Starting phenix.real_space_refine on Sat Aug 23 05:06:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ito_60873/08_2025/9ito_60873.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ito_60873/08_2025/9ito_60873.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ito_60873/08_2025/9ito_60873.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ito_60873/08_2025/9ito_60873.map" model { file = "/net/cci-nas-00/data/ceres_data/9ito_60873/08_2025/9ito_60873.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ito_60873/08_2025/9ito_60873.cif" } resolution = 3.3 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 32 5.16 5 C 6648 2.51 5 N 1605 2.21 5 O 1702 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9987 Number of models: 1 Model: "" Number of chains: 16 Chain: "H" 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: "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: "Z" Number of atoms: 2028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2028 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 14, 'TRANS': 245} Chain breaks: 1 Chain: "Y" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 423 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "V" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "X" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 179 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 2, 'TRANS': 33} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 162 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'ASN:plan1': 4, 'PHE:plan': 3, 'GLN:plan1': 1, 'ARG:plan': 3, 'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 60 Chain: "U" Number of atoms: 190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 190 Classifications: {'peptide': 38} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 1, 'TRANS': 36} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 180 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'PHE:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 3, 'ARG:plan': 5, 'TYR:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 71 Chain: "T" Number of atoms: 1630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1630 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 10, 'TRANS': 214} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 148 Unresolved non-hydrogen angles: 190 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'ARG:plan': 3, 'ASN:plan1': 4, 'GLN:plan1': 2, 'TRP:plan': 1, 'PHE:plan': 5} Unresolved non-hydrogen planarities: 74 Time building chain proxies: 2.76, per 1000 atoms: 0.28 Number of scatterers: 9987 At special positions: 0 Unit cell: (106.95, 106.95, 93, 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 32 16.00 O 1702 8.00 N 1605 7.00 C 6648 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS Z 135 " - pdb=" SG CYS Z 173 " distance=2.69 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: 0.83 Conformation dependent library (CDL) restraints added in 334.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2440 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 1 sheets defined 85.1% alpha, 0.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'H' and resid 3 through 38 removed outlier: 3.539A pdb=" N VAL H 7 " --> pdb=" O GLY H 3 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLY H 19 " --> pdb=" O LEU H 15 " (cutoff:3.500A) Proline residue: H 20 - end of helix Processing helix chain 'H' and resid 41 through 72 removed outlier: 4.444A pdb=" N THR H 47 " --> pdb=" O ASN H 43 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N PHE H 55 " --> pdb=" O ILE H 51 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU H 59 " --> pdb=" O PHE H 55 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA H 60 " --> pdb=" O THR H 56 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE H 62 " --> pdb=" O ALA H 58 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 17 removed outlier: 3.529A pdb=" N VAL I 13 " --> pdb=" O THR I 9 " (cutoff:3.500A) Processing helix chain 'I' and resid 18 through 38 removed outlier: 3.535A pdb=" N VAL I 22 " --> pdb=" O ILE I 18 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY I 25 " --> pdb=" O GLY I 21 " (cutoff:3.500A) Processing helix chain 'I' and resid 41 through 72 removed outlier: 4.562A pdb=" N TYR I 48 " --> pdb=" O ARG I 44 " (cutoff:3.500A) Processing helix chain 'J' and resid 3 through 38 removed outlier: 4.192A pdb=" N GLY J 19 " --> pdb=" O LEU J 15 " (cutoff:3.500A) Proline residue: J 20 - end of helix Processing helix chain 'J' and resid 41 through 71 removed outlier: 3.900A pdb=" N TYR J 48 " --> pdb=" O ARG J 44 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE J 51 " --> pdb=" O THR J 47 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N PHE J 55 " --> pdb=" O ILE J 51 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU J 59 " --> pdb=" O PHE J 55 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA J 60 " --> pdb=" O THR J 56 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 16 removed outlier: 3.885A pdb=" N VAL K 7 " --> pdb=" O GLY K 3 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 38 Processing helix chain 'K' and resid 41 through 72 removed outlier: 4.183A pdb=" N THR K 47 " --> pdb=" O ASN K 43 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N TYR K 48 " --> pdb=" O ARG K 44 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ILE K 51 " --> pdb=" O THR K 47 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LEU K 59 " --> pdb=" O PHE K 55 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA K 60 " --> pdb=" O THR K 56 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE K 66 " --> pdb=" O PHE K 62 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 16 Processing helix chain 'L' and resid 18 through 38 removed outlier: 4.065A pdb=" N VAL L 22 " --> pdb=" O ILE L 18 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 72 removed outlier: 4.082A pdb=" N THR L 47 " --> pdb=" O ASN L 43 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N TYR L 48 " --> pdb=" O ARG L 44 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 17 removed outlier: 3.504A pdb=" N VAL M 7 " --> pdb=" O GLY M 3 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA M 17 " --> pdb=" O VAL M 13 " (cutoff:3.500A) Processing helix chain 'M' and resid 17 through 38 removed outlier: 3.521A pdb=" N VAL M 22 " --> pdb=" O ILE M 18 " (cutoff:3.500A) Processing helix chain 'M' and resid 41 through 71 removed outlier: 3.509A pdb=" N THR M 56 " --> pdb=" O GLY M 52 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY M 63 " --> pdb=" O LEU M 59 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE M 66 " --> pdb=" O PHE M 62 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 15 Processing helix chain 'N' and resid 18 through 38 removed outlier: 5.198A pdb=" N ILE N 24 " --> pdb=" O PRO N 20 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLY N 25 " --> pdb=" O GLY N 21 " (cutoff:3.500A) Processing helix chain 'N' and resid 41 through 72 removed outlier: 4.300A pdb=" N TYR N 48 " --> pdb=" O ARG N 44 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU N 59 " --> pdb=" O PHE N 55 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 38 removed outlier: 3.715A pdb=" N VAL O 7 " --> pdb=" O GLY O 3 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLY O 19 " --> pdb=" O LEU O 15 " (cutoff:3.500A) Proline residue: O 20 - end of helix Processing helix chain 'O' and resid 42 through 72 removed outlier: 4.659A pdb=" N TYR O 48 " --> pdb=" O ARG O 44 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE O 70 " --> pdb=" O ILE O 66 " (cutoff:3.500A) Processing helix chain 'P' and resid 3 through 15 removed outlier: 3.739A pdb=" N VAL P 7 " --> pdb=" O GLY P 3 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL P 13 " --> pdb=" O THR P 9 " (cutoff:3.500A) Processing helix chain 'P' and resid 18 through 38 Processing helix chain 'P' and resid 41 through 72 removed outlier: 5.071A pdb=" N THR P 47 " --> pdb=" O ASN P 43 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N TYR P 48 " --> pdb=" O ARG P 44 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA P 54 " --> pdb=" O PHE P 50 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE P 66 " --> pdb=" O PHE P 62 " (cutoff:3.500A) Processing helix chain 'Q' and resid 3 through 16 removed outlier: 3.760A pdb=" N VAL Q 7 " --> pdb=" O GLY Q 3 " (cutoff:3.500A) Processing helix chain 'Q' and resid 17 through 38 removed outlier: 4.094A pdb=" N VAL Q 22 " --> pdb=" O ILE Q 18 " (cutoff:3.500A) Processing helix chain 'Q' and resid 44 through 72 removed outlier: 3.845A pdb=" N TYR Q 48 " --> pdb=" O ARG Q 44 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY Q 63 " --> pdb=" O LEU Q 59 " (cutoff:3.500A) Processing helix chain 'Z' and resid 49 through 71 Processing helix chain 'Z' and resid 79 through 97 Processing helix chain 'Z' and resid 102 through 124 Proline residue: Z 108 - end of helix removed outlier: 3.611A pdb=" N THR Z 112 " --> pdb=" O PRO Z 108 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE Z 119 " --> pdb=" O LEU Z 115 " (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 211 removed outlier: 3.625A pdb=" N PHE Z 195 " --> pdb=" O LEU Z 191 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA Z 196 " --> pdb=" O ASN Z 192 " (cutoff:3.500A) Processing helix chain 'Z' and resid 227 through 267 removed outlier: 3.847A pdb=" N ILE Z 233 " --> pdb=" O SER Z 229 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE Z 234 " --> pdb=" O PHE Z 230 " (cutoff:3.500A) Proline residue: Z 243 - end of helix removed outlier: 4.022A pdb=" N GLY Z 257 " --> pdb=" O ASN Z 253 " (cutoff:3.500A) Processing helix chain 'Z' and resid 273 through 304 removed outlier: 3.592A pdb=" N ALA Z 292 " --> pdb=" O ALA Z 288 " (cutoff:3.500A) Processing helix chain 'Y' and resid 10 through 29 Processing helix chain 'Y' and resid 29 through 56 Processing helix chain 'V' and resid 7 through 29 Processing helix chain 'V' and resid 29 through 50 removed outlier: 3.550A pdb=" N ASP V 50 " --> pdb=" O GLU V 46 " (cutoff:3.500A) Processing helix chain 'X' and resid 7 through 40 removed outlier: 4.572A pdb=" N ARG X 31 " --> pdb=" O ALA X 27 " (cutoff:3.500A) Proline residue: X 32 - end of helix Processing helix chain 'U' and resid 9 through 45 removed outlier: 3.879A pdb=" N LEU U 28 " --> pdb=" O ILE U 24 " (cutoff:3.500A) Proline residue: U 32 - end of helix removed outlier: 3.768A pdb=" N GLU U 45 " --> pdb=" O THR U 41 " (cutoff:3.500A) Processing helix chain 'T' and resid 49 through 72 removed outlier: 3.915A pdb=" N VAL T 53 " --> pdb=" O THR T 49 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL T 54 " --> pdb=" O ASN T 50 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ASN T 72 " --> pdb=" O ALA T 68 " (cutoff:3.500A) Processing helix chain 'T' and resid 79 through 99 removed outlier: 3.823A pdb=" N ILE T 98 " --> pdb=" O LEU T 94 " (cutoff:3.500A) Processing helix chain 'T' and resid 106 through 124 removed outlier: 3.876A pdb=" N PHE T 119 " --> pdb=" O LEU T 115 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY T 124 " --> pdb=" O GLY T 120 " (cutoff:3.500A) Processing helix chain 'T' and resid 171 through 175 removed outlier: 4.561A pdb=" N ALA T 175 " --> pdb=" O THR T 172 " (cutoff:3.500A) Processing helix chain 'T' and resid 186 through 190 removed outlier: 3.955A pdb=" N ASP T 190 " --> pdb=" O PRO T 187 " (cutoff:3.500A) Processing helix chain 'T' and resid 192 through 210 removed outlier: 3.605A pdb=" N ALA T 196 " --> pdb=" O ASN T 192 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE T 197 " --> pdb=" O PHE T 193 " (cutoff:3.500A) Processing helix chain 'T' and resid 213 through 217 Processing helix chain 'T' and resid 228 through 268 removed outlier: 4.008A pdb=" N PHE T 236 " --> pdb=" O GLY T 232 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE T 237 " --> pdb=" O ILE T 233 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER T 238 " --> pdb=" O ILE T 234 " (cutoff:3.500A) Proline residue: T 243 - end of helix Processing helix chain 'T' and resid 273 through 304 removed outlier: 3.679A pdb=" N GLY T 278 " --> pdb=" O LEU T 274 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE T 279 " --> pdb=" O PRO T 275 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA T 292 " --> pdb=" O ALA T 288 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Z' and resid 133 through 134 876 hydrogen bonds defined for protein. 2604 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: 1.36 Time building geometry restraints manager: 1.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3172 1.34 - 1.46: 2228 1.46 - 1.58: 4704 1.58 - 1.70: 0 1.70 - 1.81: 60 Bond restraints: 10164 Sorted by residual: bond pdb=" N ILE Z 39 " pdb=" CA ILE Z 39 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.19e-02 7.06e+03 1.03e+01 bond pdb=" N ILE I 70 " pdb=" CA ILE I 70 " ideal model delta sigma weight residual 1.460 1.494 -0.035 1.21e-02 6.83e+03 8.29e+00 bond pdb=" N ILE K 70 " pdb=" CA ILE K 70 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.22e-02 6.72e+03 8.22e+00 bond pdb=" N ILE H 70 " pdb=" CA ILE H 70 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.19e-02 7.06e+03 8.22e+00 bond pdb=" N VAL T 231 " pdb=" CA VAL T 231 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.21e-02 6.83e+03 7.97e+00 ... (remaining 10159 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 13330 1.39 - 2.78: 395 2.78 - 4.17: 78 4.17 - 5.56: 28 5.56 - 6.95: 2 Bond angle restraints: 13833 Sorted by residual: angle pdb=" N VAL N 22 " pdb=" CA VAL N 22 " pdb=" C VAL N 22 " ideal model delta sigma weight residual 112.96 108.02 4.94 1.00e+00 1.00e+00 2.44e+01 angle pdb=" N ILE P 70 " pdb=" CA ILE P 70 " pdb=" C ILE P 70 " ideal model delta sigma weight residual 111.67 107.08 4.59 9.50e-01 1.11e+00 2.33e+01 angle pdb=" C CYS T 135 " pdb=" CA CYS T 135 " pdb=" CB CYS T 135 " ideal model delta sigma weight residual 111.86 106.55 5.31 1.34e+00 5.57e-01 1.57e+01 angle pdb=" N ILE Q 70 " pdb=" CA ILE Q 70 " pdb=" C ILE Q 70 " ideal model delta sigma weight residual 110.72 106.75 3.97 1.01e+00 9.80e-01 1.55e+01 angle pdb=" C ASP Z 41 " pdb=" CA ASP Z 41 " pdb=" CB ASP Z 41 " ideal model delta sigma weight residual 116.63 112.11 4.52 1.16e+00 7.43e-01 1.52e+01 ... (remaining 13828 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 5045 17.35 - 34.69: 576 34.69 - 52.04: 162 52.04 - 69.38: 27 69.38 - 86.73: 11 Dihedral angle restraints: 5821 sinusoidal: 1996 harmonic: 3825 Sorted by residual: dihedral pdb=" CB CYS Z 135 " pdb=" SG CYS Z 135 " pdb=" SG CYS Z 173 " pdb=" CB CYS Z 173 " ideal model delta sinusoidal sigma weight residual 93.00 147.08 -54.08 1 1.00e+01 1.00e-02 3.97e+01 dihedral pdb=" CA MET Z 264 " pdb=" C MET Z 264 " pdb=" N ALA Z 265 " pdb=" CA ALA Z 265 " ideal model delta harmonic sigma weight residual 180.00 160.38 19.62 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA ARG H 44 " pdb=" C ARG H 44 " pdb=" N VAL H 45 " pdb=" CA VAL H 45 " ideal model delta harmonic sigma weight residual -180.00 -162.47 -17.53 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 5818 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1300 0.047 - 0.093: 336 0.093 - 0.140: 57 0.140 - 0.187: 14 0.187 - 0.233: 9 Chirality restraints: 1716 Sorted by residual: chirality pdb=" CA ILE M 70 " pdb=" N ILE M 70 " pdb=" C ILE M 70 " pdb=" CB ILE M 70 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA ILE H 70 " pdb=" N ILE H 70 " pdb=" C ILE H 70 " pdb=" CB ILE H 70 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CA ILE O 70 " pdb=" N ILE O 70 " pdb=" C ILE O 70 " pdb=" CB ILE O 70 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 1713 not shown) Planarity restraints: 1745 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY O 19 " 0.046 5.00e-02 4.00e+02 7.01e-02 7.85e+00 pdb=" N PRO O 20 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO O 20 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO O 20 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY L 19 " -0.045 5.00e-02 4.00e+02 6.85e-02 7.50e+00 pdb=" N PRO L 20 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO L 20 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO L 20 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY J 19 " -0.041 5.00e-02 4.00e+02 6.12e-02 6.00e+00 pdb=" N PRO J 20 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO J 20 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO J 20 " -0.034 5.00e-02 4.00e+02 ... (remaining 1742 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2506 2.79 - 3.32: 10665 3.32 - 3.85: 17494 3.85 - 4.37: 18894 4.37 - 4.90: 32880 Nonbonded interactions: 82439 Sorted by model distance: nonbonded pdb=" OD1 ASN V 7 " pdb=" OG1 THR V 9 " model vdw 2.264 3.040 nonbonded pdb=" OE2 GLU H 42 " pdb=" OH TYR Q 48 " model vdw 2.294 3.040 nonbonded pdb=" O GLU T 235 " pdb=" OG SER T 238 " model vdw 2.298 3.040 nonbonded pdb=" O ASN T 99 " pdb=" OH TYR T 296 " model vdw 2.318 3.040 nonbonded pdb=" O ARG T 249 " pdb=" ND2 ASN T 253 " model vdw 2.325 3.120 ... (remaining 82434 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' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' } ncs_group { reference = (chain 'T' and (resid 47 through 135 or resid 170 through 304)) selection = (chain 'Z' and ((resid 47 through 48 and (name N or name CA or name C or name O \ or name CB )) or resid 49 through 66 or (resid 67 through 78 and (name N or name \ CA or name C or name O or name CB )) or resid 79 through 120 or (resid 121 thro \ ugh 123 and (name N or name CA or name C or name O or name CB )) or resid 124 or \ (resid 125 through 127 and (name N or name CA or name C or name O or name CB )) \ or resid 128 or (resid 129 and (name N or name CA or name C or name O or name C \ B )) or resid 130 or (resid 131 through 132 and (name N or name CA or name C or \ name O or name CB )) or resid 133 or (resid 134 and (name N or name CA or name C \ or name O or name CB )) or resid 135 or resid 170 through 175 or (resid 176 and \ (name N or name CA or name C or name O or name CB )) or resid 177 through 182 o \ r (resid 183 through 189 and (name N or name CA or name C or name O or name CB ) \ ) or resid 190 through 217 or (resid 218 through 225 and (name N or name CA or n \ ame C or name O or name CB )) or resid 226 or (resid 227 through 230 and (name N \ or name CA or name C or name O or name CB )) or resid 231 through 304)) } ncs_group { reference = (chain 'U' and resid 8 through 40) selection = (chain 'X' and resid 8 through 40) } ncs_group { reference = (chain 'V' and resid 7 through 50) selection = (chain 'Y' and resid 7 through 50) } 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: 4.630 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.150 Find NCS groups from input model: 0.160 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:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 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 : 0.008 0.661 10165 Z= 0.409 Angle : 0.695 41.274 13835 Z= 0.415 Chirality : 0.045 0.233 1716 Planarity : 0.005 0.070 1745 Dihedral : 16.525 86.729 3378 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.95 % Allowed : 30.17 % Favored : 68.88 % 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: 0.55 (0.23), residues: 1342 helix: 0.92 (0.15), residues: 1131 sheet: None (None), residues: 0 loop : -2.42 (0.41), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Y 40 TYR 0.013 0.001 TYR V 30 PHE 0.026 0.001 PHE Z 276 TRP 0.014 0.001 TRP T 208 HIS 0.001 0.000 HIS Z 170 Details of bonding type rmsd covalent geometry : bond 0.00448 (10164) covalent geometry : angle 0.59998 (13833) SS BOND : bond 0.66080 ( 1) SS BOND : angle 29.25561 ( 2) hydrogen bonds : bond 0.14185 ( 876) hydrogen bonds : angle 6.16134 ( 2604) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 325 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 41 ILE cc_start: 0.9101 (tp) cc_final: 0.8788 (tp) REVERT: H 51 ILE cc_start: 0.9566 (pt) cc_final: 0.9346 (pt) REVERT: I 2 GLU cc_start: 0.8463 (mm-30) cc_final: 0.8235 (mm-30) REVERT: I 5 ASN cc_start: 0.8688 (p0) cc_final: 0.8483 (p0) REVERT: I 38 ASN cc_start: 0.9028 (t0) cc_final: 0.8716 (t0) REVERT: I 40 GLU cc_start: 0.8662 (tp30) cc_final: 0.8295 (tp30) REVERT: I 48 TYR cc_start: 0.9176 (m-80) cc_final: 0.8956 (m-80) REVERT: J 38 ASN cc_start: 0.9256 (t0) cc_final: 0.9051 (t0) REVERT: K 1 MET cc_start: 0.6821 (mpt) cc_final: 0.5842 (mpt) REVERT: K 41 ILE cc_start: 0.9541 (tp) cc_final: 0.9304 (tp) REVERT: L 1 MET cc_start: 0.7649 (mtp) cc_final: 0.7329 (mtm) REVERT: N 41 ILE cc_start: 0.9175 (tp) cc_final: 0.8866 (tp) REVERT: P 4 LEU cc_start: 0.9374 (tp) cc_final: 0.9135 (tp) REVERT: P 42 GLU cc_start: 0.8939 (tm-30) cc_final: 0.8567 (tm-30) REVERT: Z 23 PHE cc_start: 0.7247 (m-80) cc_final: 0.7015 (m-80) REVERT: Z 71 ARG cc_start: 0.7926 (ttt90) cc_final: 0.7572 (ttm-80) REVERT: Z 239 GLU cc_start: 0.9273 (tp30) cc_final: 0.8561 (tp30) REVERT: Z 242 LYS cc_start: 0.9259 (tttt) cc_final: 0.8745 (mttm) REVERT: Y 31 ARG cc_start: 0.9010 (tpp-160) cc_final: 0.8568 (tpp80) REVERT: Y 34 MET cc_start: 0.8891 (mmp) cc_final: 0.8575 (tpp) REVERT: T 246 LEU cc_start: 0.9252 (mt) cc_final: 0.9023 (mt) REVERT: T 254 ILE cc_start: 0.9036 (mm) cc_final: 0.8440 (tt) REVERT: T 264 MET cc_start: 0.4659 (tpp) cc_final: 0.4288 (tpp) REVERT: T 291 PHE cc_start: 0.9115 (t80) cc_final: 0.8798 (t80) outliers start: 9 outliers final: 4 residues processed: 329 average time/residue: 0.0810 time to fit residues: 38.1901 Evaluate side-chains 275 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 271 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 68 PHE Chi-restraints excluded: chain Z residue 109 LEU Chi-restraints excluded: chain V residue 17 ASN Chi-restraints excluded: chain T residue 135 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.2980 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 253 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.123035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.087385 restraints weight = 19424.517| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.90 r_work: 0.3132 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10165 Z= 0.161 Angle : 0.534 7.840 13835 Z= 0.285 Chirality : 0.041 0.195 1716 Planarity : 0.005 0.067 1745 Dihedral : 3.980 35.387 1435 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 4.32 % Allowed : 29.64 % Favored : 66.03 % 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 (0.23), residues: 1342 helix: 1.58 (0.15), residues: 1090 sheet: None (None), residues: 0 loop : -2.16 (0.38), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG T 96 TYR 0.016 0.002 TYR T 277 PHE 0.027 0.001 PHE J 62 TRP 0.013 0.001 TRP T 208 HIS 0.002 0.001 HIS Z 170 Details of bonding type rmsd covalent geometry : bond 0.00367 (10164) covalent geometry : angle 0.53327 (13833) SS BOND : bond 0.00219 ( 1) SS BOND : angle 2.42283 ( 2) hydrogen bonds : bond 0.04644 ( 876) hydrogen bonds : angle 3.97657 ( 2604) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 293 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 41 ILE cc_start: 0.9153 (tp) cc_final: 0.8839 (tp) REVERT: I 2 GLU cc_start: 0.8652 (mm-30) cc_final: 0.8405 (mm-30) REVERT: I 5 ASN cc_start: 0.8725 (p0) cc_final: 0.8477 (p0) REVERT: I 38 ASN cc_start: 0.9038 (t0) cc_final: 0.8704 (t0) REVERT: I 40 GLU cc_start: 0.9003 (tp30) cc_final: 0.8608 (tp30) REVERT: I 48 TYR cc_start: 0.9315 (m-80) cc_final: 0.9092 (m-80) REVERT: J 4 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8685 (mp) REVERT: J 18 ILE cc_start: 0.9039 (mt) cc_final: 0.8820 (mp) REVERT: J 38 ASN cc_start: 0.9214 (t0) cc_final: 0.8977 (t0) REVERT: K 41 ILE cc_start: 0.9533 (tp) cc_final: 0.9285 (tp) REVERT: K 43 ASN cc_start: 0.9196 (p0) cc_final: 0.8970 (p0) REVERT: P 42 GLU cc_start: 0.9088 (OUTLIER) cc_final: 0.8739 (pt0) REVERT: Q 1 MET cc_start: 0.7674 (tpt) cc_final: 0.6983 (tpt) REVERT: Q 37 ARG cc_start: 0.8489 (tpp80) cc_final: 0.8003 (mtm-85) REVERT: Q 38 ASN cc_start: 0.9099 (t0) cc_final: 0.8469 (t0) REVERT: Z 23 PHE cc_start: 0.7469 (m-80) cc_final: 0.7198 (m-80) REVERT: Z 239 GLU cc_start: 0.9242 (tp30) cc_final: 0.8555 (tp30) REVERT: Y 31 ARG cc_start: 0.9096 (tpp-160) cc_final: 0.8673 (tpp80) REVERT: Y 56 GLU cc_start: 0.6991 (OUTLIER) cc_final: 0.6469 (mm-30) REVERT: T 59 ASP cc_start: 0.5240 (OUTLIER) cc_final: 0.4799 (m-30) REVERT: T 136 HIS cc_start: 0.5953 (OUTLIER) cc_final: 0.5520 (m170) REVERT: T 253 ASN cc_start: 0.8511 (m-40) cc_final: 0.8272 (m110) REVERT: T 254 ILE cc_start: 0.8956 (mm) cc_final: 0.8479 (tt) REVERT: T 264 MET cc_start: 0.5380 (tpp) cc_final: 0.5007 (tpp) REVERT: T 272 LEU cc_start: 0.7466 (tp) cc_final: 0.6974 (tt) REVERT: T 291 PHE cc_start: 0.9260 (t80) cc_final: 0.8921 (t80) outliers start: 41 outliers final: 24 residues processed: 312 average time/residue: 0.0878 time to fit residues: 38.9568 Evaluate side-chains 304 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 275 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 18 ILE Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 53 ILE Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 68 PHE Chi-restraints excluded: chain P residue 42 GLU Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 47 THR Chi-restraints excluded: chain P residue 64 LEU Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 68 PHE Chi-restraints excluded: chain Z residue 26 TYR Chi-restraints excluded: chain Z residue 126 LEU Chi-restraints excluded: chain Z residue 240 LEU Chi-restraints excluded: chain Z residue 242 LYS Chi-restraints excluded: chain Y residue 33 VAL Chi-restraints excluded: chain Y residue 56 GLU Chi-restraints excluded: chain T residue 59 ASP Chi-restraints excluded: chain T residue 97 ASN Chi-restraints excluded: chain T residue 136 HIS Chi-restraints excluded: chain T residue 231 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 22 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 102 optimal weight: 0.6980 chunk 121 optimal weight: 10.0000 chunk 15 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.122483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.086898 restraints weight = 19409.143| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.88 r_work: 0.3116 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10165 Z= 0.159 Angle : 0.520 7.980 13835 Z= 0.277 Chirality : 0.041 0.222 1716 Planarity : 0.005 0.066 1745 Dihedral : 3.733 34.362 1430 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 5.59 % Allowed : 30.70 % Favored : 63.71 % 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 (0.23), residues: 1342 helix: 1.69 (0.15), residues: 1098 sheet: None (None), residues: 0 loop : -1.93 (0.38), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG T 96 TYR 0.019 0.002 TYR M 48 PHE 0.020 0.001 PHE Z 276 TRP 0.013 0.001 TRP T 208 HIS 0.001 0.001 HIS Z 170 Details of bonding type rmsd covalent geometry : bond 0.00369 (10164) covalent geometry : angle 0.52011 (13833) SS BOND : bond 0.00370 ( 1) SS BOND : angle 0.96156 ( 2) hydrogen bonds : bond 0.04255 ( 876) hydrogen bonds : angle 3.73061 ( 2604) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 291 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 2 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8461 (mm-30) REVERT: I 5 ASN cc_start: 0.8736 (p0) cc_final: 0.8507 (p0) REVERT: I 38 ASN cc_start: 0.9061 (t0) cc_final: 0.8705 (t0) REVERT: I 40 GLU cc_start: 0.9011 (tp30) cc_final: 0.8607 (tp30) REVERT: I 48 TYR cc_start: 0.9309 (m-80) cc_final: 0.9079 (m-80) REVERT: J 4 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8708 (mp) REVERT: J 38 ASN cc_start: 0.9229 (t0) cc_final: 0.8967 (t0) REVERT: N 41 ILE cc_start: 0.9128 (tp) cc_final: 0.8713 (tp) REVERT: Q 37 ARG cc_start: 0.8543 (tpp80) cc_final: 0.8113 (mtm-85) REVERT: Q 38 ASN cc_start: 0.9032 (t0) cc_final: 0.8386 (t0) REVERT: Z 23 PHE cc_start: 0.7581 (m-80) cc_final: 0.7282 (m-80) REVERT: Z 78 ARG cc_start: 0.4450 (tmt170) cc_final: 0.4213 (tmt170) REVERT: Z 239 GLU cc_start: 0.9229 (tp30) cc_final: 0.8545 (tp30) REVERT: Y 31 ARG cc_start: 0.9096 (tpp-160) cc_final: 0.8689 (tpp80) REVERT: Y 56 GLU cc_start: 0.7020 (OUTLIER) cc_final: 0.6504 (mm-30) REVERT: T 59 ASP cc_start: 0.5171 (OUTLIER) cc_final: 0.4714 (m-30) REVERT: T 136 HIS cc_start: 0.5935 (OUTLIER) cc_final: 0.5550 (m170) REVERT: T 253 ASN cc_start: 0.8604 (m-40) cc_final: 0.8348 (m110) REVERT: T 254 ILE cc_start: 0.8978 (mm) cc_final: 0.8506 (tt) REVERT: T 264 MET cc_start: 0.5582 (tpp) cc_final: 0.5189 (tpp) REVERT: T 272 LEU cc_start: 0.7462 (tp) cc_final: 0.6975 (tt) REVERT: T 291 PHE cc_start: 0.9284 (t80) cc_final: 0.8981 (t80) outliers start: 53 outliers final: 33 residues processed: 317 average time/residue: 0.0838 time to fit residues: 38.1836 Evaluate side-chains 310 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 273 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 18 ILE Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain L residue 38 ASN Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 66 ILE Chi-restraints excluded: chain N residue 68 PHE Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 53 ILE Chi-restraints excluded: chain P residue 64 LEU Chi-restraints excluded: chain Q residue 68 PHE Chi-restraints excluded: chain Z residue 26 TYR Chi-restraints excluded: chain Z residue 51 SER Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain Z residue 76 VAL Chi-restraints excluded: chain Z residue 126 LEU Chi-restraints excluded: chain Z residue 224 THR Chi-restraints excluded: chain Z residue 240 LEU Chi-restraints excluded: chain Z residue 266 PHE Chi-restraints excluded: chain Z residue 283 VAL Chi-restraints excluded: chain Y residue 20 LEU Chi-restraints excluded: chain Y residue 56 GLU Chi-restraints excluded: chain V residue 36 LEU Chi-restraints excluded: chain T residue 59 ASP Chi-restraints excluded: chain T residue 82 ASN Chi-restraints excluded: chain T residue 97 ASN Chi-restraints excluded: chain T residue 136 HIS Chi-restraints excluded: chain T residue 231 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 4 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 97 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 113 optimal weight: 5.9990 chunk 38 optimal weight: 0.0270 chunk 82 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.123353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.087913 restraints weight = 19592.188| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.86 r_work: 0.3140 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10165 Z= 0.142 Angle : 0.513 7.147 13835 Z= 0.272 Chirality : 0.041 0.197 1716 Planarity : 0.005 0.065 1745 Dihedral : 3.587 20.113 1428 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 5.80 % Allowed : 31.33 % Favored : 62.87 % 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 (0.23), residues: 1342 helix: 1.82 (0.15), residues: 1098 sheet: None (None), residues: 0 loop : -1.84 (0.38), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 37 TYR 0.014 0.002 TYR Z 296 PHE 0.023 0.001 PHE P 62 TRP 0.014 0.001 TRP T 208 HIS 0.001 0.000 HIS T 136 Details of bonding type rmsd covalent geometry : bond 0.00327 (10164) covalent geometry : angle 0.51303 (13833) SS BOND : bond 0.00054 ( 1) SS BOND : angle 1.21457 ( 2) hydrogen bonds : bond 0.04105 ( 876) hydrogen bonds : angle 3.62621 ( 2604) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 304 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 2 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8482 (mm-30) REVERT: I 5 ASN cc_start: 0.8789 (p0) cc_final: 0.8552 (p0) REVERT: I 38 ASN cc_start: 0.9033 (t0) cc_final: 0.8675 (t0) REVERT: I 48 TYR cc_start: 0.9276 (m-80) cc_final: 0.9069 (m-80) REVERT: J 4 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8687 (mp) REVERT: J 18 ILE cc_start: 0.9055 (OUTLIER) cc_final: 0.8852 (mp) REVERT: J 38 ASN cc_start: 0.9202 (t0) cc_final: 0.8940 (t0) REVERT: K 41 ILE cc_start: 0.9507 (OUTLIER) cc_final: 0.9272 (tp) REVERT: M 48 TYR cc_start: 0.9134 (m-80) cc_final: 0.8849 (m-80) REVERT: N 41 ILE cc_start: 0.9080 (tp) cc_final: 0.8762 (tp) REVERT: N 57 GLU cc_start: 0.8814 (mm-30) cc_final: 0.8545 (mm-30) REVERT: P 48 TYR cc_start: 0.9086 (m-10) cc_final: 0.8853 (m-10) REVERT: Q 37 ARG cc_start: 0.8526 (tpp80) cc_final: 0.8147 (mtm-85) REVERT: Q 38 ASN cc_start: 0.9001 (t0) cc_final: 0.8390 (t0) REVERT: Z 23 PHE cc_start: 0.7544 (m-80) cc_final: 0.7252 (m-80) REVERT: Z 78 ARG cc_start: 0.4512 (tmt170) cc_final: 0.4246 (tmt170) REVERT: Z 228 MET cc_start: 0.8510 (mmp) cc_final: 0.8119 (mmp) REVERT: Z 239 GLU cc_start: 0.9196 (tp30) cc_final: 0.8496 (tp30) REVERT: Z 242 LYS cc_start: 0.9158 (mttp) cc_final: 0.8874 (mttt) REVERT: Y 31 ARG cc_start: 0.9070 (tpp-160) cc_final: 0.8675 (tpp80) REVERT: Y 56 GLU cc_start: 0.6927 (OUTLIER) cc_final: 0.6433 (mm-30) REVERT: T 59 ASP cc_start: 0.5383 (OUTLIER) cc_final: 0.4939 (m-30) REVERT: T 136 HIS cc_start: 0.5991 (OUTLIER) cc_final: 0.5632 (m170) REVERT: T 253 ASN cc_start: 0.8560 (m-40) cc_final: 0.8202 (m-40) REVERT: T 254 ILE cc_start: 0.8937 (mm) cc_final: 0.8493 (tt) REVERT: T 264 MET cc_start: 0.5523 (tpp) cc_final: 0.5112 (tpp) REVERT: T 272 LEU cc_start: 0.7453 (tp) cc_final: 0.6967 (tt) REVERT: T 291 PHE cc_start: 0.9252 (t80) cc_final: 0.8939 (t80) outliers start: 55 outliers final: 33 residues processed: 330 average time/residue: 0.0795 time to fit residues: 37.7291 Evaluate side-chains 325 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 286 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain K residue 18 ILE Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain L residue 38 ASN Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 53 ILE Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 66 ILE Chi-restraints excluded: chain N residue 68 PHE Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 68 PHE Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 47 THR Chi-restraints excluded: chain P residue 53 ILE Chi-restraints excluded: chain P residue 64 LEU Chi-restraints excluded: chain Q residue 68 PHE Chi-restraints excluded: chain Z residue 26 TYR Chi-restraints excluded: chain Z residue 51 SER Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain Z residue 76 VAL Chi-restraints excluded: chain Z residue 80 LEU Chi-restraints excluded: chain Z residue 126 LEU Chi-restraints excluded: chain Z residue 224 THR Chi-restraints excluded: chain Z residue 266 PHE Chi-restraints excluded: chain Z residue 286 ILE Chi-restraints excluded: chain Y residue 20 LEU Chi-restraints excluded: chain Y residue 35 ASN Chi-restraints excluded: chain Y residue 56 GLU Chi-restraints excluded: chain V residue 36 LEU Chi-restraints excluded: chain T residue 59 ASP Chi-restraints excluded: chain T residue 84 MET Chi-restraints excluded: chain T residue 136 HIS Chi-restraints excluded: chain T residue 231 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 19 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 70 optimal weight: 5.9990 chunk 9 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 105 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 106 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.122775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.087248 restraints weight = 19400.187| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.86 r_work: 0.3126 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10165 Z= 0.160 Angle : 0.531 7.139 13835 Z= 0.282 Chirality : 0.041 0.232 1716 Planarity : 0.005 0.065 1745 Dihedral : 3.576 20.132 1428 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 6.01 % Allowed : 31.65 % Favored : 62.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.23), residues: 1342 helix: 1.82 (0.15), residues: 1099 sheet: None (None), residues: 0 loop : -1.85 (0.39), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 37 TYR 0.014 0.002 TYR T 277 PHE 0.015 0.001 PHE M 62 TRP 0.013 0.001 TRP T 208 HIS 0.001 0.000 HIS Z 170 Details of bonding type rmsd covalent geometry : bond 0.00375 (10164) covalent geometry : angle 0.53085 (13833) SS BOND : bond 0.00056 ( 1) SS BOND : angle 0.89305 ( 2) hydrogen bonds : bond 0.04104 ( 876) hydrogen bonds : angle 3.61991 ( 2604) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 284 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 2 GLU cc_start: 0.8703 (mm-30) cc_final: 0.8483 (mm-30) REVERT: I 5 ASN cc_start: 0.8756 (p0) cc_final: 0.8515 (p0) REVERT: I 38 ASN cc_start: 0.9049 (t0) cc_final: 0.8683 (t0) REVERT: I 48 TYR cc_start: 0.9259 (m-80) cc_final: 0.9043 (m-80) REVERT: J 4 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8725 (mp) REVERT: J 18 ILE cc_start: 0.9063 (OUTLIER) cc_final: 0.8850 (mp) REVERT: J 38 ASN cc_start: 0.9226 (t0) cc_final: 0.8945 (t0) REVERT: K 41 ILE cc_start: 0.9457 (OUTLIER) cc_final: 0.9222 (tp) REVERT: M 48 TYR cc_start: 0.9136 (m-80) cc_final: 0.8830 (m-80) REVERT: N 41 ILE cc_start: 0.9086 (tp) cc_final: 0.8769 (tp) REVERT: Q 37 ARG cc_start: 0.8551 (tpp80) cc_final: 0.8161 (mtm-85) REVERT: Q 38 ASN cc_start: 0.9018 (t0) cc_final: 0.8358 (t0) REVERT: Q 48 TYR cc_start: 0.8766 (m-80) cc_final: 0.8498 (m-80) REVERT: Z 23 PHE cc_start: 0.7600 (m-80) cc_final: 0.7278 (m-80) REVERT: Z 78 ARG cc_start: 0.4516 (tmt170) cc_final: 0.4152 (tmt170) REVERT: Z 239 GLU cc_start: 0.9234 (tp30) cc_final: 0.8534 (tp30) REVERT: Z 242 LYS cc_start: 0.9148 (mttp) cc_final: 0.8638 (mtpp) REVERT: Y 31 ARG cc_start: 0.9066 (tpp-160) cc_final: 0.8679 (tpp80) REVERT: T 59 ASP cc_start: 0.5293 (OUTLIER) cc_final: 0.4839 (m-30) REVERT: T 97 ASN cc_start: 0.7499 (t0) cc_final: 0.7298 (t0) REVERT: T 136 HIS cc_start: 0.6068 (OUTLIER) cc_final: 0.5731 (m170) REVERT: T 253 ASN cc_start: 0.8691 (m-40) cc_final: 0.8436 (m110) REVERT: T 254 ILE cc_start: 0.8970 (mm) cc_final: 0.8486 (tt) REVERT: T 264 MET cc_start: 0.5593 (tpp) cc_final: 0.5176 (tpp) REVERT: T 272 LEU cc_start: 0.7498 (tp) cc_final: 0.7016 (tt) REVERT: T 291 PHE cc_start: 0.9269 (t80) cc_final: 0.8990 (t80) outliers start: 57 outliers final: 41 residues processed: 316 average time/residue: 0.0771 time to fit residues: 34.9920 Evaluate side-chains 323 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 277 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain K residue 18 ILE Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain L residue 38 ASN Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 53 ILE Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 66 ILE Chi-restraints excluded: chain N residue 68 PHE Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 68 PHE Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 53 ILE Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 68 PHE Chi-restraints excluded: chain Z residue 26 TYR Chi-restraints excluded: chain Z residue 51 SER Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain Z residue 76 VAL Chi-restraints excluded: chain Z residue 80 LEU Chi-restraints excluded: chain Z residue 103 VAL Chi-restraints excluded: chain Z residue 126 LEU Chi-restraints excluded: chain Z residue 224 THR Chi-restraints excluded: chain Z residue 240 LEU Chi-restraints excluded: chain Z residue 254 ILE Chi-restraints excluded: chain Z residue 266 PHE Chi-restraints excluded: chain Z residue 286 ILE Chi-restraints excluded: chain Z residue 293 LEU Chi-restraints excluded: chain Y residue 20 LEU Chi-restraints excluded: chain Y residue 35 ASN Chi-restraints excluded: chain Y residue 56 GLU Chi-restraints excluded: chain V residue 25 LEU Chi-restraints excluded: chain V residue 36 LEU Chi-restraints excluded: chain T residue 59 ASP Chi-restraints excluded: chain T residue 82 ASN Chi-restraints excluded: chain T residue 84 MET Chi-restraints excluded: chain T residue 136 HIS Chi-restraints excluded: chain T residue 231 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 22 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 72 optimal weight: 5.9990 chunk 47 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 78 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 300 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.122921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.087614 restraints weight = 19501.362| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.87 r_work: 0.3130 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 10165 Z= 0.149 Angle : 0.528 6.506 13835 Z= 0.278 Chirality : 0.042 0.265 1716 Planarity : 0.005 0.065 1745 Dihedral : 3.588 20.190 1428 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 5.80 % