start: 0.9130 (mt) cc_final: 0.8555 (mm) REVERT: I 55 PHE cc_start: 0.9348 (m-10) cc_final: 0.8861 (m-80) REVERT: I 62 PHE cc_start: 0.9251 (m-10) cc_final: 0.8987 (m-80) REVERT: J 49 MET cc_start: 0.9575 (ttt) cc_final: 0.9295 (tmm) REVERT: K 43 ASN cc_start: 0.9200 (m-40) cc_final: 0.8880 (p0) REVERT: K 50 PHE cc_start: 0.9139 (OUTLIER) cc_final: 0.8809 (m-10) REVERT: K 57 GLU cc_start: 0.9595 (tp30) cc_final: 0.9237 (pt0) REVERT: L 15 LEU cc_start: 0.9092 (mm) cc_final: 0.8494 (tp) REVERT: L 57 GLU cc_start: 0.9506 (mm-30) cc_final: 0.9265 (mm-30) REVERT: L 66 ILE cc_start: 0.9477 (mm) cc_final: 0.9173 (mm) REVERT: M 4 LEU cc_start: 0.9344 (tp) cc_final: 0.9035 (tp) REVERT: M 29 SER cc_start: 0.9599 (t) cc_final: 0.8960 (m) REVERT: M 68 PHE cc_start: 0.8073 (m-10) cc_final: 0.7609 (m-80) REVERT: O 1 MET cc_start: 0.6479 (tpp) cc_final: 0.6199 (tpp) REVERT: O 50 PHE cc_start: 0.9158 (m-10) cc_final: 0.8627 (m-80) REVERT: O 51 ILE cc_start: 0.8649 (mm) cc_final: 0.8328 (tp) REVERT: O 62 PHE cc_start: 0.9125 (m-10) cc_final: 0.8840 (m-80) REVERT: P 1 MET cc_start: 0.6151 (mtt) cc_final: 0.5403 (tpp) REVERT: P 38 ASN cc_start: 0.8975 (t0) cc_final: 0.8117 (t0) REVERT: P 41 ILE cc_start: 0.9432 (tp) cc_final: 0.8926 (tt) REVERT: P 48 TYR cc_start: 0.9128 (m-80) cc_final: 0.8666 (m-80) REVERT: P 49 MET cc_start: 0.9708 (ttt) cc_final: 0.9350 (tmm) REVERT: Q 26 ILE cc_start: 0.9656 (mt) cc_final: 0.9280 (tp) REVERT: Q 33 GLN cc_start: 0.9290 (mm-40) cc_final: 0.9025 (mm110) REVERT: Q 38 ASN cc_start: 0.9204 (t0) cc_final: 0.8701 (t0) REVERT: Q 48 TYR cc_start: 0.8754 (m-10) cc_final: 0.8141 (m-80) REVERT: Q 49 MET cc_start: 0.9323 (tmm) cc_final: 0.8856 (tmm) REVERT: T 84 MET cc_start: 0.6315 (mtt) cc_final: 0.5862 (ptp) REVERT: T 92 TYR cc_start: 0.7735 (OUTLIER) cc_final: 0.7186 (m-80) REVERT: T 102 TYR cc_start: 0.8052 (m-80) cc_final: 0.7596 (m-80) REVERT: T 235 GLU cc_start: 0.9558 (tp30) cc_final: 0.9242 (tm-30) REVERT: T 296 TYR cc_start: 0.8666 (t80) cc_final: 0.8188 (t80) REVERT: V 34 MET cc_start: 0.9131 (mmm) cc_final: 0.8924 (mmm) REVERT: V 35 ASN cc_start: 0.9210 (m-40) cc_final: 0.8970 (p0) REVERT: Y 18 PHE cc_start: 0.9134 (t80) cc_final: 0.8923 (t80) REVERT: Y 20 LEU cc_start: 0.9432 (mm) cc_final: 0.9097 (tp) REVERT: Y 36 LEU cc_start: 0.9336 (pp) cc_final: 0.8930 (mm) REVERT: Y 42 ARG cc_start: 0.8981 (mmp80) cc_final: 0.8175 (mmp80) REVERT: Y 45 GLU cc_start: 0.7250 (pp20) cc_final: 0.6648 (pp20) REVERT: Y 46 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7834 (mm-30) REVERT: Z 190 ASP cc_start: 0.8497 (t70) cc_final: 0.7999 (p0) outliers start: 36 outliers final: 28 residues processed: 396 average time/residue: 0.1908 time to fit residues: 111.1496 Evaluate side-chains 403 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 372 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 18 ILE Chi-restraints excluded: chain H residue 49 MET Chi-restraints excluded: chain I residue 50 PHE Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain J residue 27 ILE Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 50 PHE Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 47 THR Chi-restraints excluded: chain M residue 50 PHE Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain O residue 6 LEU Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain Q residue 6 LEU Chi-restraints excluded: chain Q residue 32 VAL Chi-restraints excluded: chain T residue 92 TYR Chi-restraints excluded: chain T residue 114 PHE Chi-restraints excluded: chain T residue 240 LEU Chi-restraints excluded: chain T residue 250 LEU Chi-restraints excluded: chain T residue 274 LEU Chi-restraints excluded: chain V residue 6 ILE Chi-restraints excluded: chain V residue 11 PHE Chi-restraints excluded: chain Y residue 24 ILE Chi-restraints excluded: chain Y residue 33 VAL Chi-restraints excluded: chain Z residue 32 VAL Chi-restraints excluded: chain Z residue 48 ILE Chi-restraints excluded: chain Z residue 260 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 40 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 102 optimal weight: 0.0970 chunk 14 optimal weight: 0.9980 chunk 94 optimal weight: 0.6980 chunk 97 optimal weight: 30.0000 chunk 45 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 287 GLN ** T 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.089666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.068371 restraints weight = 45227.