Starting phenix.real_space_refine on Sat Aug 23 06:44:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9itv_60880/08_2025/9itv_60880.cif Found real_map, /net/cci-nas-00/data/ceres_data/9itv_60880/08_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_60880/08_2025/9itv_60880.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9itv_60880/08_2025/9itv_60880.map" model { file = "/net/cci-nas-00/data/ceres_data/9itv_60880/08_2025/9itv_60880.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9itv_60880/08_2025/9itv_60880.cif" } resolution = 3.97 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'PHE:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 3, 'ARG:plan': 5, 'TYR:plan': 1, 'GLU:plan': 3} 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, 'ASN:plan1': 3, 'PHE:plan': 2, 'ARG:plan': 5, 'TYR:plan': 1, 'GLU:plan': 1} 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: 2.40, per 1000 atoms: 0.23 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: 1.01 Conformation dependent library (CDL) restraints added in 354.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.22 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: 1.53 Time building geometry restraints manager: 1.22 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: 4.300 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.740 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.870 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 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 ARG 0.007 0.000 ARG H 37 TYR 0.011 0.001 TYR T 296 PHE 0.025 0.001 PHE T 230 TRP 0.004 0.001 TRP Z 122 HIS 0.001 0.000 HIS Z 31 Details of bonding type rmsd covalent geometry : bond 0.00280 (10620) covalent geometry : angle 0.57750 (14454) SS BOND : bond 0.34946 ( 1) SS BOND : angle 39.54072 ( 2) hydrogen bonds : bond 0.10350 ( 920) hydrogen bonds : angle 3.95877 ( 2739) *********************** 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 : 0.439 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: 0.0776 time to fit residues: 58.3750 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 : 0.389 ------------------------------------------------------------------------------- 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 98 optimal weight: 30.0000 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.0770 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.1140 ------------------------------------------------------------------------------- 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 = 0.3863 r_free = 0.3863 target = 0.089440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.068399 restraints weight = 44461.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.070062 restraints weight = 31308.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.071147 restraints weight = 24079.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.072008 restraints weight = 19707.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.072638 restraints weight = 16824.978| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 10621 Z= 0.188 Angle : 0.731 12.425 14456 Z= 0.368 Chirality : 0.046 0.283 1780 Planarity : 0.005 0.052 1819 Dihedral : 3.998 36.970 1478 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 20.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 4.84 % Allowed : 28.06 % Favored : 67.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.22), residues: 1388 helix: 1.54 (0.15), residues: 1124 sheet: None (None), residues: 0 loop : -1.58 (0.40), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Z 249 TYR 0.018 0.002 TYR M 48 PHE 0.044 0.002 PHE H 55 TRP 0.008 0.001 TRP T 208 HIS 0.005 0.001 HIS Z 136 Details of bonding type rmsd covalent geometry : bond 0.00432 (10620) covalent geometry : angle 0.72673 (14454) SS BOND : bond 0.00599 ( 1) SS BOND : angle 6.41069 ( 2) hydrogen bonds : bond 0.04907 ( 920) hydrogen bonds : angle 4.09078 ( 2739) *********************** 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 461 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 412 time to evaluate : 0.368 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: H 29 SER cc_start: 0.9821 (t) cc_final: 0.9523 (p) REVERT: H 44 ARG cc_start: 0.8760 (mtp85) cc_final: 0.8178 (mtp85) REVERT: H 48 TYR cc_start: 0.9058 (m-80) cc_final: 0.8400 (m-80) REVERT: H 49 MET cc_start: 0.9471 (OUTLIER) cc_final: 0.9027 (ppp) REVERT: H 55 PHE cc_start: 0.9508 (m-80) cc_final: 0.9250 (m-80) REVERT: H 59 LEU cc_start: 0.9329 (mt) cc_final: 0.8753 (mm) REVERT: H 62 PHE cc_start: 0.9391 (m-80) cc_final: 0.8992 (m-80) REVERT: I 27 ILE cc_start: 0.9486 (mt) cc_final: 0.9282 (mt) REVERT: I 33 GLN cc_start: 0.9354 (mt0) cc_final: 0.8873 (mm-40) REVERT: I 37 ARG cc_start: 0.9216 (mtt90) cc_final: 0.8861 (mpp80) REVERT: I 48 TYR cc_start: 0.9331 (m-80) cc_final: 0.8546 (m-80) REVERT: I 49 MET cc_start: 0.9586 (ttp) cc_final: 0.9016 (ppp) REVERT: I 51 ILE cc_start: 0.9109 (mt) cc_final: 0.8393 (mm) REVERT: I 53 ILE cc_start: 0.9437 (mt) cc_final: 0.9142 (mt) REVERT: I 55 PHE cc_start: 0.9426 (m-10) cc_final: 0.8902 (m-80) REVERT: I 57 GLU cc_start: 0.8495 (mt-10) cc_final: 0.8202 (tp30) REVERT: J 28 VAL cc_start: 0.9752 (t) cc_final: 0.9515 (m) REVERT: J 49 MET cc_start: 0.9502 (ttt) cc_final: 0.9174 (ppp) REVERT: J 57 GLU cc_start: 0.9761 (mm-30) cc_final: 0.9119 (pt0) REVERT: K 57 GLU cc_start: 0.9594 (tp30) cc_final: 0.9367 (pt0) REVERT: K 59 LEU cc_start: 0.9077 (mt) cc_final: 0.8707 (mm) REVERT: K 62 PHE cc_start: 0.8521 (m-10) cc_final: 0.8217 (m-10) REVERT: K 66 ILE cc_start: 0.9189 (tt) cc_final: 0.8949 (mm) REVERT: L 15 LEU cc_start: 0.9188 (mt) cc_final: 0.8640 (tp) REVERT: L 26 ILE cc_start: 0.9613 (mt) cc_final: 0.9262 (tt) REVERT: L 51 ILE cc_start: 0.9009 (mt) cc_final: 0.8796 (mt) REVERT: L 55 PHE cc_start: 0.9289 (m-80) cc_final: 0.8907 (m-80) REVERT: L 66 ILE cc_start: 0.9491 (mm) cc_final: 0.9206 (mm) REVERT: M 20 PRO cc_start: 0.9235 (Cg_exo) cc_final: 0.8778 (Cg_endo) REVERT: M 66 ILE cc_start: 0.9288 (mm) cc_final: 0.9064 (mm) REVERT: M 68 PHE cc_start: 0.8284 (m-10) cc_final: 0.7840 (m-80) REVERT: O 11 LEU cc_start: 0.9506 (tt) cc_final: 0.9303 (tp) REVERT: O 50 PHE cc_start: 0.9267 (m-10) cc_final: 0.8984 (m-80) REVERT: O 51 ILE cc_start: 0.8769 (mm) cc_final: 0.8435 (tp) REVERT: O 62 PHE cc_start: 0.9194 (m-10) cc_final: 0.8743 (m-80) REVERT: P 1 MET cc_start: 0.6251 (mtt) cc_final: 0.5140 (tpp) REVERT: P 18 ILE cc_start: 0.8583 (mt) cc_final: 0.8168 (mt) REVERT: P 24 ILE cc_start: 0.9504 (mt) cc_final: 0.9171 (tp) REVERT: P 33 GLN cc_start: 0.9351 (mt0) cc_final: 0.9035 (mm-40) REVERT: P 38 ASN cc_start: 0.8821 (t0) cc_final: 0.7832 (t0) REVERT: P 41 ILE cc_start: 0.9492 (tp) cc_final: 0.8991 (tt) REVERT: P 48 TYR cc_start: 0.9292 (m-80) cc_final: 0.8725 (m-80) REVERT: P 49 MET cc_start: 0.9579 (ttt) cc_final: 0.9184 (tmm) REVERT: P 55 PHE cc_start: 0.9664 (m-80) cc_final: 0.9458 (m-80) REVERT: P 57 GLU cc_start: 0.9500 (mm-30) cc_final: 0.9093 (tm-30) REVERT: P 61 ILE cc_start: 0.9441 (mm) cc_final: 0.9167 (mm) REVERT: P 66 ILE cc_start: 0.9599 (mm) cc_final: 0.9298 (tp) REVERT: Q 26 ILE cc_start: 0.9620 (mt) cc_final: 0.9344 (tp) REVERT: Q 38 ASN cc_start: 0.9360 (t0) cc_final: 0.8692 (t0) REVERT: Q 41 ILE cc_start: 0.8920 (tp) cc_final: 0.8255 (tp) REVERT: Q 48 TYR cc_start: 0.9001 (m-10) cc_final: 0.8239 (m-80) REVERT: Q 49 MET cc_start: 0.9383 (tmm) cc_final: 0.8944 (tmm) REVERT: Q 68 PHE cc_start: 0.9062 (m-10) cc_final: 0.8657 (m-80) REVERT: T 78 ARG cc_start: 0.8797 (ptt180) cc_final: 0.8446 (tpt170) REVERT: T 102 TYR cc_start: 0.8080 (m-80) cc_final: 0.7456 (m-80) REVERT: T 235 GLU cc_start: 0.9222 (mt-10) cc_final: 0.9020 (tp30) REVERT: T 250 LEU cc_start: 0.9363 (tp) cc_final: 0.9107 (tp) REVERT: T 291 PHE cc_start: 0.9431 (OUTLIER) cc_final: 0.9152 (m-80) REVERT: T 296 TYR cc_start: 0.9105 (t80) cc_final: 0.7780 (t80) REVERT: Y 11 PHE cc_start: 0.8986 (t80) cc_final: 0.8732 (m-80) REVERT: Z 89 GLU cc_start: 0.8484 (tp30) cc_final: 0.8246 (tp30) REVERT: Z 102 TYR cc_start: 0.8947 (m-80) cc_final: 0.8643 (m-80) REVERT: Z 125 LEU cc_start: 0.9341 (mp) cc_final: 0.9129 (mp) REVERT: Z 185 ARG cc_start: 0.8680 (ttt90) cc_final: 0.8113 (ttp-170) REVERT: Z 277 TYR cc_start: 0.8987 (m-80) cc_final: 0.8787 (m-80) outliers start: 49 outliers final: 26 residues processed: 436 average time/residue: 0.0767 time to fit residues: 49.6263 Evaluate side-chains 414 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 386 time to evaluate : 0.318 ------------------------------------------------------------------------------- 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 61 ILE Chi-restraints excluded: chain J residue 7 VAL Chi-restraints excluded: chain J residue 47 THR Chi-restraints excluded: chain J residue 64 LEU 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 Q residue 22 VAL 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 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 271 LEU Chi-restraints excluded: chain Z residue 272 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 61 optimal weight: 0.7980 chunk 90 optimal weight: 0.0870 chunk 3 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 106 optimal weight: 20.0000 chunk 112 optimal weight: 20.0000 chunk 77 optimal weight: 6.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Z 72 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.089970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.068145 restraints weight = 45450.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.069810 restraints weight = 31971.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.070968 restraints weight = 24399.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.071859 restraints weight = 19939.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.072482 restraints weight = 17023.603| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10621 Z= 0.173 Angle : 0.734 11.304 14456 Z= 0.364 Chirality : 0.046 0.255 1780 Planarity : 0.004 0.050 1819 Dihedral : 3.862 18.290 1476 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 22.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 4.74 % Allowed : 29.84 % Favored : 65.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.22), residues: 1388 helix: 1.29 (0.15), residues: 1123 sheet: None (None), residues: 0 loop : -1.65 (0.40), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Z 249 TYR 0.026 0.001 TYR K 48 PHE 0.043 0.002 PHE P 62 TRP 0.006 0.001 TRP T 208 HIS 0.001 0.000 HIS Z 136 Details of bonding type rmsd covalent geometry : bond 0.00396 (10620) covalent geometry : angle 0.73217 (14454) SS BOND : bond 0.03374 ( 1) SS BOND : angle 4.05831 ( 2) hydrogen bonds : bond 0.04865 ( 920) hydrogen bonds : angle 4.04587 ( 2739) *********************** 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 446 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 398 time to evaluate : 0.397 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: 0.9792 (t) cc_final: 0.9475 (p) REVERT: H 44 ARG cc_start: 0.8657 (mtp85) cc_final: 0.8234 (mmm-85) REVERT: H 48 TYR cc_start: 0.9031 (m-80) cc_final: 0.8319 (m-80) REVERT: H 49 MET cc_start: 0.9400 (OUTLIER) cc_final: 0.8947 (ppp) REVERT: H 51 ILE cc_start: 0.9401 (pt) cc_final: 0.9067 (pt) REVERT: H 57 GLU cc_start: 0.9257 (mt-10) cc_final: 0.8999 (mt-10) REVERT: H 59 LEU cc_start: 0.9308 (mt) cc_final: 0.8764 (mm) REVERT: H 