Starting phenix.real_space_refine on Wed Sep 17 18:56:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9itm_60871/09_2025/9itm_60871.cif Found real_map, /net/cci-nas-00/data/ceres_data/9itm_60871/09_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_60871/09_2025/9itm_60871.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9itm_60871/09_2025/9itm_60871.map" model { file = "/net/cci-nas-00/data/ceres_data/9itm_60871/09_2025/9itm_60871.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9itm_60871/09_2025/9itm_60871.cif" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.78, per 1000 atoms: 0.26 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: 1.14 Conformation dependent library (CDL) restraints added in 429.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2776 Ramachandran restraints generated. 1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 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: 0.31 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: 1.87 Time building geometry restraints manager: 1.46 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: 5.380 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.960 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.230 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (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 ARG 0.002 0.000 ARG M 44 TYR 0.011 0.001 TYR Z 296 PHE 0.008 0.001 PHE T 276 TRP 0.029 0.002 TRP T 208 HIS 0.001 0.000 HIS Z 31 Details of bonding type rmsd covalent geometry : bond 0.00395 (10903) covalent geometry : angle 0.59260 (14823) SS BOND : bond 0.74898 ( 2) SS BOND : angle 15.64313 ( 4) hydrogen bonds : bond 0.15155 ( 921) hydrogen bonds : angle 6.69737 ( 2724) *********************** 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 : 0.409 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: 0.1108 time to fit residues: 49.8459 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 : 0.412 ------------------------------------------------------------------------------- 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 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.3829 r_free = 0.3829 target = 0.120737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.086960 restraints weight = 18916.804| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.52 r_work: 0.3244 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1352 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= 0.194 Angle : 0.590 9.081 14827 Z= 0.317 Chirality : 0.042 0.166 1821 Planarity : 0.006 0.073 1852 Dihedral : 3.910 29.571 1491 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.24 % Allowed : 29.22 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.22), residues: 1388 helix: 1.38 (0.15), residues: 1122 sheet: None (None), residues: 0 loop : -1.01 (0.40), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG T 22 TYR 0.015 0.002 TYR V 30 PHE 0.023 0.001 PHE T 230 TRP 0.019 0.002 TRP T 208 HIS 0.002 0.001 HIS T 136 Details of bonding type rmsd covalent geometry : bond 0.00429 (10903) covalent geometry : angle 0.58957 (14823) SS BOND : bond 0.02404 ( 2) SS BOND : angle 1.13754 ( 4) hydrogen bonds : bond 0.06357 ( 921) hydrogen bonds : angle 4.51575 ( 2724) *********************** 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: 46 poor density : 283 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 57 GLU cc_start: 0.8749 (tp30) cc_final: 0.8539 (tp30) REVERT: K 70 ILE cc_start: 0.9418 (mm) cc_final: 0.9188 (mt) REVERT: M 41 ILE cc_start: 0.9209 (tp) cc_final: 0.8957 (tp) REVERT: O 1 MET cc_start: 0.7582 (tpp) cc_final: 0.7311 (tpp) REVERT: O 38 ASN cc_start: 0.8275 (t0) cc_final: 0.7606 (t0) REVERT: O 41 ILE cc_start: 0.9137 (tp) cc_final: 0.8685 (tp) REVERT: P 41 ILE cc_start: 0.9084 (tp) cc_final: 0.8818 (tp) REVERT: Q 41 ILE cc_start: 0.9333 (tp) cc_final: 0.9060 (tp) REVERT: T 25 LEU cc_start: 0.7535 (OUTLIER) cc_final: 0.7210 (pp) REVERT: T 255 PHE cc_start: 0.8978 (t80) cc_final: 0.8546 (t80) REVERT: U 31 ARG cc_start: 0.8637 (tpp-160) cc_final: 0.8386 (tpp80) REVERT: V 24 ILE cc_start: 0.8617 (tt) cc_final: 0.8304 (mm) REVERT: Z 26 TYR cc_start: 0.7789 (t80) cc_final: 0.7440 (t80) REVERT: Z 179 LYS cc_start: 0.7404 (tptp) cc_final: 0.7095 (ttpt) REVERT: Z 236 PHE cc_start: 0.8791 (t80) cc_final: 0.8274 (t80) REVERT: Z 258 GLU cc_start: 0.8285 (tm-30) cc_final: 0.7943 (tm-30) outliers start: 46 outliers final: 26 residues processed: 307 average time/residue: 0.1162 time to fit residues: 50.1788 Evaluate side-chains 295 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 268 time to evaluate : 0.256 ------------------------------------------------------------------------------- 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 J residue 46 VAL 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 N residue 59 LEU 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 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 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 11 optimal weight: 0.5980 chunk 111 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 118 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 5 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 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 = 0.3815 r_free = 0.3815 target = 0.121264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.087659 restraints weight = 18842.246| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.53 r_work: 0.3148 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10905 Z= 0.169 Angle : 0.574 10.188 14827 Z= 0.301 Chirality : 0.041 0.162 1821 Planarity : 0.005 0.073 1852 Dihedral : 3.843 30.996 1490 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 4.79 % Allowed : 28.85 % Favored : 66.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.52 (0.22), residues: 1388 helix: 1.51 (0.15), residues: 1132 sheet: None (None), residues: 0 loop : -1.13 (0.42), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 44 TYR 0.014 0.002 TYR Q 48 PHE 0.024 0.001 PHE T 24 TRP 0.020 0.002 TRP T 208 HIS 0.001 0.001 HIS Z 31 Details of bonding type rmsd covalent geometry : bond 0.00365 (10903) covalent geometry : angle 0.57355 (14823) SS BOND : bond 0.00412 ( 2) SS BOND : angle 1.39341 ( 4) hydrogen bonds : bond 0.05870 ( 921) hydrogen bonds : angle 4.25595 ( 2724) *********************** 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 343 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 291 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 70 ILE cc_start: 0.9339 (mm) cc_final: 0.9136 (mt) REVERT: M 41 ILE cc_start: 0.9173 (OUTLIER) cc_final: 0.8897 (tp) REVERT: O 1 MET cc_start: 0.7591 (tpp) cc_final: 0.7237 (tpp) REVERT: O 38 ASN cc_start: 0.8208 (t0) cc_final: 0.7955 (t0) REVERT: O 41 ILE cc_start: 0.9118 (tp) cc_final: 0.8840 (tp) REVERT: P 41 ILE cc_start: 0.9000 (tp) cc_final: 0.8749 (tp) REVERT: P 48 TYR cc_start: 0.9117 (m-80) cc_final: 0.8890 (m-80) REVERT: Q 41 ILE cc_start: 0.9288 (tp) cc_final: 0.8976 (tp) REVERT: T 25 LEU cc_start: 0.7505 (OUTLIER) cc_final: 0.7167 (pp) REVERT: T 180 LEU cc_start: 0.8493 (tt) cc_final: 0.8079 (mp) REVERT: T 255 PHE cc_start: 0.8963 (t80) cc_final: 0.8570 (t80) REVERT: U 31 ARG cc_start: 0.8619 (tpp-160) cc_final: 0.8373 (tpp80) REVERT: V 24 ILE cc_start: 0.8592 (tt) cc_final: 0.8276 (mm) REVERT: Z 26 TYR cc_start: 0.7772 (t80) cc_final: 0.7396 (t80) REVERT: Z 85 GLU cc_start: 0.8870 (tt0) cc_final: 0.8533 (tt0) REVERT: Z 179 LYS cc_start: 0.7410 (tptp) cc_final: 0.7156 (ttpt) REVERT: Z 236 PHE cc_start: 0.8793 (t80) cc_final: 0.8311 (t80) REVERT: Z 258 GLU cc_start: 0.8244 (tm-30) cc_final: 0.7890 (tm-30) outliers start: 52 outliers final: 40 residues processed: 317 average time/residue: 0.1171 time to fit residues: 52.0301 Evaluate side-chains 317 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 275 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 J residue 41 ILE 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 M residue 41 ILE Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 61 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 O residue 32 VAL Chi-restraints excluded: chain P residue 49 MET 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 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 52 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 116 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 112 optimal weight: 10.0000 chunk 81 optimal weight: 9.9990 chunk 12 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 70 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3813 r_free = 0.3813 target = 0.121048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.087540 restraints weight = 19039.402| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.52 r_work: 0.3141 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 10905 Z= 0.173 Angle : 0.576 10.728 14827 Z= 0.301 Chirality : 0.041 0.164 1821 Planarity : 0.005 0.073 1852 Dihedral : 3.847 32.141 1490 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 5.81 % Allowed : 28.29 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.57 (0.22), residues: 1388 helix: 1.52 (0.15), residues: 1123 sheet: None (None), residues: 0 loop : -0.90 (0.41), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Z 78 TYR 0.013 0.002 TYR N 48 PHE 0.027 0.001 PHE T 230 TRP 0.022 0.002 TRP T 208 HIS 0.001 0.001 HIS Z 170 Details of bonding type rmsd covalent geometry : bond 0.00387 (10903) covalent geometry : angle 0.57578 (14823) SS BOND : bond 0.00256 ( 2) SS BOND : angle 1.23868 ( 4) hydrogen bonds : bond 0.05687 ( 921) hydrogen bonds : angle 4.15690 ( 2724) *********************** 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 348 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 285 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 2 GLU cc_start: 0.8252 (pm20) cc_final: 0.8010 (pm20) REVERT: J 44 ARG cc_start: 0.7127 (OUTLIER) cc_final: 0.6589 (tpt170) REVERT: M 41 ILE cc_start: 0.9215 (OUTLIER) cc_final: 0.8941 (tp) REVERT: O 1 MET cc_start: 0.7508 (tpp) cc_final: 0.7207 (tpp) REVERT: O 41 ILE cc_start: 0.9158 (tp) cc_final: 0.8880 (tp) REVERT: P 41 ILE cc_start: 0.9027 (tp) cc_final: 0.8813 (tp) REVERT: P 57 GLU cc_start: 0.8977 (mm-30) cc_final: 0.8716 (mm-30) REVERT: Q 41 ILE cc_start: 0.9297 (tp) cc_final: 0.8984 (tp) REVERT: T 25 LEU cc_start: 0.7490 (OUTLIER) cc_final: 0.7077 (pp) REVERT: T 239 GLU cc_start: 0.9240 (tp30) cc_final: 0.8861 (tp30) REVERT: T 255 PHE cc_start: 0.8984 (t80) cc_final: 0.8596 (t80) REVERT: U 31 ARG cc_start: 0.8615 (tpp-160) cc_final: 0.8373 (tpp80) REVERT: Z 26 TYR cc_start: 0.7723 (t80) cc_final: 0.7307 (t80) REVERT: Z 85 GLU cc_start: 0.8887 (OUTLIER) cc_final: 0.8532 (tt0) REVERT: Z 179 LYS cc_start: 0.7447 (tptp) cc_final: 0.7106 (ttpt) REVERT: Z 236 PHE cc_start: 0.8788 (t80) cc_final: 0.8306 (t80) REVERT: Z 258 GLU cc_start: 0.8280 (tm-30) cc_final: 0.7906 (tm-30) outliers start: 63 outliers final: 44 residues processed: 317 average time/residue: 0.1133 time to fit residues: 50.5876 Evaluate side-chains 309 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 261 time to evaluate : 0.395 ------------------------------------------------------------------------------- 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 44 ARG 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 32 VAL Chi-restraints excluded: chain O residue 32 VAL 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 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 283 VAL 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 68 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 102 optimal weight: 0.4980 chunk 88 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 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 = 0.3817 r_free = 0.3817 target = 0.121465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.087771 restraints weight = 18767.844| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.51 r_work: 0.3151 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 10905 Z= 0.163 Angle : 0.581 13.037 14827 Z= 0.300 Chirality : 0.041 0.163 1821 Planarity : 0.005 0.073 1852 Dihedral : 3.843 32.731 1490 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 6.08 % Allowed : 28.76 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.59 (0.22), residues: 1388 helix: 1.54 (0.15), residues: 1133 sheet: None (None), residues: 0 loop : -1.05 (0.42), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 44 TYR 0.014 0.002 TYR Q 48 PHE 0.025 0.001 PHE T 230 TRP 0.022 0.002 TRP T 208 HIS 0.001 0.000 HIS T 136 Details of bonding type rmsd covalent geometry : bond 0.00362 (10903) covalent geometry : angle 0.58070 (14823) SS BOND : bond 0.00269 ( 2) SS BOND : angle 1.17909 ( 4) hydrogen bonds : bond 0.05552 ( 921) hydrogen bonds : angle 4.09428 ( 2724) *********************** 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 341 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 275 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 1 MET cc_start: 0.7782 (OUTLIER) cc_final: 0.6567 (mpt) REVERT: J 2 GLU cc_start: 0.8444 (mp0) cc_final: 0.7913 (pm20) REVERT: J 44 ARG cc_start: 0.6998 (OUTLIER) cc_final: 0.6566 (tpt170) REVERT: K 1 MET cc_start: 0.7583 (tpp) cc_final: 0.7243 (mmt) REVERT: K 42 GLU cc_start: 0.8205 (tt0) cc_final: 0.7920 (tt0) REVERT: K 66 ILE cc_start: 0.9236 (tt) cc_final: 0.9019 (tt) REVERT: M 41 ILE cc_start: 0.9210 (OUTLIER) cc_final: 0.8924 (tp) REVERT: O 1 MET cc_start: 0.7511 (tpp) cc_final: 0.7116 (tpp) REVERT: Q 41 ILE cc_start: 0.9273 (tp) cc_final: 0.8968 (tp) REVERT: T 25 LEU cc_start: 0.7489 (OUTLIER) cc_final: 0.7049 (pp) REVERT: T 92 TYR cc_start: 0.8680 (t80) cc_final: 0.8196 (t80) REVERT: T 239 GLU cc_start: 0.9240 (tp30) cc_final: 0.8840 (tp30) REVERT: T 255 PHE cc_start: 0.8978 (t80) cc_final: 0.8589 (t80) REVERT: Z 179 LYS cc_start: 0.7366 (tptp) cc_final: 0.7036 (ttpt) REVERT: Z 236 PHE cc_start: 0.8802 (t80) cc_final: 0.8322 (t80) REVERT: Z 258 GLU cc_start: 0.8272 (tm-30) cc_final: 0.7886 (tm-30) outliers start: 66 outliers final: 50 residues processed: 313 average time/residue: 0.1055 time to fit residues: 46.6412 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 : 0.383 ------------------------------------------------------------------------------- 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 1 MET 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 44 ARG 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 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 32 VAL Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain O residue 56 THR 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 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 Y residue 25 LEU Chi-restraints excluded: chain Z residue 15 LEU Chi-restraints excluded: chain Z residue 19 ILE Chi-restraints excluded: chain Z residue 40 PHE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 56 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 43 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 49 optimal weight: 0.4980 chunk 107 optimal weight: 0.9980 chunk 96 optimal weight: 6.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3833 r_free = 0.3833 target = 0.122510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.088731 restraints weight = 18964.182| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.54 r_work: 0.3166 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2044 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= 0.152 Angle : 0.580 10.760 14827 Z= 0.299 Chirality : 0.041 0.175 1821 Planarity : 0.005 0.073 1852 Dihedral : 3.861 33.723 1490 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 5.81 % Allowed : 29.77 % Favored : 64.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.70 (0.22), residues: 1388 helix: 1.62 (0.15), residues: 1133 sheet: None (None), residues: 0 loop : -1.03 (0.42), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 44 TYR 0.013 0.002 TYR Z 207 PHE 0.025 0.001 PHE T 230 TRP 0.023 0.002 TRP T 208 HIS 0.001 0.000 HIS T 136 Details of bonding type rmsd covalent geometry : bond 0.00325 (10903) covalent geometry : angle 0.57987 (14823) SS BOND : bond 0.00322 ( 2) SS BOND : angle 1.06117 ( 4) hydrogen bonds : bond 0.05370 ( 921) hydrogen bonds : angle 4.01150 ( 2724) *********************** 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 350 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 287 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 1 MET cc_start: 0.7762 (OUTLIER) cc_final: 0.6717 (mpt) REVERT: K 1 MET cc_start: 0.7798 (tpp) cc_final: 0.7501 (mmt) REVERT: M 41 ILE cc_start: 0.9215 (OUTLIER) cc_final: 0.8894 (tp) REVERT: M 61 ILE cc_start: 0.8790 (OUTLIER) cc_final: 0.8584 (mm) REVERT: N 35 ILE cc_start: 0.9249 (mm) cc_final: 0.9014 (mm) REVERT: O 1 MET cc_start: 0.7541 (tpp) cc_final: 0.6968 (tpp) REVERT: P 57 GLU cc_start: 0.8986 (mm-30) cc_final: 0.8758 (mm-30) REVERT: Q 41 ILE cc_start: 0.9259 (tp) cc_final: 0.8954 (tp) REVERT: T 25 LEU cc_start: 0.7418 (OUTLIER) cc_final: 0.6997 (pp) REVERT: T 92 TYR cc_start: 0.8692 (t80) cc_final: 0.8195 (t80) REVERT: T 239 GLU cc_start: 0.9238 (tp30) cc_final: 0.8841 (tp30) REVERT: T 255 PHE cc_start: 0.8963 (t80) cc_final: 0.8521 (t80) REVERT: Z 179 LYS cc_start: 0.7370 (tptp) cc_final: 0.7058 (ttpt) REVERT: Z 236 PHE cc_start: 0.8752 (t80) cc_final: 0.8261 (t80) REVERT: Z 258 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7845 (tm-30) outliers start: 63 outliers final: 47 residues processed: 322 average time/residue: 0.1012 time to fit residues: 46.8484 Evaluate side-chains 317 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 265 time to evaluate : 0.398 ------------------------------------------------------------------------------- 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 1 MET 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 49 MET 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 61 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 O residue 32 VAL Chi-restraints excluded: chain O residue 56 THR 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 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 T residue 283 VAL Chi-restraints excluded: chain T residue 286 ILE Chi-restraints excluded: chain T residue 289 LEU Chi-restraints excluded: chain T residue 290 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 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 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 78 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 115 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 59 optimal weight: 0.1980 chunk 120 optimal weight: 2.9990 chunk 85 optimal weight: 0.0870 chunk 123 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 overall best weight: 0.4958 ------------------------------------------------------------------------------- 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 = 0.3839 r_free = 0.3839 target = 0.122866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.089551 restraints weight = 18802.855| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.52 r_work: 0.3180 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10905 Z= 0.148 Angle : 0.601 12.133 14827 Z= 0.306 Chirality : 0.041 0.183 1821 Planarity : 0.005 0.072 1852 Dihedral : 3.882 33.743 1490 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 5.81 % Allowed : 30.51 % Favored : 63.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.76 (0.22), residues: 1388 helix: 1.66 (0.15), residues: 1133 sheet: None (None), residues: 0 loop : -1.00 (0.42), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG Z 78 TYR 0.017 0.002 TYR Q 48 PHE 0.028 0.001 PHE T 24 TRP 0.023 0.002 TRP T 208 HIS 0.002 0.001 HIS T 136 Details of bonding type rmsd covalent geometry : bond 0.00315 (10903) covalent geometry : angle 0.59936 (14823) SS BOND : bond 0.01355 ( 2) SS BOND : angle 2.97912 ( 4) hydrogen bonds : bond 0.05260 ( 921) hydrogen bonds : angle 3.96741 ( 2724) *********************** 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 349 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 286 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 1 MET cc_start: 0.7782 (OUTLIER) cc_final: 0.6675 (mpt) REVERT: K 1 MET cc_start: 0.7853 (tpp) cc_final: 0.7558 (tpp) REVERT: K 66 ILE cc_start: 0.9218 (tt) cc_final: 0.9007 (tt) REVERT: M 40 GLU cc_start: 0.8015 (tm-30) cc_final: 0.7706 (tm-30) REVERT: M 41 ILE cc_start: 0.9203 (OUTLIER) cc_final: 0.8846 (tp) REVERT: P 57 GLU cc_start: 0.8935 (mm-30) cc_final: 0.8642 (mm-30) REVERT: Q 41 ILE cc_start: 0.9240 (tp) cc_final: 0.8941 (tp) REVERT: T 25 LEU cc_start: 0.7357 (OUTLIER) cc_final: 0.6951 (pp) REVERT: T 92 TYR cc_start: 0.8692 (t80) cc_final: 0.8176 (t80) REVERT: T 239 GLU cc_start: 0.9231 (tp30) cc_final: 0.8836 (tp30) REVERT: T 255 PHE cc_start: 0.8948 (t80) cc_final: 0.8493 (t80) REVERT: Z 179 LYS cc_start: 0.7382 (tptp) cc_final: 0.7051 (ttpt) REVERT: Z 236 PHE cc_start: 0.8737 (t80) cc_final: 0.8269 (t80) REVERT: Z 239 GLU cc_start: 0.9142 (mm-30) cc_final: 0.8837 (mm-30) REVERT: Z 242 LYS cc_start: 0.8767 (mttt) cc_final: 0.8513 (mtmt) REVERT: Z 258 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7806 (tm-30) outliers start: 63 outliers final: 51 residues processed: 321 average time/residue: 0.1064 time to fit residues: 48.7440 Evaluate side-chains 328 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 273 time to evaluate : 0.457 ------------------------------------------------------------------------------- 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 1 MET 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 49 MET Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain K residue 13 VAL 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 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 283 VAL 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 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 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 15 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 111 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 129 optimal weight: 6.9990 chunk 47 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3831 r_free = 0.3831 target = 0.122258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.088885 restraints weight = 18789.890| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.52 r_work: 0.3168 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 10905 Z= 0.161 Angle : 0.610 12.004 14827 Z= 0.312 Chirality : 0.042 0.167 1821 Planarity : 0.005 0.072 1852 Dihedral : 3.889 34.089 1490 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 5.81 % Allowed : 30.51 % Favored : 63.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.78 (0.22), residues: 1388 helix: 1.67 (0.15), residues: 1132 sheet: None (None), residues: 0 loop : -0.92 (0.43), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Z 78 TYR 0.012 0.002 TYR Z 296 PHE 0.024 0.001 PHE X 11 TRP 0.024 0.002 TRP T 208 HIS 0.001 0.001 HIS T 136 Details of bonding type rmsd covalent geometry : bond 0.00356 (10903) covalent geometry : angle 0.60923 (14823) SS BOND : bond 0.00838 ( 2) SS BOND : angle 2.38500 ( 4) hydrogen bonds : bond 0.05297 ( 921) hydrogen bonds : angle 3.97652 ( 2724) *********************** 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 343 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 280 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 1 MET cc_start: 0.7734 (OUTLIER) cc_final: 0.6640 (mpt) REVERT: K 1 MET cc_start: 0.7875 (tpp) cc_final: 0.7081 (mmt) REVERT: K 66 ILE cc_start: 0.9218 (tt) cc_final: 0.9013 (tt) REVERT: M 40 GLU cc_start: 0.8009 (tm-30) cc_final: 0.7703 (tm-30) REVERT: M 41 ILE cc_start: 0.9213 (OUTLIER) cc_final: 0.8881 (tp) REVERT: O 1 MET cc_start: 0.7405 (tpp) cc_final: 0.6601 (tmm) REVERT: Q 41 ILE cc_start: 0.9237 (tp) cc_final: 0.8961 (tp) REVERT: T 25 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.6949 (pp) REVERT: T 92 TYR cc_start: 0.8693 (t80) cc_final: 0.8208 (t80) REVERT: T 239 GLU cc_start: 0.9225 (tp30) cc_final: 0.8808 (tp30) REVERT: T 255 PHE cc_start: 0.8960 (t80) cc_final: 0.8502 (t80) REVERT: Z 179 LYS cc_start: 0.7444 (tptp) cc_final: 0.7033 (ttpt) REVERT: Z 236 PHE cc_start: 0.8724 (t80) cc_final: 0.8247 (t80) REVERT: Z 239 GLU cc_start: 0.9120 (mm-30) cc_final: 0.8786 (mm-30) REVERT: Z 242 LYS cc_start: 0.8716 (mttt) cc_final: 0.8453 (mtmt) REVERT: Z 258 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7766 (tm-30) outliers start: 63 outliers final: 53 residues processed: 315 average time/residue: 0.1084 time to fit residues: 48.5691 Evaluate side-chains 328 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 271 time to evaluate : 0.402 ------------------------------------------------------------------------------- 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 1 MET 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 49 MET 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 61 ILE Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain O residue 56 THR 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 37 GLU 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 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 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 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 107 optimal weight: 0.0870 chunk 112 optimal weight: 9.9990 chunk 121 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 83 optimal weight: 4.9990 chunk 108 optimal weight: 0.0040 chunk 46 optimal weight: 0.6980 chunk 87 optimal weight: 0.8980 chunk 86 optimal weight: 0.6980 chunk 61 optimal weight: 0.5980 overall best weight: 0.4170 ------------------------------------------------------------------------------- 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 = 0.3850 r_free = 0.3850 target = 0.123774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.090520 restraints weight = 18678.435| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.52 r_work: 0.3196 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 10905 Z= 0.147 Angle : 0.616 12.855 14827 Z= 0.312 Chirality : 0.041 0.169 1821 Planarity : 0.005 0.072 1852 Dihedral : 3.876 34.333 1490 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 5.35 % Allowed : 30.41 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.81 (0.22), residues: 1388 helix: 1.69 (0.15), residues: 1131 sheet: None (None), residues: 0 loop : -0.93 (0.43), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Z 78 TYR 0.015 0.002 TYR Q 48 PHE 0.030 0.001 PHE T 24 TRP 0.023 0.002 TRP T 208 HIS 0.001 0.000 HIS Z 170 Details of bonding type rmsd covalent geometry : bond 0.00316 (10903) covalent geometry : angle 0.61504 (14823) SS BOND : bond 0.00821 ( 2) SS BOND : angle 1.78190 ( 4) hydrogen bonds : bond 0.05126 ( 921) hydrogen bonds : angle 3.93338 ( 2724) *********************** 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 342 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 284 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 1 MET cc_start: 0.7643 (OUTLIER) cc_final: 0.6464 (mpt) REVERT: J 2 GLU cc_start: 0.8373 (mp0) cc_final: 0.8062 (pm20) REVERT: K 1 MET cc_start: 0.7862 (tpp) cc_final: 0.7197 (mmt) REVERT: M 40 GLU cc_start: 0.8042 (tm-30) cc_final: 0.7733 (tm-30) REVERT: M 41 ILE cc_start: 0.9184 (OUTLIER) cc_final: 0.8858 (tp) REVERT: Q 41 ILE cc_start: 0.9217 (tp) cc_final: 0.8934 (tp) REVERT: T 92 TYR cc_start: 0.8692 (t80) cc_final: 0.8155 (t80) REVERT: T 239 GLU cc_start: 0.9221 (tp30) cc_final: 0.8837 (tp30) REVERT: T 255 PHE cc_start: 0.8950 (t80) cc_final: 0.8485 (t80) REVERT: T 280 GLU cc_start: 0.8713 (tm-30) cc_final: 0.8423 (tm-30) REVERT: U 31 ARG cc_start: 0.8590 (tpp-160) cc_final: 0.8388 (tpp80) REVERT: Z 179 LYS cc_start: 0.7429 (tptp) cc_final: 0.6970 (ttpt) REVERT: Z 236 PHE cc_start: 0.8683 (t80) cc_final: 0.8225 (t80) REVERT: Z 239 GLU cc_start: 0.9141 (mm-30) cc_final: 0.8825 (mm-30) REVERT: Z 242 LYS cc_start: 0.8673 (mttt) cc_final: 0.8460 (mtmt) REVERT: Z 258 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7785 (tm-30) REVERT: Z 296 TYR cc_start: 0.8177 (t80) cc_final: 0.7373 (t80) outliers start: 58 outliers final: 47 residues processed: 314 average time/residue: 0.1086 time to fit residues: 48.5112 Evaluate side-chains 323 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 273 time to evaluate : 0.401 ------------------------------------------------------------------------------- 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 1 MET Chi-restraints excluded: chain I residue 18 ILE 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 49 MET 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 61 ILE 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 Q residue 44 ARG Chi-restraints excluded: chain Q residue 45 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 283 VAL 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 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 26 optimal weight: 0.0870 chunk 133 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 14 optimal weight: 0.1980 chunk 67 optimal weight: 0.0770 chunk 10 optimal weight: 0.4980 chunk 72 optimal weight: 0.0470 chunk 120 optimal weight: 0.1980 chunk 25 optimal weight: 0.8980 chunk 106 optimal weight: 0.8980 overall best weight: 0.1214 ------------------------------------------------------------------------------- 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 = 0.3890 r_free = 0.3890 target = 0.126711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.093844 restraints weight = 18743.919| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.54 r_work: 0.3249 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10905 Z= 0.136 Angle : 0.617 13.762 14827 Z= 0.311 Chirality : 0.042 0.187 1821 Planarity : 0.005 0.071 1852 Dihedral : 3.831 33.533 1490 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.78 % Allowed : 32.44 % Favored : 63.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.86 (0.23), residues: 1388 helix: 1.73 (0.15), residues: 1132 sheet: None (None), residues: 0 loop : -0.95 (0.43), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Z 78 TYR 0.012 0.002 TYR Q 48 PHE 0.022 0.001 PHE X 11 TRP 0.022 0.002 TRP T 208 HIS 0.001 0.000 HIS Z 31 Details of bonding type rmsd covalent geometry : bond 0.00276 (10903) covalent geometry : angle 0.61620 (14823) SS BOND : bond 0.00743 ( 2) SS BOND : angle 1.61987 ( 4) hydrogen bonds : bond 0.04795 ( 921) hydrogen bonds : angle 3.84350 ( 2724) ********************** 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 342 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 301 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 1 MET cc_start: 0.7645 (OUTLIER) cc_final: 0.6458 (mpt) REVERT: J 2 GLU cc_start: 0.8314 (mp0) cc_final: 0.8006 (pm20) REVERT: M 41 ILE cc_start: 0.9137 (OUTLIER) cc_final: 0.8909 (tp) REVERT: Q 41 ILE cc_start: 0.9124 (tp) cc_final: 0.8875 (tp) REVERT: T 92 TYR cc_start: 0.8682 (t80) cc_final: 0.8117 (t80) REVERT: T 136 HIS cc_start: 0.5620 (OUTLIER) cc_final: 0.5397 (m-70) REVERT: T 239 GLU cc_start: 0.9207 (tp30) cc_final: 0.8866 (tp30) REVERT: T 255 PHE cc_start: 0.8892 (t80) cc_final: 0.8420 (t80) REVERT: T 280 GLU cc_start: 0.8696 (tm-30) cc_final: 0.8380 (tm-30) REVERT: Z 26 TYR cc_start: 0.7403 (t80) cc_final: 0.7004 (t80) REVERT: Z 179 LYS cc_start: 0.7455 (tptp) cc_final: 0.7002 (ttpt) REVERT: Z 236 PHE cc_start: 0.8685 (t80) cc_final: 0.8227 (t80) REVERT: Z 239 GLU cc_start: 0.9166 (mm-30) cc_final: 0.8874 (mm-30) REVERT: Z 258 GLU cc_start: 0.8304 (tm-30) cc_final: 0.7925 (tm-30) REVERT: Z 296 TYR cc_start: 0.8100 (t80) cc_final: 0.7382 (t80) outliers start: 41 outliers final: 32 residues processed: 320 average time/residue: 0.1074 time to fit residues: 49.1568 Evaluate side-chains 319 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 284 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain I residue 1 MET 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 49 MET 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 18 ILE Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 68 PHE Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain Q residue 44 ARG 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 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 260 LEU Chi-restraints excluded: chain T residue 289 LEU Chi-restraints excluded: chain V residue 11 PHE 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 85 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 82 optimal weight: 5.9990 chunk 44 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 128 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- 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 = 0.121798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.088321 restraints weight = 19061.735| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.58 r_work: 0.3156 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 10905 Z= 0.199 Angle : 0.660 13.359 14827 Z= 0.333 Chirality : 0.044 0.189 1821 Planarity : 0.005 0.072 1852 Dihedral : 3.854 32.152 1490 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 4.15 % Allowed : 32.44 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.81 (0.22), residues: 1388 helix: 1.66 (0.15), residues: 1121 sheet: None (None), residues: 0 loop : -0.66 (0.42), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Z 249 TYR 0.020 0.002 TYR Q 48 PHE 0.027 0.001 PHE T 24 TRP 0.024 0.002 TRP T 208 HIS 0.001 0.001 HIS Z 170 Details of bonding type rmsd covalent geometry : bond 0.00467 (10903) covalent geometry : angle 0.65977 (14823) SS BOND : bond 0.00662 ( 2) SS BOND : angle 1.44558 ( 4) hydrogen bonds : bond 0.05380 ( 921) hydrogen bonds : angle 3.94623 ( 2724) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2660.01 seconds wall clock time: 46 minutes 24.63 seconds (2784.63 seconds total)