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.069999 restraints weight = 32660.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.071127 restraints weight = 25516.431| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.5005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 10621 Z= 0.184 Angle : 0.926 15.438 14456 Z= 0.439 Chirality : 0.053 0.464 1780 Planarity : 0.005 0.056 1819 Dihedral : 4.140 22.504 1476 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 24.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.56 % Allowed : 42.39 % Favored : 54.05 % 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 (0.22), residues: 1388 helix: 0.71 (0.15), residues: 1128 sheet: None (None), residues: 0 loop : -1.80 (0.41), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP T 208 HIS 0.001 0.000 HIS Z 31 PHE 0.059 0.001 PHE T 282 TYR 0.015 0.001 TYR M 48 ARG 0.015 0.000 ARG Z 249 Details of bonding type rmsd hydrogen bonds : bond 0.05087 ( 920) hydrogen bonds : angle 4.42864 ( 2739) SS BOND : bond 0.00119 ( 1) SS BOND : angle 1.95528 ( 2) covalent geometry : bond 0.00436 (10620) covalent geometry : angle 0.92614 (14454) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 384 time to evaluate : 1.139 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 29 SER cc_start: 0.9761 (t) cc_final: 0.9296 (p) REVERT: H 33 GLN cc_start: 0.9339 (mt0) cc_final: 0.8970 (mm-40) REVERT: H 44 ARG cc_start: 0.8592 (mtp85) cc_final: 0.8190 (mmm-85) REVERT: H 48 TYR cc_start: 0.9026 (m-80) cc_final: 0.8305 (m-80) REVERT: H 49 MET cc_start: 0.9373 (OUTLIER) cc_final: 0.9008 (ppp) REVERT: H 57 GLU cc_start: 0.9243 (mt-10) cc_final: 0.8931 (mt-10) REVERT: H 59 LEU cc_start: 0.9224 (mt) cc_final: 0.8745 (mm) REVERT: H 62 PHE cc_start: 0.9350 (m-80) cc_final: 0.9088 (m-80) REVERT: I 33 GLN cc_start: 0.9270 (mt0) cc_final: 0.8790 (mm-40) REVERT: I 37 ARG cc_start: 0.9098 (mtt90) cc_final: 0.8725 (mpp80) REVERT: I 48 TYR cc_start: 0.9281 (m-80) cc_final: 0.8694 (m-80) REVERT: I 49 MET cc_start: 0.9504 (ttp) cc_final: 0.9233 (ppp) REVERT: I 51 ILE cc_start: 0.9109 (mt) cc_final: 0.8565 (mm) REVERT: I 55 PHE cc_start: 0.9342 (m-10) cc_final: 0.8895 (m-80) REVERT: I 62 PHE cc_start: 0.9199 (m-10) cc_final: 0.8943 (m-80) REVERT: J 49 MET cc_start: 0.9588 (ttt) cc_final: 0.9323 (tmm) REVERT: K 43 ASN cc_start: 0.9201 (m-40) cc_final: 0.8896 (p0) REVERT: K 50 PHE cc_start: 0.9137 (OUTLIER) cc_final: 0.8820 (m-10) REVERT: K 57 GLU cc_start: 0.9575 (tp30) cc_final: 0.9232 (pt0) REVERT: L 15 LEU cc_start: 0.9147 (mm) cc_final: 0.8655 (tp) REVERT: L 66 ILE cc_start: 0.9480 (mm) cc_final: 0.9173 (mm) REVERT: M 4 LEU cc_start: 0.9357 (tp) cc_final: 0.9049 (tp) REVERT: M 29 SER cc_start: 0.9524 (t) cc_final: 0.9045 (p) REVERT: M 68 PHE cc_start: 0.8032 (m-10) cc_final: 0.7570 (m-80) REVERT: O 50 PHE cc_start: 0.9154 (m-10) cc_final: 0.8652 (m-80) REVERT: O 51 ILE cc_start: 0.8670 (mm) cc_final: 0.8367 (tp) REVERT: O 62 PHE cc_start: 0.9079 (m-10) cc_final: 0.8824 (m-80) REVERT: P 1 MET cc_start: 0.6111 (mtt) cc_final: 0.5366 (tpp) REVERT: P 38 ASN cc_start: 0.8914 (t0) cc_final: 0.8055 (t0) REVERT: P 41 ILE cc_start: 0.9428 (tp) cc_final: 0.8917 (tt) REVERT: P 48 TYR cc_start: 0.9171 (m-80) cc_final: 0.8605 (m-80) REVERT: P 49 MET cc_start: 0.9701 (ttt) cc_final: 0.9325 (tmm) REVERT: P 55 PHE cc_start: 0.9564 (m-80) cc_final: 0.9281 (m-80) REVERT: Q 26 ILE cc_start: 0.9646 (mt) cc_final: 0.9238 (tp) REVERT: Q 33 GLN cc_start: 0.9325 (mm-40) cc_final: 0.9036 (mm110) REVERT: Q 38 ASN cc_start: 0.9202 (t0) cc_final: 0.8689 (t0) REVERT: Q 48 TYR cc_start: 0.8776 (m-10) cc_final: 0.8163 (m-80) REVERT: Q 49 MET cc_start: 0.9302 (tmm) cc_final: 0.8840 (tmm) REVERT: T 84 MET cc_start: 0.6323 (mtt) cc_final: 0.5881 (ptp) REVERT: T 92 TYR cc_start: 0.7733 (OUTLIER) cc_final: 0.7195 (m-80) REVERT: T 102 TYR cc_start: 0.8092 (m-80) cc_final: 0.7655 (m-80) REVERT: T 235 GLU cc_start: 0.9562 (tp30) cc_final: 0.9243 (tm-30) REVERT: T 296 TYR cc_start: 0.8710 (t80) cc_final: 0.8312 (t80) REVERT: V 35 ASN cc_start: 0.9163 (m-40) cc_final: 0.8943 (p0) REVERT: Y 20 LEU cc_start: 0.9468 (mm) cc_final: 0.9126 (tp) REVERT: Y 36 LEU cc_start: 0.9328 (pp) cc_final: 0.8906 (mm) REVERT: Y 42 ARG cc_start: 0.8982 (mmp80) cc_final: 0.8181 (mmp80) REVERT: Y 45 GLU cc_start: 0.7294 (pp20) cc_final: 0.6644 (pp20) REVERT: Y 46 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7916 (mm-30) REVERT: Z 190 ASP cc_start: 0.8546 (t70) cc_final: 0.8172 (p0) outliers start: 36 outliers final: 30 residues processed: 398 average time/residue: 0.1832 time to fit residues: 107.1928 Evaluate side-chains 405 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 372 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 49 MET Chi-restraints excluded: chain I residue 35 ILE Chi-restraints excluded: chain I residue 50 PHE Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain J residue 27 ILE Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 50 PHE Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 28 VAL Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 47 THR Chi-restraints excluded: chain M residue 50 PHE Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain O residue 6 LEU Chi-restraints excluded: chain P residue 18 ILE Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain Q residue 6 LEU Chi-restraints excluded: chain Q residue 32 VAL Chi-restraints excluded: chain T residue 92 TYR Chi-restraints excluded: chain T residue 114 PHE Chi-restraints excluded: chain T residue 240 LEU Chi-restraints excluded: chain T residue 250 LEU Chi-restraints excluded: chain T residue 274 LEU Chi-restraints excluded: chain V residue 6 ILE Chi-restraints excluded: chain V residue 11 PHE Chi-restraints excluded: chain Y residue 24 ILE Chi-restraints excluded: chain Y residue 33 VAL Chi-restraints excluded: chain Z residue 32 VAL Chi-restraints excluded: chain Z residue 260 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 103 optimal weight: 0.0270 chunk 85 optimal weight: 5.9990 chunk 115 optimal weight: 0.9980 chunk 126 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 chunk 79 optimal weight: 8.9990 chunk 40 optimal weight: 0.9990 chunk 83 optimal weight: 7.9990 chunk 91 optimal weight: 0.8980 chunk 88 optimal weight: 8.9990 chunk 39 optimal weight: 0.8980 overall best weight: 0.7640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 300 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 = 0.3863 r_free = 0.3863 target = 0.089579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.068371 restraints weight = 45022.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.069953 restraints weight = 32813.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.071003 restraints weight = 25740.201| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.5127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 10621 Z= 0.183 Angle : 0.940 15.979 14456 Z= 0.445 Chirality : 0.052 0.362 1780 Planarity : 0.005 0.057 1819 Dihedral : 4.131 20.955 1476 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 24.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.87 % Allowed : 43.08 % Favored : 54.05 % 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: 0.26 (0.22), residues: 1388 helix: 0.68 (0.15), residues: 1128 sheet: None (None), residues: 0 loop : -1.81 (0.40), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP T 208 HIS 0.001 0.000 HIS Z 31 PHE 0.061 0.002 PHE T 282 TYR 0.021 0.001 TYR K 48 ARG 0.015 0.000 ARG Z 249 Details of bonding type rmsd hydrogen bonds : bond 0.05041 ( 920) hydrogen bonds : angle 4.48679 ( 2739) SS BOND : bond 0.00127 ( 1) SS BOND : angle 1.88601 ( 2) covalent geometry : bond 0.00436 (10620) covalent geometry : angle 0.94016 (14454) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4104.23 seconds wall clock time: 73 minutes 51.52 seconds (4431.52 seconds total)