62 PHE cc_start: 0.9403 (m-80) cc_final: 0.9044 (m-80) REVERT: I 33 GLN cc_start: 0.9323 (mt0) cc_final: 0.8913 (mm-40) REVERT: I 37 ARG cc_start: 0.9168 (mtt90) cc_final: 0.8809 (mpp80) REVERT: I 48 TYR cc_start: 0.9302 (m-80) cc_final: 0.8506 (m-80) REVERT: I 49 MET cc_start: 0.9571 (ttp) cc_final: 0.8980 (ppp) REVERT: I 51 ILE cc_start: 0.9095 (mt) cc_final: 0.8301 (mm) REVERT: I 53 ILE cc_start: 0.9416 (mt) cc_final: 0.9117 (mt) REVERT: I 55 PHE cc_start: 0.9453 (m-10) cc_final: 0.8917 (m-80) REVERT: I 62 PHE cc_start: 0.9231 (m-10) cc_final: 0.9008 (m-10) REVERT: J 49 MET cc_start: 0.9547 (ttt) cc_final: 0.9121 (tmm) REVERT: J 57 GLU cc_start: 0.9775 (mm-30) cc_final: 0.9499 (mm-30) REVERT: K 26 ILE cc_start: 0.9306 (mm) cc_final: 0.9100 (tp) REVERT: K 57 GLU cc_start: 0.9580 (tp30) cc_final: 0.9325 (pt0) REVERT: K 59 LEU cc_start: 0.9082 (mt) cc_final: 0.8675 (mt) REVERT: K 62 PHE cc_start: 0.8558 (m-10) cc_final: 0.8231 (m-10) REVERT: K 66 ILE cc_start: 0.9205 (tt) cc_final: 0.8993 (mm) REVERT: L 11 LEU cc_start: 0.9428 (tp) cc_final: 0.9211 (tt) REVERT: L 51 ILE cc_start: 0.9030 (mt) cc_final: 0.8818 (mt) REVERT: L 55 PHE cc_start: 0.9346 (m-80) cc_final: 0.8999 (m-80) REVERT: L 66 ILE cc_start: 0.9469 (mm) cc_final: 0.9175 (mm) REVERT: M 29 SER cc_start: 0.9575 (t) cc_final: 0.9104 (p) REVERT: M 66 ILE cc_start: 0.9305 (mm) cc_final: 0.9060 (mm) REVERT: M 68 PHE cc_start: 0.8256 (m-10) cc_final: 0.7867 (m-80) REVERT: O 50 PHE cc_start: 0.9270 (m-10) cc_final: 0.8958 (m-80) REVERT: O 51 ILE cc_start: 0.8656 (mm) cc_final: 0.8372 (tp) REVERT: O 62 PHE cc_start: 0.9199 (m-10) cc_final: 0.8757 (m-80) REVERT: P 1 MET cc_start: 0.6199 (mtt) cc_final: 0.5068 (tpp) REVERT: P 24 ILE cc_start: 0.9487 (mt) cc_final: 0.9181 (tp) REVERT: P 33 GLN cc_start: 0.9311 (mt0) cc_final: 0.8829 (mt0) REVERT: P 38 ASN cc_start: 0.8902 (t0) cc_final: 0.7942 (t0) REVERT: P 41 ILE cc_start: 0.9460 (tp) cc_final: 0.8999 (tt) REVERT: P 48 TYR cc_start: 0.9233 (m-80) cc_final: 0.8696 (m-80) REVERT: P 49 MET cc_start: 0.9598 (ttt) cc_final: 0.9226 (tmm) REVERT: P 57 GLU cc_start: 0.9394 (mm-30) cc_final: 0.9027 (tm-30) REVERT: P 61 ILE cc_start: 0.9394 (mm) cc_final: 0.9117 (mm) REVERT: P 66 ILE cc_start: 0.9611 (mm) cc_final: 0.9325 (tp) REVERT: Q 26 ILE cc_start: 0.9666 (mt) cc_final: 0.9319 (tp) REVERT: Q 38 ASN cc_start: 0.9259 (t0) cc_final: 0.8553 (t0) REVERT: Q 41 ILE cc_start: 0.8922 (tp) cc_final: 0.8216 (tp) REVERT: Q 48 TYR cc_start: 0.8982 (m-10) cc_final: 0.8257 (m-80) REVERT: Q 49 MET cc_start: 0.9372 (tmm) cc_final: 0.8804 (tmm) REVERT: Q 53 ILE cc_start: 0.9453 (mt) cc_final: 0.9208 (mt) REVERT: Q 64 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.9077 (pp) REVERT: Q 68 PHE cc_start: 0.9213 (m-10) cc_final: 0.8613 (m-80) REVERT: T 78 ARG cc_start: 0.8798 (ptt180) cc_final: 0.8382 (tpt170) REVERT: T 102 TYR cc_start: 0.8048 (m-80) cc_final: 0.7426 (m-80) REVERT: T 235 GLU cc_start: 0.9471 (mt-10) cc_final: 0.9158 (tp30) REVERT: T 291 PHE cc_start: 0.9393 (OUTLIER) cc_final: 0.9189 (m-80) REVERT: T 296 TYR cc_start: 0.9018 (t80) cc_final: 0.7916 (t80) REVERT: Y 36 LEU cc_start: 0.9286 (pp) cc_final: 0.8934 (mm) REVERT: Y 45 GLU cc_start: 0.7108 (pp20) cc_final: 0.6782 (pp20) REVERT: Y 46 GLU cc_start: 0.8843 (mt-10) cc_final: 0.8583 (mt-10) REVERT: Z 102 TYR cc_start: 0.8937 (m-80) cc_final: 0.8665 (m-80) REVERT: Z 132 ILE cc_start: 0.8343 (mm) cc_final: 0.7944 (mt) REVERT: Z 185 ARG cc_start: 0.8779 (ttt90) cc_final: 0.8234 (ttp-110) REVERT: Z 190 ASP cc_start: 0.8461 (t70) cc_final: 0.8022 (p0) REVERT: Z 286 ILE cc_start: 0.9527 (mm) cc_final: 0.9324 (mm) outliers start: 48 outliers final: 25 residues processed: 420 average time/residue: 0.0834 time to fit residues: 52.4568 Evaluate side-chains 408 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 380 time to evaluate : 0.334 ------------------------------------------------------------------------------- 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 I residue 69 LEU 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 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 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 7 VAL Chi-restraints excluded: chain Q residue 64 LEU 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 T residue 291 PHE Chi-restraints excluded: chain V residue 11 PHE Chi-restraints excluded: chain Y residue 6 ILE Chi-restraints excluded: chain Y residue 24 ILE Chi-restraints excluded: chain Z residue 48 ILE Chi-restraints excluded: chain Z residue 109 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 113 optimal weight: 10.0000 chunk 86 optimal weight: 3.9990 chunk 89 optimal weight: 0.5980 chunk 71 optimal weight: 4.9990 chunk 22 optimal weight: 0.2980 chunk 35 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 70 optimal weight: 7.9990 chunk 87 optimal weight: 0.0570 chunk 34 optimal weight: 1.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- 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 Y 17 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.090205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.068246 restraints weight = 45840.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.069886 restraints weight = 32056.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.071081 restraints weight = 24625.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.071990 restraints weight = 20059.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.072680 restraints weight = 17046.463| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10621 Z= 0.164 Angle : 0.747 12.316 14456 Z= 0.366 Chirality : 0.047 0.295 1780 Planarity : 0.004 0.051 1819 Dihedral : 3.908 16.754 1476 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 21.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.05 % Allowed : 32.11 % Favored : 63.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.22), residues: 1388 helix: 1.13 (0.15), residues: 1123 sheet: None (None), residues: 0 loop : -1.67 (0.40), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 37 TYR 0.031 0.002 TYR K 48 PHE 0.045 0.001 PHE T 282 TRP 0.005 0.001 TRP T 208 HIS 0.001 0.000 HIS Z 31 Details of bonding type rmsd covalent geometry : bond 0.00376 (10620) covalent geometry : angle 0.74598 (14454) SS BOND : bond 0.00733 ( 1) SS BOND : angle 3.26517 ( 2) hydrogen bonds : bond 0.04868 ( 920) hydrogen bonds : angle 4.06182 ( 2739) *********************** 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 449 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 408 time to evaluate : 0.243 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: 0.9774 (t) cc_final: 0.9494 (p) REVERT: H 44 ARG cc_start: 0.8565 (mtp85) cc_final: 0.8135 (mmm-85) REVERT: H 48 TYR cc_start: 0.8963 (m-80) cc_final: 0.8317 (m-80) REVERT: H 49 MET cc_start: 0.9389 (OUTLIER) cc_final: 0.8885 (ppp) REVERT: H 57 GLU cc_start: 0.9247 (mt-10) cc_final: 0.8930 (mt-10) REVERT: H 59 LEU cc_start: 0.9284 (mt) cc_final: 0.8874 (mt) REVERT: H 62 PHE cc_start: 0.9339 (m-80) cc_final: 0.9046 (m-80) REVERT: I 33 GLN cc_start: 0.9303 (mt0) cc_final: 0.8909 (mm-40) REVERT: I 37 ARG cc_start: 0.9126 (mtt90) cc_final: 0.8763 (mpp80) REVERT: I 48 TYR cc_start: 0.9267 (m-80) cc_final: 0.8626 (m-80) REVERT: I 49 MET cc_start: 0.9553 (ttp) cc_final: 0.9007 (ppp) REVERT: I 51 ILE cc_start: 0.9080 (mt) cc_final: 0.8251 (mm) REVERT: I 55 PHE cc_start: 0.9431 (m-10) cc_final: 0.8835 (m-80) REVERT: J 28 VAL cc_start: 0.9704 (t) cc_final: 0.9457 (m) REVERT: J 49 MET cc_start: 0.9541 (ttt) cc_final: 0.9261 (ppp) REVERT: J 57 GLU cc_start: 0.9720 (mm-30) cc_final: 0.9511 (mm-30) REVERT: K 43 ASN cc_start: 0.9196 (m-40) cc_final: 0.8871 (p0) REVERT: K 57 GLU cc_start: 0.9515 (tp30) cc_final: 0.9307 (pt0) REVERT: K 59 LEU cc_start: 0.9091 (mt) cc_final: 0.8644 (mt) REVERT: K 62 PHE cc_start: 0.8564 (m-10) cc_final: 0.8249 (m-10) REVERT: K 66 ILE cc_start: 0.9226 (tt) cc_final: 0.8991 (mm) REVERT: L 15 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8628 (tp) REVERT: L 66 ILE cc_start: 0.9495 (mm) cc_final: 0.9216 (mm) REVERT: M 29 SER cc_start: 0.9593 (t) cc_final: 0.8953 (m) REVERT: M 48 TYR cc_start: 0.8839 (m-80) cc_final: 0.8631 (m-80) REVERT: M 66 ILE cc_start: 0.9318 (mm) cc_final: 0.9048 (mm) REVERT: M 68 PHE cc_start: 0.8203 (m-10) cc_final: 0.7847 (m-80) REVERT: N 41 ILE cc_start: 0.8643 (tp) cc_final: 0.8183 (pt) REVERT: O 1 MET cc_start: 0.6933 (tpp) cc_final: 0.6523 (tpt) REVERT: O 38 ASN cc_start: 0.8672 (t0) cc_final: 0.8379 (t0) REVERT: O 49 MET cc_start: 0.9328 (ttp) cc_final: 0.9113 (ttm) REVERT: O 50 PHE cc_start: 0.9173 (m-10) cc_final: 0.8733 (m-80) REVERT: O 51 ILE cc_start: 0.8687 (mm) cc_final: 0.8395 (tp) REVERT: O 62 PHE cc_start: 0.9174 (m-10) cc_final: 0.8699 (m-80) REVERT: P 1 MET cc_start: 0.6169 (mtt) cc_final: 0.5823 (ptp) REVERT: P 33 GLN cc_start: 0.9263 (mt0) cc_final: 0.8801 (mt0) REVERT: P 38 ASN cc_start: 0.8878 (t0) cc_final: 0.7911 (t0) REVERT: P 41 ILE cc_start: 0.9403 (tp) cc_final: 0.8991 (tt) REVERT: P 48 TYR cc_start: 0.9160 (m-80) cc_final: 0.8635 (m-80) REVERT: P 49 MET cc_start: 0.9650 (ttt) cc_final: 0.9298 (tmm) REVERT: P 62 PHE cc_start: 0.9249 (m-10) cc_final: 0.8766 (m-10) REVERT: P 66 ILE cc_start: 0.9623 (mm) cc_final: 0.9330 (tp) REVERT: Q 26 ILE cc_start: 0.9671 (mt) cc_final: 0.9318 (tp) REVERT: Q 38 ASN cc_start: 0.9184 (t0) cc_final: 0.8616 (t0) REVERT: Q 48 TYR cc_start: 0.8883 (m-10) cc_final: 0.8233 (m-80) REVERT: Q 49 MET cc_start: 0.9362 (tmm) cc_final: 0.9019 (ppp) REVERT: Q 64 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.9050 (pp) REVERT: Q 68 PHE cc_start: 0.9194 (m-10) cc_final: 0.8627 (m-80) REVERT: T 102 TYR cc_start: 0.8003 (m-80) cc_final: 0.7403 (m-80) REVERT: T 235 GLU cc_start: 0.9525 (mt-10) cc_final: 0.9193 (tp30) REVERT: T 238 SER cc_start: 0.8898 (p) cc_final: 0.8615 (p) REVERT: T 264 MET cc_start: 0.7512 (ptp) cc_final: 0.7252 (ptp) REVERT: T 296 TYR cc_start: 0.8934 (t80) cc_final: 0.7865 (t80) REVERT: V 35 ASN cc_start: 0.9194 (m-40) cc_final: 0.8900 (p0) REVERT: Y 20 LEU cc_start: 0.9410 (mm) cc_final: 0.9057 (tp) REVERT: Y 36 LEU cc_start: 0.9221 (pp) cc_final: 0.8743 (mm) REVERT: Z 102 TYR cc_start: 0.8787 (m-80) cc_final: 0.8570 (m-80) REVERT: Z 185 ARG cc_start: 0.8716 (ttt90) cc_final: 0.8232 (ttp-110) REVERT: Z 190 ASP cc_start: 0.8466 (t70) cc_final: 0.8113 (p0) REVERT: Z 235 GLU cc_start: 0.9581 (mm-30) cc_final: 0.8927 (pt0) REVERT: Z 286 ILE cc_start: 0.9569 (mm) cc_final: 0.9357 (mm) outliers start: 41 outliers final: 24 residues processed: 424 average time/residue: 0.0783 time to fit residues: 49.4861 Evaluate side-chains 415 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 388 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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 57 GLU Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 47 THR Chi-restraints excluded: chain K residue 24 ILE 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 56 THR Chi-restraints excluded: chain O residue 6 LEU Chi-restraints excluded: chain O residue 18 ILE Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 32 VAL Chi-restraints excluded: chain Q residue 64 LEU 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 260 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 27 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 130 optimal weight: 0.2980 chunk 6 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 53 optimal weight: 0.0020 chunk 33 optimal weight: 0.9980 overall best weight: 0.5388 ------------------------------------------------------------------------------- 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 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 = 0.3873 r_free = 0.3873 target = 0.089996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.068343 restraints weight = 45352.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.069972 restraints weight = 32025.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.071142 restraints weight = 24778.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.072000 restraints weight = 20207.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.072648 restraints weight = 17306.222| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10621 Z= 0.163 Angle : 0.763 12.822 14456 Z= 0.372 Chirality : 0.046 0.316 1780 Planarity : 0.004 0.053 1819 Dihedral : 3.922 16.437 1476 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 21.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 4.25 % Allowed : 34.98 % Favored : 60.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.22), residues: 1388 helix: 1.06 (0.15), residues: 1124 sheet: None (None), residues: 0 loop : -1.72 (0.41), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG T 78 TYR 0.027 0.001 TYR K 48 PHE 0.048 0.001 PHE T 282 TRP 0.005 0.001 TRP T 208 HIS 0.001 0.000 HIS Z 31 Details of bonding type rmsd covalent geometry : bond 0.00376 (10620) covalent geometry : angle 0.76205 (14454) SS BOND : bond 0.00197 ( 1) SS BOND : angle 2.92036 ( 2) hydrogen bonds : bond 0.04853 ( 920) hydrogen bonds : angle 4.12249 ( 2739) *********************** 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 450 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 407 time to evaluate : 0.399 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: 0.9764 (t) cc_final: 0.9489 (p) REVERT: H 44 ARG cc_start: 0.8566 (mtp85) cc_final: 0.8109 (mmm-85) REVERT: H 48 TYR cc_start: 0.8949 (m-80) cc_final: 0.8382 (m-80) REVERT: H 49 MET cc_start: 0.9380 (OUTLIER) cc_final: 0.8861 (ppp) REVERT: H 59 LEU cc_start: 0.9233 (mt) cc_final: 0.8851 (mt) REVERT: H 62 PHE cc_start: 0.9329 (m-80) cc_final: 0.9023 (m-80) REVERT: I 33 GLN cc_start: 0.9292 (mt0) cc_final: 0.8899 (mm-40) REVERT: I 37 ARG cc_start: 0.9102 (mtt90) cc_final: 0.8730 (mpp80) REVERT: I 48 TYR cc_start: 0.9202 (m-80) cc_final: 0.8626 (m-80) REVERT: I 49 MET cc_start: 0.9548 (ttp) cc_final: 0.9332 (ppp) REVERT: I 51 ILE cc_start: 0.9118 (mt) cc_final: 0.8286 (mm) REVERT: I 55 PHE cc_start: 0.9372 (m-10) cc_final: 0.8753 (m-80) REVERT: I 62 PHE cc_start: 0.9239 (m-10) cc_final: 0.9032 (m-10) REVERT: J 57 GLU cc_start: 0.9725 (mm-30) cc_final: 0.9499 (mm-30) REVERT: J 64 LEU cc_start: 0.9556 (mm) cc_final: 0.9352 (mm) REVERT: K 26 ILE cc_start: 0.9352 (mm) cc_final: 0.9129 (tp) REVERT: K 43 ASN cc_start: 0.9168 (m-40) cc_final: 0.8848 (p0) REVERT: K 57 GLU cc_start: 0.9581 (tp30) cc_final: 0.9321 (pt0) REVERT: K 59 LEU cc_start: 0.9072 (mt) cc_final: 0.8562 (mt) REVERT: K 62 PHE cc_start: 0.8597 (m-10) cc_final: 0.8271 (m-10) REVERT: L 55 PHE cc_start: 0.9390 (m-80) cc_final: 0.9188 (m-80) REVERT: L 66 ILE cc_start: 0.9483 (mm) cc_final: 0.9210 (mm) REVERT: M 4 LEU cc_start: 0.9324 (tp) cc_final: 0.9008 (tp) REVERT: M 29 SER cc_start: 0.9554 (t) cc_final: 0.9090 (p) REVERT: M 66 ILE cc_start: 0.9314 (mm) cc_final: 0.9091 (mm) REVERT: M 68 PHE cc_start: 0.8163 (m-10) cc_final: 0.7818 (m-80) REVERT: O 1 MET cc_start: 0.6719 (tpp) cc_final: 0.6416 (tpt) REVERT: O 49 MET cc_start: 0.9324 (ttp) cc_final: 0.9104 (ttm) REVERT: O 50 PHE cc_start: 0.9132 (m-10) cc_final: 0.8675 (m-80) REVERT: O 51 ILE cc_start: 0.8666 (mm) cc_final: 0.8395 (tp) REVERT: O 62 PHE cc_start: 0.9201 (m-10) cc_final: 0.8715 (m-80) REVERT: P 1 MET cc_start: 0.6153 (mtt) cc_final: 0.5804 (ptp) REVERT: P 33 GLN cc_start: 0.9267 (mt0) cc_final: 0.8870 (mt0) REVERT: P 38 ASN cc_start: 0.8897 (t0) cc_final: 0.7966 (t0) REVERT: P 41 ILE cc_start: 0.9386 (tp) cc_final: 0.8986 (tt) REVERT: P 48 TYR cc_start: 0.9118 (m-80) cc_final: 0.8595 (m-80) REVERT: P 49 MET cc_start: 0.9663 (ttt) cc_final: 0.9311 (tmm) REVERT: P 51 ILE cc_start: 0.9513 (mm) cc_final: 0.9098 (tt) REVERT: P 62 PHE cc_start: 0.9214 (m-10) cc_final: 0.8850 (m-10) REVERT: P 66 ILE cc_start: 0.9623 (mm) cc_final: 0.9342 (tp) REVERT: Q 26 ILE cc_start: 0.9669 (mt) cc_final: 0.9305 (tp) REVERT: Q 38 ASN cc_start: 0.9166 (t0) cc_final: 0.8461 (t0) REVERT: Q 41 ILE cc_start: 0.8844 (tp) cc_final: 0.8133 (tp) REVERT: Q 48 TYR cc_start: 0.8850 (m-10) cc_final: 0.8236 (m-80) REVERT: Q 49 MET cc_start: 0.9352 (OUTLIER) cc_final: 0.8826 (tmm) REVERT: Q 68 PHE cc_start: 0.9176 (m-10) cc_final: 0.8620 (m-80) REVERT: T 84 MET cc_start: 0.6229 (mtt) cc_final: 0.5695 (ptp) REVERT: T 102 TYR cc_start: 0.7951 (m-80) cc_final: 0.7422 (m-80) REVERT: T 119 PHE cc_start: 0.2985 (m-80) cc_final: 0.2763 (m-80) REVERT: T 235 GLU cc_start: 0.9500 (mt-10) cc_final: 0.9209 (tp30) REVERT: T 238 SER cc_start: 0.8885 (p) cc_final: 0.8587 (p) REVERT: T 296 TYR cc_start: 0.8863 (t80) cc_final: 0.8028 (t80) REVERT: V 37 LEU cc_start: 0.9516 (tt) cc_final: 0.9266 (tp) REVERT: Y 18 PHE cc_start: 0.9062 (t80) cc_final: 0.8700 (t80) REVERT: Y 20 LEU cc_start: 0.9381 (mm) cc_final: 0.9031 (tp) REVERT: Y 36 LEU cc_start: 0.9268 (pp) cc_final: 0.8812 (mm) REVERT: Y 42 ARG cc_start: 0.8967 (mmp80) cc_final: 0.8749 (mmp80) REVERT: Z 102 TYR cc_start: 0.8720 (m-80) cc_final: 0.8502 (m-80) REVERT: Z 185 ARG cc_start: 0.8668 (ttt90) cc_final: 0.8204 (ttp-110) REVERT: Z 190 ASP cc_start: 0.8452 (t70) cc_final: 0.8094 (p0) REVERT: Z 235 GLU cc_start: 0.9598 (mm-30) cc_final: 0.8988 (pt0) REVERT: Z 239 GLU cc_start: 0.9350 (mm-30) cc_final: 0.9125 (mm-30) outliers start: 43 outliers final: 26 residues processed: 423 average time/residue: 0.0791 time to fit residues: 50.0659 Evaluate side-chains 409 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 381 time to evaluate : 0.319 ------------------------------------------------------------------------------- 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 24 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 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 O residue 18 ILE 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 Q residue 49 MET 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 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 81 optimal weight: 30.0000 chunk 89 optimal weight: 0.9980 chunk 71 optimal weight: 8.9990 chunk 119 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 115 optimal weight: 5.9990 chunk 121 optimal weight: 0.5980 chunk 134 optimal weight: 2.9990 chunk 102 optimal weight: 0.0570 chunk 52 optimal weight: 0.8980 chunk 80 optimal weight: 4.9990 overall best weight: 0.7100 ------------------------------------------------------------------------------- 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 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 = 0.3867 r_free = 0.3867 target = 0.089533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.068167 restraints weight = 45598.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.069753 restraints weight = 32399.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.070961 restraints weight = 25003.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.071643 restraints weight = 20440.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.072216 restraints weight = 17744.701| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10621 Z= 0.169 Angle : 0.773 13.624 14456 Z= 0.380 Chirality : 0.047 0.322 1780 Planarity : 0.004 0.053 1819 Dihedral : 3.937 17.122 1476 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 22.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.15 % Allowed : 37.55 % Favored : 58.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.22), residues: 1388 helix: 1.00 (0.15), residues: 1124 sheet: None (None), residues: 0 loop : -1.71 (0.41), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG V 40 TYR 0.026 0.001 TYR K 48 PHE 0.046 0.001 PHE T 282 TRP 0.006 0.001 TRP T 208 HIS 0.001 0.000 HIS Z 31 Details of bonding type rmsd covalent geometry : bond 0.00397 (10620) covalent geometry : angle 0.77210 (14454) SS BOND : bond 0.00145 ( 1) SS BOND : angle 2.58210 ( 2) hydrogen bonds : bond 0.04893 ( 920) hydrogen bonds : angle 4.18409 ( 2739) *********************** 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 444 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 402 time to evaluate : 0.354 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: H 29 SER cc_start: 0.9767 (t) cc_final: 0.9480 (p) REVERT: H 44 ARG cc_start: 0.8578 (mtp85) cc_final: 0.8117 (mmm-85) REVERT: H 48 TYR cc_start: 0.9039 (m-80) cc_final: 0.8364 (m-80) REVERT: H 49 MET cc_start: 0.9362 (OUTLIER) cc_final: 0.9040 (ppp) REVERT: H 57 GLU cc_start: 0.9316 (mt-10) cc_final: 0.8740 (mt-10) REVERT: H 59 LEU cc_start: 0.9205 (mt) cc_final: 0.8826 (mt) REVERT: H 62 PHE cc_start: 0.9341 (m-80) cc_final: 0.9032 (m-80) REVERT: I 33 GLN cc_start: 0.9297 (mt0) cc_final: 0.8737 (mm-40) REVERT: I 37 ARG cc_start: 0.9127 (mtt90) cc_final: 0.8647 (mpp80) REVERT: I 48 TYR cc_start: 0.9230 (m-80) cc_final: 0.8634 (m-80) REVERT: I 49 MET cc_start: 0.9582 (ttp) cc_final: 0.9356 (ppp) REVERT: I 51 ILE cc_start: 0.9157 (mt) cc_final: 0.8294 (mm) REVERT: I 55 PHE cc_start: 0.9350 (m-10) cc_final: 0.8710 (m-80) REVERT: I 62 PHE cc_start: 0.9263 (m-10) cc_final: 0.8978 (m-10) REVERT: J 49 MET cc_start: 0.9574 (ttt) cc_final: 0.9240 (tmm) REVERT: J 57 GLU cc_start: 0.9720 (mm-30) cc_final: 0.9435 (mm-30) REVERT: K 26 ILE cc_start: 0.9368 (mm) cc_final: 0.9150 (tp) REVERT: K 43 ASN cc_start: 0.9183 (m-40) cc_final: 0.8857 (p0) REVERT: K 48 TYR cc_start: 0.9460 (m-80) cc_final: 0.9255 (m-80) REVERT: K 50 PHE cc_start: 0.9092 (OUTLIER) cc_final: 0.8790 (m-80) REVERT: K 57 GLU cc_start: 0.9565 (tp30) cc_final: 0.9282 (pt0) REVERT: L 1 MET cc_start: 0.5371 (OUTLIER) cc_final: 0.4904 (mmp) REVERT: L 11 LEU cc_start: 0.9246 (tt) cc_final: 0.9038 (tt) REVERT: L 15 LEU cc_start: 0.9091 (mm) cc_final: 0.8677 (tp) REVERT: L 66 ILE cc_start: 0.9441 (mm) cc_final: 0.9101 (mm) REVERT: M 1 MET cc_start: 0.6295 (mmt) cc_final: 0.6061 (mtt) REVERT: M 4 LEU cc_start: 0.9329 (tp) cc_final: 0.9013 (tp) REVERT: M 29 SER cc_start: 0.9563 (t) cc_final: 0.8894 (m) REVERT: M 42 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8545 (tt0) REVERT: M 68 PHE cc_start: 0.8170 (m-10) cc_final: 0.7791 (m-80) REVERT: N 48 TYR cc_start: 0.8933 (m-10) cc_final: 0.8343 (m-80) REVERT: N 55 PHE cc_start: 0.9351 (OUTLIER) cc_final: 0.8740 (m-80) REVERT: O 49 MET cc_start: 0.9302 (ttp) cc_final: 0.9070 (ttm) REVERT: O 50 PHE cc_start: 0.9109 (m-10) cc_final: 0.8676 (m-80) REVERT: O 51 ILE cc_start: 0.8689 (mm) cc_final: 0.8429 (tp) REVERT: O 62 PHE cc_start: 0.9200 (m-10) cc_final: 0.8714 (m-80) REVERT: P 1 MET cc_start: 0.6060 (mtt) cc_final: 0.5748 (ptp) REVERT: P 38 ASN cc_start: 0.8948 (t0) cc_final: 0.7996 (t0) REVERT: P 41 ILE cc_start: 0.9432 (tp) cc_final: 0.9031 (tt) REVERT: P 48 TYR cc_start: 0.9122 (m-80) cc_final: 0.8632 (m-80) REVERT: P 49 MET cc_start: 0.9680 (ttt) cc_final: 0.9325 (tmm) REVERT: P 51 ILE cc_start: 0.9530 (mm) cc_final: 0.9133 (tt) REVERT: P 62 PHE cc_start: 0.9191 (m-10) cc_final: 0.8851 (m-10) REVERT: P 66 ILE cc_start: 0.9614 (mm) cc_final: 0.9362 (tp) REVERT: Q 26 ILE cc_start: 0.9676 (mt) cc_final: 0.9318 (tp) REVERT: Q 38 ASN cc_start: 0.9162 (t0) cc_final: 0.8473 (t0) REVERT: Q 41 ILE cc_start: 0.8893 (tp) cc_final: 0.8181 (tp) REVERT: Q 45 VAL cc_start: 0.9631 (OUTLIER) cc_final: 0.9414 (t) REVERT: Q 48 TYR cc_start: 0.8866 (m-10) cc_final: 0.8255 (m-80) REVERT: Q 49 MET cc_start: 0.9335 (OUTLIER) cc_final: 0.8821 (tmm) REVERT: Q 68 PHE cc_start: 0.9156 (m-10) cc_final: 0.8536 (m-80) REVERT: T 102 TYR cc_start: 0.7938 (m-80) cc_final: 0.7419 (m-80) REVERT: T 235 GLU cc_start: 0.9481 (mt-10) cc_final: 0.9208 (tp30) REVERT: T 238 SER cc_start: 0.8909 (p) cc_final: 0.8614 (p) REVERT: T 296 TYR cc_start: 0.8827 (t80) cc_final: 0.8008 (t80) REVERT: V 34 MET cc_start: 0.9154 (mmm) cc_final: 0.8905 (mmm) REVERT: V 35 ASN cc_start: 0.9267 (m-40) cc_final: 0.8595 (p0) REVERT: V 37 LEU cc_start: 0.9578 (tt) cc_final: 0.9302 (tp) REVERT: V 39 GLU cc_start: 0.8772 (mm-30) cc_final: 0.8281 (mm-30) REVERT: Y 18 PHE cc_start: 0.9075 (t80) cc_final: 0.8704 (t80) REVERT: Y 20 LEU cc_start: 0.9373 (mm) cc_final: 0.9048 (tp) REVERT: Y 36 LEU cc_start: 0.9289 (pp) cc_final: 0.8796 (mm) REVERT: Z 102 TYR cc_start: 0.8694 (m-80) cc_final: 0.8472 (m-80) REVERT: Z 185 ARG cc_start: 0.8680 (ttt90) cc_final: 0.8232 (ttp-110) REVERT: Z 190 ASP cc_start: 0.8432 (t70) cc_final: 0.8045 (p0) REVERT: Z 235 GLU cc_start: 0.9614 (mm-30) cc_final: 0.9003 (pt0) outliers start: 42 outliers final: 26 residues processed: 418 average time/residue: 0.0821 time to fit residues: 51.1980 Evaluate side-chains 416 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 383 time to evaluate : 0.398 ------------------------------------------------------------------------------- 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 24 ILE 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 42 GLU 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 55 PHE Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain N residue 64 LEU Chi-restraints excluded: chain O residue 6 LEU Chi-restraints excluded: chain P residue 45 VAL 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 Q residue 45 VAL Chi-restraints excluded: chain Q residue 49 MET 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 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 69 optimal weight: 0.9980 chunk 98 optimal weight: 8.9990 chunk 123 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 107 optimal weight: 8.9990 chunk 96 optimal weight: 30.0000 chunk 51 optimal weight: 0.7980 chunk 134 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 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 = 0.3833 r_free = 0.3833 target = 0.087512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.066303 restraints weight = 46997.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.067886 restraints weight = 33189.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.069036 restraints weight = 25488.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.069605 restraints weight = 20753.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.070255 restraints weight = 18197.167| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.4374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 10621 Z= 0.206 Angle : 0.816 13.565 14456 Z= 0.407 Chirality : 0.049 0.328 1780 Planarity : 0.005 0.051 1819 Dihedral : 4.023 17.580 1476 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 23.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 4.35 % Allowed : 38.74 % Favored : 56.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.22), residues: 1388 helix: 0.86 (0.15), residues: 1131 sheet: None (None), residues: 0 loop : -1.71 (0.42), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG V 40 TYR 0.027 0.002 TYR K 48 PHE 0.058 0.002 PHE T 282 TRP 0.008 0.001 TRP Z 208 HIS 0.003 0.001 HIS Z 136 Details of bonding type rmsd covalent geometry : bond 0.00470 (10620) covalent geometry : angle 0.81580 (14454) SS BOND : bond 0.00062 ( 1) SS BOND : angle 2.30248 ( 2) hydrogen bonds : bond 0.04981 ( 920) hydrogen bonds : angle 4.32367 ( 2739) *********************** 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 442 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 398 time to evaluate : 0.234 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: H 29 SER cc_start: 0.9769 (t) cc_final: 0.9337 (p) REVERT: H 33 GLN cc_start: 0.9342 (mt0) cc_final: 0.9010 (mm-40) REVERT: H 37 ARG cc_start: 0.8965 (mtt90) cc_final: 0.8653 (mtt90) REVERT: H 44 ARG cc_start: 0.8634 (mtp85) cc_final: 0.8251 (mmm-85) REVERT: H 48 TYR cc_start: 0.8996 (m-80) cc_final: 0.8340 (m-80) REVERT: H 49 MET cc_start: 0.9373 (OUTLIER) cc_final: 0.9010 (ppp) REVERT: H 62 PHE cc_start: 0.9364 (m-80) cc_final: 0.9082 (m-80) REVERT: I 33 GLN cc_start: 0.9319 (mt0) cc_final: 0.8808 (mm-40) REVERT: I 37 ARG cc_start: 0.9150 (mtt90) cc_final: 0.8742 (mpp80) REVERT: I 48 TYR cc_start: 0.9263 (m-80) cc_final: 0.8697 (m-80) REVERT: I 49 MET cc_start: 0.9584 (OUTLIER) cc_final: 0.9189 (ppp) REVERT: I 51 ILE cc_start: 0.9216 (mt) cc_final: 0.8471 (mm) REVERT: I 55 PHE cc_start: 0.9319 (m-10) cc_final: 0.8750 (m-80) REVERT: I 62 PHE cc_start: 0.9266 (m-10) cc_final: 0.9003 (m-10) REVERT: J 49 MET cc_start: 0.9584 (ttt) cc_final: 0.9295 (tmm) REVERT: K 43 ASN cc_start: 0.9208 (m-40) cc_final: 0.8922 (p0) REVERT: K 50 PHE cc_start: 0.9154 (OUTLIER) cc_final: 0.8800 (m-80) REVERT: K 57 GLU cc_start: 0.9568 (tp30) cc_final: 0.9256 (pt0) REVERT: L 1 MET cc_start: 0.5918 (mmt) cc_final: 0.5491 (mmp) REVERT: L 11 LEU cc_start: 0.9323 (tt) cc_final: 0.9098 (tt) REVERT: L 66 ILE cc_start: 0.9502 (mm) cc_final: 0.9177 (mm) REVERT: M 4 LEU cc_start: 0.9381 (tp) cc_final: 0.9085 (tp) REVERT: M 29 SER cc_start: 0.9597 (t) cc_final: 0.8897 (m) REVERT: M 68 PHE cc_start: 0.8229 (m-10) cc_final: 0.7760 (m-80) REVERT: N 48 TYR cc_start: 0.8987 (m-10) cc_final: 0.8392 (m-80) REVERT: N 55 PHE cc_start: 0.9360 (OUTLIER) cc_final: 0.8718 (m-80) REVERT: O 50 PHE cc_start: 0.9167 (m-10) cc_final: 0.8868 (m-80) REVERT: O 51 ILE cc_start: 0.8719 (mm) cc_final: 0.8475 (tp) REVERT: P 1 MET cc_start: 0.6146 (mtt) cc_final: 0.5142 (tpp) REVERT: P 33 GLN cc_start: 0.9299 (mt0) cc_final: 0.8936 (mt0) REVERT: P 38 ASN cc_start: 0.9003 (t0) cc_final: 0.8096 (t0) REVERT: P 41 ILE cc_start: 0.9444 (tp) cc_final: 0.8891 (tt) REVERT: P 48 TYR cc_start: 0.9166 (m-80) cc_final: 0.8611 (m-80) REVERT: P 49 MET cc_start: 0.9713 (ttt) cc_final: 0.9364 (tmm) REVERT: P 51 ILE cc_start: 0.9548 (mm) cc_final: 0.9079 (tt) REVERT: P 62 PHE cc_start: 0.9137 (m-10) cc_final: 0.8848 (m-10) REVERT: Q 26 ILE cc_start: 0.9686 (mt) cc_final: 0.9319 (tp) REVERT: Q 38 ASN cc_start: 0.9240 (t0) cc_final: 0.8726 (t0) REVERT: Q 48 TYR cc_start: 0.8886 (m-10) cc_final: 0.8308 (m-80) REVERT: Q 49 MET cc_start: 0.9309 (OUTLIER) cc_final: 0.8853 (tmm) REVERT: Q 68 PHE cc_start: 0.9297 (m-10) cc_final: 0.8698 (m-80) REVERT: T 84 MET cc_start: 0.6357 (mtt) cc_final: 0.5822 (ptp) REVERT: T 92 TYR cc_start: 0.7651 (OUTLIER) cc_final: 0.7038 (m-80) REVERT: T 102 TYR cc_start: 0.8225 (m-80) cc_final: 0.7686 (m-80) REVERT: T 235 GLU cc_start: 0.9505 (mt-10) cc_final: 0.9211 (tp30) REVERT: T 238 SER cc_start: 0.8938 (p) cc_final: 0.8665 (p) REVERT: T 296 TYR cc_start: 0.8868 (t80) cc_final: 0.8217 (t80) REVERT: V 35 ASN cc_start: 0.9225 (m-40) cc_final: 0.8539 (p0) REVERT: V 39 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8329 (mm-30) REVERT: Y 18 PHE cc_start: 0.9102 (t80) cc_final: 0.8860 (t80) REVERT: Y 42 ARG cc_start: 0.8939 (mmp80) cc_final: 0.8256 (mmp80) REVERT: Y 45 GLU cc_start: 0.6924 (pp20) cc_final: 0.5732 (pp20) REVERT: Z 102 TYR cc_start: 0.8789 (m-80) cc_final: 0.8467 (m-80) REVERT: Z 190 ASP cc_start: 0.8538 (t70) cc_final: 0.8079 (p0) outliers start: 44 outliers final: 30 residues processed: 414 average time/residue: 0.0727 time to fit residues: 44.9397 Evaluate side-chains 415 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 379 time to evaluate : 0.432 ------------------------------------------------------------------------------- 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 49 MET Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 27 ILE Chi-restraints excluded: chain K residue 24 ILE Chi-restraints excluded: chain K residue 50 PHE Chi-restraints excluded: chain L 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 51 ILE Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain N residue 55 PHE 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 P residue 56 THR Chi-restraints excluded: chain Q residue 6 LEU Chi-restraints excluded: chain Q residue 32 VAL Chi-restraints excluded: chain Q residue 49 MET Chi-restraints excluded: chain T residue 92 TYR Chi-restraints excluded: chain T residue 114 PHE 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 260 LEU Chi-restraints excluded: chain Z residue 289 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.6878 > 50: distance: 46 - 70: 35.210 distance: 50 - 76: 20.218 distance: 55 - 85: 31.049 distance: 65 - 70: 33.434 distance: 66 - 93: 22.408 distance: 70 - 71: 48.449 distance: 71 - 72: 32.837 distance: 71 - 74: 16.518 distance: 72 - 73: 45.015 distance: 72 - 76: 44.986 distance: 73 - 100: 16.529 distance: 74 - 75: 36.044 distance: 76 - 77: 38.424 distance: 77 - 78: 55.941 distance: 77 - 80: 60.119 distance: 78 - 79: 53.944 distance: 78 - 85: 42.245 distance: 80 - 81: 24.578 distance: 82 - 83: 42.401 distance: 82 - 84: 21.147 distance: 85 - 86: 45.966 distance: 86 - 87: 34.408 distance: 87 - 88: 49.590 distance: 87 - 93: 36.148 distance: 89 - 90: 15.968 distance: 90 - 91: 35.040 distance: 90 - 92: 40.833 distance: 93 - 94: 54.151 distance: 94 - 95: 44.687 distance: 94 - 97: 32.856 distance: 95 - 96: 49.750 distance: 95 - 100: 49.561 distance: 97 - 98: 30.266 distance: 97 - 99: 46.422 distance: 100 - 101: 37.138 distance: 101 - 102: 53.452 distance: 101 - 104: 24.051 distance: 102 - 103: 35.159 distance: 102 - 109: 32.740 distance: 103 - 132: 44.626 distance: 104 - 105: 32.168 distance: 105 - 106: 24.114 distance: 106 - 107: 30.984 distance: 107 - 108: 21.171 distance: 109 - 110: 62.596 distance: 109 - 115: 57.490 distance: 110 - 111: 56.186 distance: 110 - 113: 63.514 distance: 111 - 112: 55.859 distance: 111 - 116: 42.153 distance: 112 - 140: 33.925 distance: 113 - 114: 25.232 distance: 114 - 115: 33.404 distance: 116 - 117: 19.963 distance: 117 - 118: 15.941 distance: 117 - 120: 42.932 distance: 118 - 119: 5.494 distance: 118 - 127: 23.389 distance: 119 - 145: 28.062 distance: 120 - 121: 26.391 distance: 121 - 122: 20.204 distance: 121 - 123: 23.919 distance: 122 - 124: 8.293 distance: 123 - 125: 19.449 distance: 124 - 126: 36.708 distance: 125 - 126: 35.692 distance: 127 - 128: 18.569 distance: 128 - 129: 16.204 distance: 128 - 131: 12.875 distance: 129 - 130: 36.117 distance: 129 - 132: 31.307 distance: 130 - 156: 30.369 distance: 132 - 133: 5.667 distance: 133 - 134: 31.862 distance: 133 - 136: 13.994 distance: 134 - 135: 44.248 distance: 134 - 140: 14.676 distance: 135 - 167: 33.491 distance: 136 - 137: 49.187 distance: 137 - 138: 28.039 distance: 137 - 139: 22.870 distance: 140 - 141: 25.090 distance: 141 - 142: 18.509 distance: 141 - 144: 30.923 distance: 142 - 143: 44.282 distance: 142 - 145: 24.491 distance: 143 - 171: 35.909