Starting phenix.real_space_refine on Tue May 13 13:25:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9itm_60871/05_2025/9itm_60871.cif Found real_map, /net/cci-nas-00/data/ceres_data/9itm_60871/05_2025/9itm_60871.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9itm_60871/05_2025/9itm_60871.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9itm_60871/05_2025/9itm_60871.map" model { file = "/net/cci-nas-00/data/ceres_data/9itm_60871/05_2025/9itm_60871.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9itm_60871/05_2025/9itm_60871.cif" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.011 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 36 5.16 5 C 7167 2.51 5 N 1706 2.21 5 O 1783 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 10692 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: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "L" 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: "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: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "O" 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: "P" 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: "Q" 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: "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: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 396 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} 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: 348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 348 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 2, 'TRANS': 39} 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: 7.42, per 1000 atoms: 0.69 Number of scatterers: 10692 At special positions: 0 Unit cell: (86.49, 127.41, 82.77, 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 36 16.00 O 1783 8.00 N 1706 7.00 C 7167 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS T 135 " - pdb=" SG CYS T 173 " distance=2.86 Simple disulfide: pdb=" SG CYS Z 135 " - pdb=" SG CYS Z 173 " distance=2.70 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.10 Conformation dependent library (CDL) restraints added in 1.4 seconds 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2520 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 3 sheets defined 84.5% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'H' and resid 4 through 38 Proline residue: H 20 - end of helix Processing helix chain 'H' and resid 41 through 72 removed outlier: 3.882A pdb=" N ALA H 58 " --> pdb=" O ALA H 54 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA H 60 " --> pdb=" O THR H 56 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 38 Proline residue: I 20 - end of helix Processing helix chain 'I' and resid 41 through 71 removed outlier: 3.914A pdb=" N ALA I 58 " --> pdb=" O ALA I 54 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA I 60 " --> pdb=" O THR I 56 " (cutoff:3.500A) 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 removed outlier: 3.815A pdb=" N ALA J 58 " --> pdb=" O ALA J 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 16 removed outlier: 3.604A pdb=" N GLY K 16 " --> pdb=" O ALA K 12 " (cutoff:3.500A) Processing helix chain 'K' and resid 17 through 38 removed outlier: 3.736A pdb=" N GLY K 21 " --> pdb=" O ALA K 17 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N VAL K 22 " --> pdb=" O ILE K 18 " (cutoff:3.500A) Processing helix chain 'K' and resid 41 through 72 removed outlier: 3.674A pdb=" N ALA K 58 " --> pdb=" O ALA K 54 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA K 67 " --> pdb=" O GLY K 63 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU K 69 " --> pdb=" O VAL K 65 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 17 Processing helix chain 'L' and resid 18 through 37 removed outlier: 3.537A 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 removed outlier: 3.696A pdb=" N ALA L 58 " --> pdb=" O ALA L 54 " (cutoff:3.500A) 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: 4.683A pdb=" N THR M 47 " --> pdb=" O ASN M 43 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N TYR M 48 " --> pdb=" O ARG M 44 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU M 57 " --> pdb=" O ILE M 53 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA M 58 " --> pdb=" O ALA M 54 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 38 removed outlier: 3.988A 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 removed outlier: 3.590A pdb=" N ALA N 60 " --> pdb=" O THR N 56 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 38 Proline residue: O 20 - end of helix Processing helix chain 'O' and resid 41 through 72 removed outlier: 4.724A pdb=" N LEU O 59 " --> pdb=" O PHE O 55 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA O 60 " --> pdb=" O THR O 56 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE O 72 " --> pdb=" O PHE O 68 " (cutoff:3.500A) Processing helix chain 'P' and resid 3 through 38 removed outlier: 3.891A pdb=" N VAL P 7 " --> pdb=" O GLY P 3 " (cutoff:3.500A) Proline residue: P 20 - end of helix Processing helix chain 'P' and resid 41 through 71 removed outlier: 4.153A pdb=" N THR P 47 " --> pdb=" O ASN P 43 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N TYR P 48 " --> pdb=" O ARG P 44 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA P 58 " --> pdb=" O ALA P 54 " (cutoff:3.500A) Processing helix chain 'Q' and resid 3 through 38 removed outlier: 3.674A 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: 3.932A pdb=" N THR Q 47 " --> pdb=" O ASN Q 43 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU Q 59 " --> pdb=" O PHE Q 55 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA Q 60 " --> pdb=" O THR Q 56 " (cutoff:3.500A) Processing helix chain 'T' and resid 19 through 23 removed outlier: 3.953A pdb=" N ARG T 22 " --> pdb=" O ILE T 19 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE T 23 " --> pdb=" O ALA T 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 19 through 23' Processing helix chain 'T' and resid 50 through 71 removed outlier: 5.197A pdb=" N ILE T 56 " --> pdb=" O PHE T 52 " (cutoff:3.500A) Processing helix chain 'T' and resid 79 through 97 Processing helix chain 'T' and resid 106 through 125 removed outlier: 3.521A pdb=" N VAL T 110 " --> pdb=" O ALA T 106 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N PHE T 114 " --> pdb=" O VAL T 110 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N PHE T 119 " --> pdb=" O LEU T 115 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY T 124 " --> pdb=" O GLY T 120 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU T 125 " --> pdb=" O ASN T 121 " (cutoff:3.500A) Processing helix chain 'T' and resid 171 through 178 removed outlier: 3.928A pdb=" N ALA T 175 " --> pdb=" O THR T 172 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N GLN T 176 " --> pdb=" O CYS T 173 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS T 178 " --> pdb=" O ALA T 175 " (cutoff:3.500A) Processing helix chain 'T' and resid 186 through 190 Processing helix chain 'T' and resid 192 through 212 removed outlier: 4.269A 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: 3.536A 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 272 through 304 removed outlier: 4.579A pdb=" N PHE T 276 " --> pdb=" O LEU T 272 " (cutoff:3.500A) removed outlier: 3.700A 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 29 Processing helix chain 'X' and resid 29 through 43 Processing helix chain 'Y' and resid 7 through 29 Processing helix chain 'Y' and resid 30 through 47 removed outlier: 3.608A pdb=" N SER Y 47 " --> pdb=" O ARG Y 43 " (cutoff:3.500A) Processing helix chain 'Z' and resid 17 through 24 removed outlier: 3.846A pdb=" N ALA Z 20 " --> pdb=" O ILE Z 17 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ARG Z 22 " --> pdb=" O ILE Z 19 " (cutoff:3.500A) Processing helix chain 'Z' and resid 50 through 71 removed outlier: 3.898A pdb=" N VAL Z 54 " --> pdb=" O ASN Z 50 " (cutoff:3.500A) Processing helix chain 'Z' and resid 79 through 99 Processing helix chain 'Z' and resid 102 through 125 Proline residue: Z 108 - end of helix removed outlier: 4.108A 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 186 through 189 Processing helix chain 'Z' and resid 190 through 214 removed outlier: 3.565A pdb=" N THR Z 194 " --> pdb=" O ASP Z 190 " (cutoff:3.500A) Processing helix chain 'Z' and resid 215 through 220 removed outlier: 3.724A pdb=" N LYS Z 219 " --> pdb=" O PRO Z 215 " (cutoff:3.500A) Processing helix chain 'Z' and resid 221 through 225 removed outlier: 3.798A pdb=" N ASN Z 225 " --> pdb=" O PHE Z 222 " (cutoff:3.500A) Processing helix chain 'Z' and resid 229 through 268 removed outlier: 3.998A pdb=" N ILE Z 233 " --> pdb=" O SER Z 229 " (cutoff:3.500A) Proline residue: Z 243 - end of helix removed outlier: 3.777A pdb=" N LEU Z 250 " --> pdb=" O LEU Z 246 " (cutoff:3.500A) Processing helix chain 'Z' and resid 273 through 304 removed outlier: 3.926A pdb=" N PHE Z 285 " --> pdb=" O VAL Z 281 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'T' and resid 132 through 133 Processing sheet with id=AA2, first strand: chain 'Y' and resid 4 through 5 Processing sheet with id=AA3, first strand: chain 'Z' and resid 39 through 41 removed outlier: 7.236A pdb=" N ILE Z 48 " --> pdb=" O PHE Z 40 " (cutoff:3.500A) 921 hydrogen bonds defined for protein. 2724 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.36 Time building geometry restraints manager: 3.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3313 1.34 - 1.46: 1617 1.46 - 1.58: 5905 1.58 - 1.69: 0 1.69 - 1.81: 68 Bond restraints: 10903 Sorted by residual: bond pdb=" N ILE O 70 " pdb=" CA ILE O 70 " ideal model delta sigma weight residual 1.455 1.495 -0.040 1.06e-02 8.90e+03 1.41e+01 bond pdb=" N ILE M 70 " pdb=" CA ILE M 70 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.19e-02 7.06e+03 8.60e+00 bond pdb=" N ILE Q 70 " pdb=" CA ILE Q 70 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.19e-02 7.06e+03 8.46e+00 bond pdb=" N ILE K 70 " pdb=" CA ILE K 70 " ideal model delta sigma weight residual 1.460 1.495 -0.034 1.19e-02 7.06e+03 8.40e+00 bond pdb=" N ILE N 70 " pdb=" CA ILE N 70 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.22e-02 6.72e+03 8.21e+00 ... (remaining 10898 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 14553 1.99 - 3.99: 241 3.99 - 5.98: 27 5.98 - 7.98: 1 7.98 - 9.97: 1 Bond angle restraints: 14823 Sorted by residual: angle pdb=" C THR T 172 " pdb=" N CYS T 173 " pdb=" CA CYS T 173 " ideal model delta sigma weight residual 122.62 112.65 9.97 1.78e+00 3.16e-01 3.14e+01 angle pdb=" N ILE O 70 " pdb=" CA ILE O 70 " pdb=" C ILE O 70 " ideal model delta sigma weight residual 112.12 108.50 3.62 8.40e-01 1.42e+00 1.86e+01 angle pdb=" N ILE P 70 " pdb=" CA ILE P 70 " pdb=" C ILE P 70 " ideal model delta sigma weight residual 113.42 108.55 4.87 1.17e+00 7.31e-01 1.74e+01 angle pdb=" C CYS T 173 " pdb=" CA CYS T 173 " pdb=" CB CYS T 173 " ideal model delta sigma weight residual 111.40 116.64 -5.24 1.29e+00 6.01e-01 1.65e+01 angle pdb=" N ILE L 70 " pdb=" CA ILE L 70 " pdb=" C ILE L 70 " ideal model delta sigma weight residual 111.67 108.19 3.48 9.50e-01 1.11e+00 1.34e+01 ... (remaining 14818 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 5386 17.77 - 35.53: 706 35.53 - 53.30: 141 53.30 - 71.07: 16 71.07 - 88.83: 15 Dihedral angle restraints: 6264 sinusoidal: 2310 harmonic: 3954 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 93.00 173.86 -80.86 1 1.00e+01 1.00e-02 8.07e+01 dihedral pdb=" CA CYS T 173 " pdb=" C CYS T 173 " pdb=" N ALA T 174 " pdb=" CA ALA T 174 " ideal model delta harmonic sigma weight residual 180.00 156.52 23.48 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA PHE T 52 " pdb=" C PHE T 52 " pdb=" N VAL T 53 " pdb=" CA VAL T 53 " ideal model delta harmonic sigma weight residual 180.00 157.05 22.95 0 5.00e+00 4.00e-02 2.11e+01 ... (remaining 6261 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1330 0.043 - 0.086: 381 0.086 - 0.129: 88 0.129 - 0.172: 11 0.172 - 0.215: 11 Chirality restraints: 1821 Sorted by residual: chirality pdb=" CA ILE K 70 " pdb=" N ILE K 70 " pdb=" C ILE K 70 " pdb=" CB ILE K 70 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA ILE L 70 " pdb=" N ILE L 70 " pdb=" C ILE L 70 " pdb=" CB ILE L 70 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA CYS Z 135 " pdb=" N CYS Z 135 " pdb=" C CYS Z 135 " pdb=" CB CYS Z 135 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.84e-01 ... (remaining 1818 not shown) Planarity restraints: 1852 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY Q 19 " 0.048 5.00e-02 4.00e+02 7.34e-02 8.62e+00 pdb=" N PRO Q 20 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO Q 20 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO Q 20 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY M 19 " -0.044 5.00e-02 4.00e+02 6.66e-02 7.09e+00 pdb=" N PRO M 20 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO M 20 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO M 20 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY H 19 " 0.043 5.00e-02 4.00e+02 6.52e-02 6.79e+00 pdb=" N PRO H 20 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO H 20 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO H 20 " 0.036 5.00e-02 4.00e+02 ... (remaining 1849 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2295 2.77 - 3.30: 11530 3.30 - 3.84: 18620 3.84 - 4.37: 20861 4.37 - 4.90: 36088 Nonbonded interactions: 89394 Sorted by model distance: nonbonded pdb=" OH TYR L 48 " pdb=" OE2 GLU M 42 " model vdw 2.239 3.040 nonbonded pdb=" O PRO Z 108 " pdb=" OG1 THR Z 112 " model vdw 2.249 3.040 nonbonded pdb=" O PHE T 86 " pdb=" OG SER T 90 " model vdw 2.279 3.040 nonbonded pdb=" O ASN T 99 " pdb=" OH TYR T 296 " model vdw 2.294 3.040 nonbonded pdb=" OE1 GLU T 85 " pdb=" NH2 ARG X 40 " model vdw 2.304 3.120 ... (remaining 89389 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 3 through 44) selection = chain 'X' selection = (chain 'Y' and resid 3 through 44) } 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 individual isotropic 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: 5.930 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 27.520 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 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 : 0.011 0.824 10905 Z= 0.554 Angle : 0.646 30.404 14827 Z= 0.395 Chirality : 0.043 0.215 1821 Planarity : 0.006 0.073 1852 Dihedral : 16.324 88.834 3738 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.28 % Allowed : 29.68 % Favored : 70.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.22), residues: 1388 helix: 0.53 (0.15), residues: 1112 sheet: None (None), residues: 0 loop : -1.20 (0.39), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP T 208 HIS 0.001 0.000 HIS Z 31 PHE 0.008 0.001 PHE T 276 TYR 0.011 0.001 TYR Z 296 ARG 0.002 0.000 ARG M 44 Details of bonding type rmsd hydrogen bonds : bond 0.15155 ( 921) hydrogen bonds : angle 6.69737 ( 2724) SS BOND : bond 0.74898 ( 2) SS BOND : angle 15.64313 ( 4) covalent geometry : bond 0.00395 (10903) covalent geometry : angle 0.59260 (14823) *********************** 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 318 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 315 time to evaluate : 1.151 Fit side-chains revert: symmetry clash REVERT: J 24 ILE cc_start: 0.9394 (mm) cc_final: 0.9187 (mt) REVERT: O 1 MET cc_start: 0.7541 (tpp) cc_final: 0.7293 (tpp) REVERT: O 38 ASN cc_start: 0.8270 (t0) cc_final: 0.7915 (t0) REVERT: O 41 ILE cc_start: 0.9071 (tp) cc_final: 0.8730 (tp) REVERT: P 41 ILE cc_start: 0.9022 (tp) cc_final: 0.8677 (tt) REVERT: Q 41 ILE cc_start: 0.9388 (tp) cc_final: 0.9012 (tp) REVERT: T 37 GLU cc_start: 0.6779 (tm-30) cc_final: 0.6464 (pm20) REVERT: T 96 ARG cc_start: 0.9046 (ttm-80) cc_final: 0.8833 (ttm110) REVERT: T 180 LEU cc_start: 0.8008 (tt) cc_final: 0.7798 (tt) REVERT: T 255 PHE cc_start: 0.8990 (t80) cc_final: 0.8565 (t80) REVERT: T 264 MET cc_start: 0.9046 (mmt) cc_final: 0.8812 (mmt) REVERT: T 280 GLU cc_start: 0.8866 (tm-30) cc_final: 0.8653 (tm-30) REVERT: V 24 ILE cc_start: 0.8568 (tt) cc_final: 0.8253 (mm) REVERT: V 28 LEU cc_start: 0.8827 (tt) cc_final: 0.8592 (tt) REVERT: Z 179 LYS cc_start: 0.7327 (tptp) cc_final: 0.7102 (ttpt) REVERT: Z 236 PHE cc_start: 0.8802 (t80) cc_final: 0.8305 (t80) outliers start: 3 outliers final: 2 residues processed: 318 average time/residue: 0.2286 time to fit residues: 101.5594 Evaluate side-chains 267 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 265 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 283 VAL Chi-restraints excluded: chain Z residue 169 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 58 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 70 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 65 optimal weight: 0.5980 chunk 80 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.121500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.087757 restraints weight = 18746.979| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.51 r_work: 0.3258 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10905 Z= 0.175 Angle : 0.581 9.399 14827 Z= 0.312 Chirality : 0.042 0.169 1821 Planarity : 0.006 0.073 1852 Dihedral : 3.907 29.270 1491 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.96 % Allowed : 29.49 % Favored : 66.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.22), residues: 1388 helix: 1.37 (0.15), residues: 1132 sheet: None (None), residues: 0 loop : -1.19 (0.41), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP T 208 HIS 0.002 0.001 HIS T 136 PHE 0.023 0.001 PHE T 230 TYR 0.019 0.002 TYR V 30 ARG 0.005 0.000 ARG Z 249 Details of bonding type rmsd hydrogen bonds : bond 0.06317 ( 921) hydrogen bonds : angle 4.50985 ( 2724) SS BOND : bond 0.00569 ( 2) SS BOND : angle 1.44250 ( 4) covalent geometry : bond 0.00378 (10903) covalent geometry : angle 0.58045 (14823) *********************** 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 329 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 286 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 57 GLU cc_start: 0.8729 (tp30) cc_final: 0.8517 (tp30) REVERT: K 70 ILE cc_start: 0.9404 (mm) cc_final: 0.9163 (mt) REVERT: O 1 MET cc_start: 0.7587 (tpp) cc_final: 0.7354 (tpp) REVERT: O 38 ASN cc_start: 0.8251 (t0) cc_final: 0.7638 (t0) REVERT: O 41 ILE cc_start: 0.9135 (tp) cc_final: 0.8736 (tp) REVERT: P 41 ILE cc_start: 0.9087 (tp) cc_final: 0.8804 (tp) REVERT: Q 41 ILE cc_start: 0.9318 (tp) cc_final: 0.9045 (tp) REVERT: T 25 LEU cc_start: 0.7541 (OUTLIER) cc_final: 0.7207 (pp) REVERT: T 255 PHE cc_start: 0.8974 (t80) cc_final: 0.8538 (t80) REVERT: T 280 GLU cc_start: 0.8780 (tm-30) cc_final: 0.8568 (tm-30) REVERT: U 31 ARG cc_start: 0.8632 (tpp-160) cc_final: 0.8379 (tpp80) REVERT: V 24 ILE cc_start: 0.8605 (tt) cc_final: 0.8290 (mm) REVERT: Z 26 TYR cc_start: 0.7751 (t80) cc_final: 0.7410 (t80) REVERT: Z 179 LYS cc_start: 0.7395 (tptp) cc_final: 0.7139 (ttpt) REVERT: Z 236 PHE cc_start: 0.8820 (t80) cc_final: 0.8298 (t80) REVERT: Z 258 GLU cc_start: 0.8263 (tm-30) cc_final: 0.7920 (tm-30) outliers start: 43 outliers final: 22 residues processed: 308 average time/residue: 0.2231 time to fit residues: 95.5296 Evaluate side-chains 295 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 272 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 49 MET Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain J residue 41 ILE Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 66 ILE Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain T residue 25 LEU Chi-restraints excluded: chain T residue 32 VAL Chi-restraints excluded: chain T residue 200 ILE Chi-restraints excluded: chain T residue 206 GLU Chi-restraints excluded: chain T residue 208 TRP Chi-restraints excluded: chain T residue 289 LEU Chi-restraints excluded: chain V residue 11 PHE Chi-restraints excluded: chain V residue 16 ILE Chi-restraints excluded: chain X residue 37 LEU Chi-restraints excluded: chain Y residue 4 LEU Chi-restraints excluded: chain Y residue 6 ILE Chi-restraints excluded: chain Z residue 169 ILE Chi-restraints excluded: chain Z residue 205 ILE Chi-restraints excluded: chain Z residue 290 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 77 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 39 optimal weight: 0.2980 chunk 106 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 131 optimal weight: 3.9990 chunk 7 optimal weight: 0.0970 chunk 117 optimal weight: 1.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.122846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.089009 restraints weight = 18830.564| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.56 r_work: 0.3169 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10905 Z= 0.152 Angle : 0.563 9.964 14827 Z= 0.295 Chirality : 0.041 0.167 1821 Planarity : 0.005 0.072 1852 Dihedral : 3.823 30.720 1490 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 4.70 % Allowed : 28.85 % Favored : 66.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.22), residues: 1388 helix: 1.54 (0.15), residues: 1132 sheet: None (None), residues: 0 loop : -1.13 (0.42), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP T 208 HIS 0.001 0.000 HIS Z 31 PHE 0.025 0.001 PHE T 230 TYR 0.014 0.002 TYR N 48 ARG 0.006 0.000 ARG M 44 Details of bonding type rmsd hydrogen bonds : bond 0.05686 ( 921) hydrogen bonds : angle 4.20988 ( 2724) SS BOND : bond 0.00362 ( 2) SS BOND : angle 1.36551 ( 4) covalent geometry : bond 0.00315 (10903) covalent geometry : angle 0.56213 (14823) *********************** 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 344 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 293 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 70 ILE cc_start: 0.9341 (mm) cc_final: 0.9136 (mt) REVERT: M 41 ILE cc_start: 0.9179 (OUTLIER) cc_final: 0.8887 (tp) REVERT: O 1 MET cc_start: 0.7583 (tpp) cc_final: 0.7225 (tpp) REVERT: O 38 ASN cc_start: 0.8189 (t0) cc_final: 0.7953 (t0) REVERT: O 41 ILE cc_start: 0.9108 (tp) cc_final: 0.8842 (tp) REVERT: P 41 ILE cc_start: 0.9001 (tp) cc_final: 0.8734 (tp) REVERT: P 48 TYR cc_start: 0.9080 (m-80) cc_final: 0.8875 (m-80) REVERT: Q 41 ILE cc_start: 0.9264 (tp) cc_final: 0.8966 (tp) REVERT: T 25 LEU cc_start: 0.7451 (OUTLIER) cc_final: 0.7111 (pp) REVERT: T 180 LEU cc_start: 0.8466 (tt) cc_final: 0.8068 (mp) REVERT: T 239 GLU cc_start: 0.9195 (tp30) cc_final: 0.8737 (tp30) REVERT: T 242 LYS cc_start: 0.8846 (mttt) cc_final: 0.8345 (mttt) REVERT: T 255 PHE cc_start: 0.8935 (t80) cc_final: 0.8541 (t80) REVERT: T 280 GLU cc_start: 0.8797 (tm-30) cc_final: 0.8573 (tm-30) REVERT: U 31 ARG cc_start: 0.8602 (tpp-160) cc_final: 0.8351 (tpp80) REVERT: V 24 ILE cc_start: 0.8575 (tt) cc_final: 0.8255 (mm) REVERT: Z 26 TYR cc_start: 0.7563 (t80) cc_final: 0.7181 (t80) REVERT: Z 179 LYS cc_start: 0.7394 (tptp) cc_final: 0.7098 (ttpt) REVERT: Z 236 PHE cc_start: 0.8786 (t80) cc_final: 0.8301 (t80) REVERT: Z 258 GLU cc_start: 0.8260 (tm-30) cc_final: 0.7904 (tm-30) REVERT: Z 296 TYR cc_start: 0.8163 (t80) cc_final: 0.7299 (t80) outliers start: 51 outliers final: 36 residues processed: 318 average time/residue: 0.2343 time to fit residues: 103.4393 Evaluate side-chains 312 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 274 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 49 MET Chi-restraints excluded: chain H residue 66 ILE Chi-restraints excluded: chain J residue 41 ILE Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 49 MET Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain M residue 41 ILE Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 66 ILE Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain O residue 53 ILE Chi-restraints excluded: chain P residue 49 MET Chi-restraints excluded: chain Q residue 44 ARG Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain T residue 25 LEU Chi-restraints excluded: chain T residue 53 VAL Chi-restraints excluded: chain T residue 65 LEU Chi-restraints excluded: chain T residue 89 GLU Chi-restraints excluded: chain T residue 200 ILE Chi-restraints excluded: chain T residue 206 GLU Chi-restraints excluded: chain T residue 208 TRP Chi-restraints excluded: chain T residue 260 LEU Chi-restraints excluded: chain T residue 286 ILE Chi-restraints excluded: chain T residue 289 LEU Chi-restraints excluded: chain V residue 11 PHE Chi-restraints excluded: chain V residue 16 ILE Chi-restraints excluded: chain X residue 25 LEU Chi-restraints excluded: chain X residue 37 LEU Chi-restraints excluded: chain Y residue 4 LEU Chi-restraints excluded: chain Y residue 6 ILE Chi-restraints excluded: chain Z residue 15 LEU Chi-restraints excluded: chain Z residue 136 HIS Chi-restraints excluded: chain Z residue 169 ILE Chi-restraints excluded: chain Z residue 205 ILE Chi-restraints excluded: chain Z residue 290 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 37 optimal weight: 0.7980 chunk 137 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 111 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.121985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.088297 restraints weight = 18741.922| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.52 r_work: 0.3154 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10905 Z= 0.167 Angle : 0.570 10.839 14827 Z= 0.297 Chirality : 0.041 0.167 1821 Planarity : 0.005 0.072 1852 Dihedral : 3.818 31.705 1490 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 5.90 % Allowed : 28.20 % Favored : 65.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.22), residues: 1388 helix: 1.53 (0.15), residues: 1134 sheet: None (None), residues: 0 loop : -1.05 (0.42), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP T 208 HIS 0.001 0.001 HIS Z 31 PHE 0.026 0.001 PHE T 230 TYR 0.014 0.002 TYR N 48 ARG 0.007 0.000 ARG Z 78 Details of bonding type rmsd hydrogen bonds : bond 0.05591 ( 921) hydrogen bonds : angle 4.12051 ( 2724) SS BOND : bond 0.00256 ( 2) SS BOND : angle 1.22575 ( 4) covalent geometry : bond 0.00366 (10903) covalent geometry : angle 0.56964 (14823) *********************** 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 346 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 282 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 41 ILE cc_start: 0.9195 (OUTLIER) cc_final: 0.8911 (tp) REVERT: O 1 MET cc_start: 0.7517 (tpp) cc_final: 0.7042 (tmm) REVERT: O 41 ILE cc_start: 0.9110 (tp) cc_final: 0.8846 (tp) REVERT: P 41 ILE cc_start: 0.9021 (tp) cc_final: 0.8810 (tp) REVERT: P 57 GLU cc_start: 0.8980 (mm-30) cc_final: 0.8705 (mm-30) REVERT: Q 41 ILE cc_start: 0.9284 (tp) cc_final: 0.8990 (tp) REVERT: T 25 LEU cc_start: 0.7523 (OUTLIER) cc_final: 0.7107 (pp) REVERT: T 255 PHE cc_start: 0.8954 (t80) cc_final: 0.8540 (t80) REVERT: T 280 GLU cc_start: 0.8803 (tm-30) cc_final: 0.8589 (tm-30) REVERT: V 24 ILE cc_start: 0.8584 (tt) cc_final: 0.8268 (mm) REVERT: Z 85 GLU cc_start: 0.8879 (OUTLIER) cc_final: 0.8526 (tt0) REVERT: Z 179 LYS cc_start: 0.7360 (tptp) cc_final: 0.7047 (ttpt) REVERT: Z 236 PHE cc_start: 0.8795 (t80) cc_final: 0.8310 (t80) REVERT: Z 258 GLU cc_start: 0.8249 (tm-30) cc_final: 0.7880 (tm-30) outliers start: 64 outliers final: 44 residues processed: 316 average time/residue: 0.2252 time to fit residues: 99.6136 Evaluate side-chains 312 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 265 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 49 MET Chi-restraints excluded: chain H residue 66 ILE Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 49 MET Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 68 PHE Chi-restraints excluded: chain L residue 49 MET Chi-restraints excluded: chain M residue 41 ILE Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 66 ILE Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 18 ILE Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain Q residue 44 ARG Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain T residue 25 LEU Chi-restraints excluded: chain T residue 32 VAL Chi-restraints excluded: chain T residue 53 VAL Chi-restraints excluded: chain T residue 65 LEU Chi-restraints excluded: chain T residue 89 GLU Chi-restraints excluded: chain T residue 110 VAL Chi-restraints excluded: chain T residue 200 ILE Chi-restraints excluded: chain T residue 206 GLU Chi-restraints excluded: chain T residue 208 TRP Chi-restraints excluded: chain T residue 260 LEU Chi-restraints excluded: chain T residue 286 ILE Chi-restraints excluded: chain T residue 289 LEU Chi-restraints excluded: chain V residue 11 PHE Chi-restraints excluded: chain V residue 16 ILE Chi-restraints excluded: chain X residue 25 LEU Chi-restraints excluded: chain X residue 37 LEU Chi-restraints excluded: chain Y residue 4 LEU Chi-restraints excluded: chain Y residue 6 ILE Chi-restraints excluded: chain Y residue 25 LEU Chi-restraints excluded: chain Z residue 15 LEU Chi-restraints excluded: chain Z residue 85 GLU Chi-restraints excluded: chain Z residue 136 HIS Chi-restraints excluded: chain Z residue 169 ILE Chi-restraints excluded: chain Z residue 205 ILE Chi-restraints excluded: chain Z residue 290 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 17 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 chunk 97 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 128 optimal weight: 0.8980 chunk 106 optimal weight: 0.8980 chunk 104 optimal weight: 4.9990 chunk 85 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.122056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.088484 restraints weight = 18663.010| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.52 r_work: 0.3155 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 10905 Z= 0.162 Angle : 0.572 11.074 14827 Z= 0.297 Chirality : 0.041 0.166 1821 Planarity : 0.005 0.072 1852 Dihedral : 3.820 33.008 1490 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 5.35 % Allowed : 29.49 % Favored : 65.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.22), residues: 1388 helix: 1.57 (0.15), residues: 1133 sheet: None (None), residues: 0 loop : -1.06 (0.42), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP T 208 HIS 0.001 0.000 HIS T 136 PHE 0.026 0.001 PHE T 24 TYR 0.014 0.002 TYR Q 48 ARG 0.005 0.000 ARG M 44 Details of bonding type rmsd hydrogen bonds : bond 0.05490 ( 921) hydrogen bonds : angle 4.07519 ( 2724) SS BOND : bond 0.00262 ( 2) SS BOND : angle 1.17090 ( 4) covalent geometry : bond 0.00360 (10903) covalent geometry : angle 0.57130 (14823) *********************** 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 340 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 282 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 2 GLU cc_start: 0.8505 (mp0) cc_final: 0.8004 (pm20) REVERT: K 66 ILE cc_start: 0.9221 (tt) cc_final: 0.9003 (tt) REVERT: M 41 ILE cc_start: 0.9206 (OUTLIER) cc_final: 0.8913 (tp) REVERT: Q 41 ILE cc_start: 0.9272 (tp) cc_final: 0.8965 (tp) REVERT: T 25 LEU cc_start: 0.7489 (OUTLIER) cc_final: 0.7084 (pp) REVERT: T 255 PHE cc_start: 0.8962 (t80) cc_final: 0.8549 (t80) REVERT: T 280 GLU cc_start: 0.8821 (tm-30) cc_final: 0.8599 (tm-30) REVERT: V 24 ILE cc_start: 0.8552 (tt) cc_final: 0.8241 (mm) REVERT: Z 179 LYS cc_start: 0.7328 (tptp) cc_final: 0.7033 (ttpt) REVERT: Z 236 PHE cc_start: 0.8797 (t80) cc_final: 0.8326 (t80) REVERT: Z 258 GLU cc_start: 0.8244 (tm-30) cc_final: 0.7852 (tm-30) outliers start: 58 outliers final: 46 residues processed: 313 average time/residue: 0.2369 time to fit residues: 103.8534 Evaluate side-chains 315 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 267 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 49 MET Chi-restraints excluded: chain H residue 66 ILE Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 49 MET Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain K residue 68 PHE Chi-restraints excluded: chain L residue 49 MET Chi-restraints excluded: chain M residue 41 ILE Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 66 ILE Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 18 ILE Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 59 LEU Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain Q residue 44 ARG Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain T residue 25 LEU Chi-restraints excluded: chain T residue 32 VAL Chi-restraints excluded: chain T residue 53 VAL Chi-restraints excluded: chain T residue 65 LEU Chi-restraints excluded: chain T residue 89 GLU Chi-restraints excluded: chain T residue 110 VAL Chi-restraints excluded: chain T residue 200 ILE Chi-restraints excluded: chain T residue 206 GLU Chi-restraints excluded: chain T residue 208 TRP Chi-restraints excluded: chain T residue 258 GLU Chi-restraints excluded: chain T residue 260 LEU Chi-restraints excluded: chain T residue 286 ILE Chi-restraints excluded: chain T residue 289 LEU Chi-restraints excluded: chain V residue 11 PHE Chi-restraints excluded: chain V residue 16 ILE Chi-restraints excluded: chain X residue 25 LEU Chi-restraints excluded: chain X residue 37 LEU Chi-restraints excluded: chain Y residue 4 LEU Chi-restraints excluded: chain Y residue 6 ILE Chi-restraints excluded: chain Z residue 15 LEU Chi-restraints excluded: chain Z residue 85 GLU Chi-restraints excluded: chain Z residue 136 HIS Chi-restraints excluded: chain Z residue 169 ILE Chi-restraints excluded: chain Z residue 171 ASP Chi-restraints excluded: chain Z residue 205 ILE Chi-restraints excluded: chain Z residue 283 VAL Chi-restraints excluded: chain Z residue 290 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 2 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.121769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.088217 restraints weight = 18836.610| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.52 r_work: 0.3150 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 10905 Z= 0.170 Angle : 0.586 10.735 14827 Z= 0.304 Chirality : 0.042 0.184 1821 Planarity : 0.005 0.073 1852 Dihedral : 3.889 33.598 1490 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 5.81 % Allowed : 29.86 % Favored : 64.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.22), residues: 1388 helix: 1.57 (0.15), residues: 1134 sheet: None (None), residues: 0 loop : -1.05 (0.42), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP T 208 HIS 0.003 0.001 HIS T 136 PHE 0.024 0.001 PHE T 230 TYR 0.014 0.002 TYR O 48 ARG 0.005 0.000 ARG M 44 Details of bonding type rmsd hydrogen bonds : bond 0.05481 ( 921) hydrogen bonds : angle 4.04574 ( 2724) SS BOND : bond 0.01311 ( 2) SS BOND : angle 2.52716 ( 4) covalent geometry : bond 0.00381 (10903) covalent geometry : angle 0.58456 (14823) *********************** 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 338 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 275 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 66 ILE cc_start: 0.9227 (tt) cc_final: 0.9006 (tt) REVERT: M 41 ILE cc_start: 0.9221 (OUTLIER) cc_final: 0.8947 (tp) REVERT: N 59 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8597 (mp) REVERT: O 1 MET cc_start: 0.7576 (tpp) cc_final: 0.7169 (tpp) REVERT: P 57 GLU cc_start: 0.8993 (mm-30) cc_final: 0.8756 (mm-30) REVERT: Q 41 ILE cc_start: 0.9271 (tp) cc_final: 0.8965 (tp) REVERT: T 25 LEU cc_start: 0.7467 (OUTLIER) cc_final: 0.7060 (pp) REVERT: T 92 TYR cc_start: 0.8672 (t80) cc_final: 0.8191 (t80) REVERT: T 239 GLU cc_start: 0.9242 (tp30) cc_final: 0.8840 (tp30) REVERT: T 255 PHE cc_start: 0.8968 (t80) cc_final: 0.8569 (t80) REVERT: T 280 GLU cc_start: 0.8830 (tm-30) cc_final: 0.8583 (tm-30) REVERT: V 24 ILE cc_start: 0.8562 (tt) cc_final: 0.8243 (mm) REVERT: Z 179 LYS cc_start: 0.7348 (tptp) cc_final: 0.7031 (ttpt) REVERT: Z 236 PHE cc_start: 0.8790 (t80) cc_final: 0.8305 (t80) REVERT: Z 258 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7835 (tm-30) outliers start: 63 outliers final: 49 residues processed: 313 average time/residue: 0.2197 time to fit residues: 96.3916 Evaluate side-chains 317 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 264 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 49 MET Chi-restraints excluded: chain H residue 66 ILE Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain K residue 68 PHE Chi-restraints excluded: chain L residue 49 MET Chi-restraints excluded: chain M residue 41 ILE Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 66 ILE Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 18 ILE Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 59 LEU Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain O residue 56 THR Chi-restraints excluded: chain P residue 64 LEU Chi-restraints excluded: chain P residue 69 LEU Chi-restraints excluded: chain Q residue 44 ARG Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain T residue 25 LEU Chi-restraints excluded: chain T residue 32 VAL Chi-restraints excluded: chain T residue 53 VAL Chi-restraints excluded: chain T residue 65 LEU Chi-restraints excluded: chain T residue 89 GLU Chi-restraints excluded: chain T residue 110 VAL Chi-restraints excluded: chain T residue 200 ILE Chi-restraints excluded: chain T residue 206 GLU Chi-restraints excluded: chain T residue 208 TRP Chi-restraints excluded: chain T residue 258 GLU Chi-restraints excluded: chain T residue 260 LEU Chi-restraints excluded: chain T residue 286 ILE Chi-restraints excluded: chain T residue 289 LEU Chi-restraints excluded: chain V residue 11 PHE Chi-restraints excluded: chain V residue 16 ILE Chi-restraints excluded: chain X residue 25 LEU Chi-restraints excluded: chain X residue 37 LEU Chi-restraints excluded: chain Y residue 4 LEU Chi-restraints excluded: chain Y residue 6 ILE Chi-restraints excluded: chain Y residue 25 LEU Chi-restraints excluded: chain Z residue 15 LEU Chi-restraints excluded: chain Z residue 169 ILE Chi-restraints excluded: chain Z residue 171 ASP Chi-restraints excluded: chain Z residue 205 ILE Chi-restraints excluded: chain Z residue 258 GLU Chi-restraints excluded: chain Z residue 283 VAL Chi-restraints excluded: chain Z residue 290 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 48 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 134 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 104 optimal weight: 0.4980 chunk 38 optimal weight: 0.6980 chunk 125 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.121422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.087887 restraints weight = 19110.007| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.56 r_work: 0.3149 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 10905 Z= 0.172 Angle : 0.602 12.224 14827 Z= 0.309 Chirality : 0.042 0.180 1821 Planarity : 0.005 0.073 1852 Dihedral : 3.908 34.336 1490 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 5.90 % Allowed : 29.59 % Favored : 64.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.22), residues: 1388 helix: 1.61 (0.15), residues: 1133 sheet: None (None), residues: 0 loop : -0.98 (0.43), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP T 208 HIS 0.002 0.001 HIS T 136 PHE 0.028 0.001 PHE T 24 TYR 0.014 0.002 TYR Z 296 ARG 0.005 0.000 ARG M 44 Details of bonding type rmsd hydrogen bonds : bond 0.05480 ( 921) hydrogen bonds : angle 4.03904 ( 2724) SS BOND : bond 0.00792 ( 2) SS BOND : angle 2.21024 ( 4) covalent geometry : bond 0.00386 (10903) covalent geometry : angle 0.60086 (14823) *********************** 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 338 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 274 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 66 ILE cc_start: 0.9229 (tt) cc_final: 0.9014 (tt) REVERT: M 40 GLU cc_start: 0.8013 (tm-30) cc_final: 0.7719 (tm-30) REVERT: M 41 ILE cc_start: 0.9208 (OUTLIER) cc_final: 0.8851 (tp) REVERT: N 59 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8654 (mp) REVERT: Q 41 ILE cc_start: 0.9274 (tp) cc_final: 0.8963 (tp) REVERT: T 25 LEU cc_start: 0.7462 (OUTLIER) cc_final: 0.7022 (pp) REVERT: T 92 TYR cc_start: 0.8686 (t80) cc_final: 0.8178 (t80) REVERT: T 239 GLU cc_start: 0.9248 (tp30) cc_final: 0.8843 (tp30) REVERT: T 255 PHE cc_start: 0.8976 (t80) cc_final: 0.8578 (t80) REVERT: T 280 GLU cc_start: 0.8828 (tm-30) cc_final: 0.8577 (tm-30) REVERT: Y 34 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.8387 (ttp) REVERT: Z 179 LYS cc_start: 0.7358 (tptp) cc_final: 0.6995 (ttpt) REVERT: Z 236 PHE cc_start: 0.8726 (t80) cc_final: 0.8252 (t80) REVERT: Z 239 GLU cc_start: 0.9144 (mm-30) cc_final: 0.8857 (mm-30) REVERT: Z 242 LYS cc_start: 0.8807 (mttt) cc_final: 0.8570 (mtmt) REVERT: Z 258 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7815 (tm-30) outliers start: 64 outliers final: 56 residues processed: 311 average time/residue: 0.2201 time to fit residues: 96.4268 Evaluate side-chains 321 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 260 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 49 MET Chi-restraints excluded: chain H residue 66 ILE Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain K residue 68 PHE Chi-restraints excluded: chain L residue 49 MET Chi-restraints excluded: chain M residue 41 ILE Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 66 ILE Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 18 ILE Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 59 LEU Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain O residue 56 THR Chi-restraints excluded: chain P residue 69 LEU Chi-restraints excluded: chain Q residue 44 ARG Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain T residue 25 LEU Chi-restraints excluded: chain T residue 32 VAL Chi-restraints excluded: chain T residue 53 VAL Chi-restraints excluded: chain T residue 65 LEU Chi-restraints excluded: chain T residue 89 GLU Chi-restraints excluded: chain T residue 110 VAL Chi-restraints excluded: chain T residue 136 HIS Chi-restraints excluded: chain T residue 172 THR Chi-restraints excluded: chain T residue 200 ILE Chi-restraints excluded: chain T residue 206 GLU Chi-restraints excluded: chain T residue 208 TRP Chi-restraints excluded: chain T residue 258 GLU Chi-restraints excluded: chain T residue 260 LEU Chi-restraints excluded: chain T residue 283 VAL Chi-restraints excluded: chain T residue 286 ILE Chi-restraints excluded: chain T residue 289 LEU Chi-restraints excluded: chain U residue 24 ILE Chi-restraints excluded: chain V residue 11 PHE Chi-restraints excluded: chain V residue 16 ILE Chi-restraints excluded: chain X residue 25 LEU Chi-restraints excluded: chain X residue 37 LEU Chi-restraints excluded: chain Y residue 4 LEU Chi-restraints excluded: chain Y residue 6 ILE Chi-restraints excluded: chain Y residue 25 LEU Chi-restraints excluded: chain Y residue 34 MET Chi-restraints excluded: chain Z residue 15 LEU Chi-restraints excluded: chain Z residue 19 ILE Chi-restraints excluded: chain Z residue 85 GLU Chi-restraints excluded: chain Z residue 169 ILE Chi-restraints excluded: chain Z residue 171 ASP Chi-restraints excluded: chain Z residue 205 ILE Chi-restraints excluded: chain Z residue 258 GLU Chi-restraints excluded: chain Z residue 283 VAL Chi-restraints excluded: chain Z residue 286 ILE Chi-restraints excluded: chain Z residue 290 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 61 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 70 optimal weight: 0.5980 chunk 74 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 102 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 87 optimal weight: 0.0770 chunk 54 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.123180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.089606 restraints weight = 18707.313| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.53 r_work: 0.3181 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10905 Z= 0.148 Angle : 0.597 12.236 14827 Z= 0.305 Chirality : 0.041 0.173 1821 Planarity : 0.005 0.072 1852 Dihedral : 3.895 34.614 1490 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 6.08 % Allowed : 29.68 % Favored : 64.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.22), residues: 1388 helix: 1.68 (0.15), residues: 1132 sheet: None (None), residues: 0 loop : -0.92 (0.44), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP T 208 HIS 0.001 0.000 HIS Z 170 PHE 0.023 0.001 PHE X 11 TYR 0.011 0.002 TYR Z 296 ARG 0.005 0.000 ARG M 44 Details of bonding type rmsd hydrogen bonds : bond 0.05238 ( 921) hydrogen bonds : angle 3.96713 ( 2724) SS BOND : bond 0.00815 ( 2) SS BOND : angle 1.44858 ( 4) covalent geometry : bond 0.00314 (10903) covalent geometry : angle 0.59706 (14823) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 283 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 1 MET cc_start: 0.7280 (mmt) cc_final: 0.6883 (mmt) REVERT: M 40 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7746 (tm-30) REVERT: M 41 ILE cc_start: 0.9192 (OUTLIER) cc_final: 0.8871 (tp) REVERT: O 1 MET cc_start: 0.7312 (tpp) cc_final: 0.7056 (tpt) REVERT: Q 41 ILE cc_start: 0.9237 (tp) cc_final: 0.8932 (tp) REVERT: T 25 LEU cc_start: 0.7359 (OUTLIER) cc_final: 0.6928 (pp) REVERT: T 92 TYR cc_start: 0.8696 (t80) cc_final: 0.8186 (t80) REVERT: T 239 GLU cc_start: 0.9234 (tp30) cc_final: 0.8831 (tp30) REVERT: T 255 PHE cc_start: 0.8940 (t80) cc_final: 0.8537 (t80) REVERT: T 280 GLU cc_start: 0.8816 (tm-30) cc_final: 0.8531 (tm-30) REVERT: Z 179 LYS cc_start: 0.7412 (tptp) cc_final: 0.6974 (ttpt) REVERT: Z 236 PHE cc_start: 0.8686 (t80) cc_final: 0.8222 (t80) REVERT: Z 239 GLU cc_start: 0.9129 (mm-30) cc_final: 0.8801 (mm-30) REVERT: Z 242 LYS cc_start: 0.8721 (mttt) cc_final: 0.8455 (mtmt) REVERT: Z 258 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7788 (tm-30) outliers start: 66 outliers final: 51 residues processed: 318 average time/residue: 0.2296 time to fit residues: 103.1507 Evaluate side-chains 325 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 271 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 49 MET Chi-restraints excluded: chain H residue 66 ILE Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain K residue 68 PHE Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 49 MET Chi-restraints excluded: chain M residue 41 ILE Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 66 ILE Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 18 ILE Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 59 LEU Chi-restraints excluded: chain N residue 68 PHE Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain O residue 56 THR Chi-restraints excluded: chain P residue 69 LEU Chi-restraints excluded: chain Q residue 44 ARG Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain T residue 25 LEU Chi-restraints excluded: chain T residue 32 VAL Chi-restraints excluded: chain T residue 37 GLU Chi-restraints excluded: chain T residue 65 LEU Chi-restraints excluded: chain T residue 89 GLU Chi-restraints excluded: chain T residue 110 VAL Chi-restraints excluded: chain T residue 136 HIS Chi-restraints excluded: chain T residue 200 ILE Chi-restraints excluded: chain T residue 206 GLU Chi-restraints excluded: chain T residue 208 TRP Chi-restraints excluded: chain T residue 258 GLU Chi-restraints excluded: chain T residue 260 LEU Chi-restraints excluded: chain T residue 286 ILE Chi-restraints excluded: chain T residue 289 LEU Chi-restraints excluded: chain V residue 11 PHE Chi-restraints excluded: chain V residue 16 ILE Chi-restraints excluded: chain X residue 25 LEU Chi-restraints excluded: chain X residue 37 LEU Chi-restraints excluded: chain Y residue 4 LEU Chi-restraints excluded: chain Y residue 6 ILE Chi-restraints excluded: chain Z residue 85 GLU Chi-restraints excluded: chain Z residue 136 HIS Chi-restraints excluded: chain Z residue 169 ILE Chi-restraints excluded: chain Z residue 171 ASP Chi-restraints excluded: chain Z residue 205 ILE Chi-restraints excluded: chain Z residue 258 GLU Chi-restraints excluded: chain Z residue 286 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 6 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 44 optimal weight: 0.5980 chunk 90 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.121635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.088248 restraints weight = 19131.294| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.55 r_work: 0.3162 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10905 Z= 0.173 Angle : 0.614 12.975 14827 Z= 0.314 Chirality : 0.042 0.189 1821 Planarity : 0.005 0.073 1852 Dihedral : 3.897 34.332 1490 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 5.44 % Allowed : 30.41 % Favored : 64.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.22), residues: 1388 helix: 1.63 (0.15), residues: 1133 sheet: None (None), residues: 0 loop : -0.89 (0.43), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP T 208 HIS 0.001 0.001 HIS Z 170 PHE 0.027 0.001 PHE T 24 TYR 0.017 0.002 TYR Q 48 ARG 0.008 0.000 ARG Z 78 Details of bonding type rmsd hydrogen bonds : bond 0.05389 ( 921) hydrogen bonds : angle 3.97637 ( 2724) SS BOND : bond 0.00683 ( 2) SS BOND : angle 1.52670 ( 4) covalent geometry : bond 0.00389 (10903) covalent geometry : angle 0.61352 (14823) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 273 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 57 GLU cc_start: 0.8629 (tp30) cc_final: 0.8405 (tp30) REVERT: M 40 GLU cc_start: 0.8050 (tm-30) cc_final: 0.7709 (tm-30) REVERT: M 41 ILE cc_start: 0.9188 (OUTLIER) cc_final: 0.8840 (tp) REVERT: O 1 MET cc_start: 0.7551 (tpp) cc_final: 0.7010 (mmm) REVERT: Q 41 ILE cc_start: 0.9262 (tp) cc_final: 0.8981 (tp) REVERT: T 25 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.7001 (pp) REVERT: T 92 TYR cc_start: 0.8699 (t80) cc_final: 0.8213 (t80) REVERT: T 239 GLU cc_start: 0.9246 (tp30) cc_final: 0.8835 (tp30) REVERT: T 255 PHE cc_start: 0.8977 (t80) cc_final: 0.8571 (t80) REVERT: T 280 GLU cc_start: 0.8826 (tm-30) cc_final: 0.8539 (tm-30) REVERT: Z 179 LYS cc_start: 0.7427 (tptp) cc_final: 0.6984 (ttpt) REVERT: Z 236 PHE cc_start: 0.8684 (t80) cc_final: 0.8217 (t80) REVERT: Z 239 GLU cc_start: 0.9166 (mm-30) cc_final: 0.8858 (mm-30) REVERT: Z 242 LYS cc_start: 0.8718 (mttt) cc_final: 0.8505 (mtmt) REVERT: Z 258 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7797 (tm-30) outliers start: 59 outliers final: 51 residues processed: 308 average time/residue: 0.2181 time to fit residues: 95.0194 Evaluate side-chains 317 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 263 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 49 MET Chi-restraints excluded: chain H residue 66 ILE Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain I residue 66 ILE Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain K residue 68 PHE Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 49 MET Chi-restraints excluded: chain M residue 41 ILE Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 66 ILE Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 18 ILE Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 59 LEU Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain O residue 56 THR Chi-restraints excluded: chain P residue 69 LEU Chi-restraints excluded: chain Q residue 44 ARG Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain T residue 25 LEU Chi-restraints excluded: chain T residue 32 VAL Chi-restraints excluded: chain T residue 65 LEU Chi-restraints excluded: chain T residue 89 GLU Chi-restraints excluded: chain T residue 110 VAL Chi-restraints excluded: chain T residue 136 HIS Chi-restraints excluded: chain T residue 172 THR Chi-restraints excluded: chain T residue 200 ILE Chi-restraints excluded: chain T residue 206 GLU Chi-restraints excluded: chain T residue 208 TRP Chi-restraints excluded: chain T residue 258 GLU Chi-restraints excluded: chain T residue 260 LEU Chi-restraints excluded: chain T residue 283 VAL Chi-restraints excluded: chain T residue 286 ILE Chi-restraints excluded: chain T residue 289 LEU Chi-restraints excluded: chain V residue 11 PHE Chi-restraints excluded: chain V residue 16 ILE Chi-restraints excluded: chain X residue 25 LEU Chi-restraints excluded: chain X residue 37 LEU Chi-restraints excluded: chain Y residue 4 LEU Chi-restraints excluded: chain Y residue 6 ILE Chi-restraints excluded: chain Z residue 15 LEU Chi-restraints excluded: chain Z residue 85 GLU Chi-restraints excluded: chain Z residue 169 ILE Chi-restraints excluded: chain Z residue 171 ASP Chi-restraints excluded: chain Z residue 205 ILE Chi-restraints excluded: chain Z residue 258 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 15 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 116 optimal weight: 0.3980 chunk 37 optimal weight: 0.8980 chunk 135 optimal weight: 0.5980 chunk 82 optimal weight: 20.0000 chunk 7 optimal weight: 0.0970 chunk 31 optimal weight: 0.7980 chunk 113 optimal weight: 0.0010 chunk 40 optimal weight: 0.5980 overall best weight: 0.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.123824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.091877 restraints weight = 18585.474| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.51 r_work: 0.3208 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 10905 Z= 0.145 Angle : 0.625 13.454 14827 Z= 0.317 Chirality : 0.042 0.193 1821 Planarity : 0.005 0.072 1852 Dihedral : 3.877 34.518 1490 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 4.06 % Allowed : 31.80 % Favored : 64.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.22), residues: 1388 helix: 1.71 (0.15), residues: 1132 sheet: None (None), residues: 0 loop : -0.96 (0.43), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP T 208 HIS 0.001 0.000 HIS Z 31 PHE 0.022 0.001 PHE X 11 TYR 0.012 0.002 TYR O 48 ARG 0.007 0.000 ARG Z 78 Details of bonding type rmsd hydrogen bonds : bond 0.05074 ( 921) hydrogen bonds : angle 3.91653 ( 2724) SS BOND : bond 0.00729 ( 2) SS BOND : angle 1.16634 ( 4) covalent geometry : bond 0.00309 (10903) covalent geometry : angle 0.62430 (14823) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 286 time to evaluate : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 1 MET cc_start: 0.6966 (mmt) cc_final: 0.6705 (mmt) REVERT: M 40 GLU cc_start: 0.8027 (tm-30) cc_final: 0.7709 (tm-30) REVERT: M 41 ILE cc_start: 0.9157 (OUTLIER) cc_final: 0.8815 (tp) REVERT: N 35 ILE cc_start: 0.9229 (mm) cc_final: 0.9013 (mm) REVERT: Q 41 ILE cc_start: 0.9195 (tp) cc_final: 0.8920 (tp) REVERT: T 25 LEU cc_start: 0.7268 (OUTLIER) cc_final: 0.6876 (pp) REVERT: T 92 TYR cc_start: 0.8664 (t80) cc_final: 0.8143 (t80) REVERT: T 239 GLU cc_start: 0.9226 (tp30) cc_final: 0.8833 (tp30) REVERT: T 255 PHE cc_start: 0.8925 (t80) cc_final: 0.8519 (t80) REVERT: T 280 GLU cc_start: 0.8820 (tm-30) cc_final: 0.8528 (tm-30) REVERT: V 23 PHE cc_start: 0.7035 (m-80) cc_final: 0.6590 (t80) REVERT: Z 179 LYS cc_start: 0.7442 (tptp) cc_final: 0.7008 (ttpt) REVERT: Z 236 PHE cc_start: 0.8691 (t80) cc_final: 0.8228 (t80) REVERT: Z 239 GLU cc_start: 0.9166 (mm-30) cc_final: 0.8870 (mm-30) REVERT: Z 258 GLU cc_start: 0.8212 (tm-30) cc_final: 0.7829 (tm-30) REVERT: Z 296 TYR cc_start: 0.8126 (t80) cc_final: 0.7349 (t80) outliers start: 44 outliers final: 38 residues processed: 311 average time/residue: 0.2201 time to fit residues: 96.4087 Evaluate side-chains 319 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 279 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 49 MET Chi-restraints excluded: chain H residue 66 ILE Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain I residue 66 ILE Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain K residue 68 PHE Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 49 MET Chi-restraints excluded: chain M residue 41 ILE Chi-restraints excluded: chain M residue 66 ILE Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 59 LEU Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain Q residue 44 ARG Chi-restraints excluded: chain T residue 25 LEU Chi-restraints excluded: chain T residue 32 VAL Chi-restraints excluded: chain T residue 65 LEU Chi-restraints excluded: chain T residue 89 GLU Chi-restraints excluded: chain T residue 110 VAL Chi-restraints excluded: chain T residue 172 THR Chi-restraints excluded: chain T residue 200 ILE Chi-restraints excluded: chain T residue 206 GLU Chi-restraints excluded: chain T residue 208 TRP Chi-restraints excluded: chain T residue 260 LEU Chi-restraints excluded: chain V residue 11 PHE Chi-restraints excluded: chain X residue 25 LEU Chi-restraints excluded: chain Y residue 4 LEU Chi-restraints excluded: chain Y residue 6 ILE Chi-restraints excluded: chain Z residue 15 LEU Chi-restraints excluded: chain Z residue 85 GLU Chi-restraints excluded: chain Z residue 169 ILE Chi-restraints excluded: chain Z residue 171 ASP Chi-restraints excluded: chain Z residue 205 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 131 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 69 optimal weight: 0.6980 chunk 94 optimal weight: 0.6980 chunk 101 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.123113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.089992 restraints weight = 18710.909| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.54 r_work: 0.3183 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10905 Z= 0.164 Angle : 0.641 16.898 14827 Z= 0.322 Chirality : 0.042 0.219 1821 Planarity : 0.005 0.073 1852 Dihedral : 3.869 33.628 1490 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.87 % Allowed : 32.72 % Favored : 63.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.22), residues: 1388 helix: 1.67 (0.15), residues: 1133 sheet: None (None), residues: 0 loop : -0.97 (0.43), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP T 208 HIS 0.001 0.001 HIS T 136 PHE 0.027 0.001 PHE T 24 TYR 0.017 0.002 TYR Q 48 ARG 0.008 0.000 ARG Z 78 Details of bonding type rmsd hydrogen bonds : bond 0.05218 ( 921) hydrogen bonds : angle 3.91797 ( 2724) SS BOND : bond 0.00625 ( 2) SS BOND : angle 1.20364 ( 4) covalent geometry : bond 0.00367 (10903) covalent geometry : angle 0.64044 (14823) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5047.10 seconds wall clock time: 88 minutes 16.09 seconds (5296.09 seconds total)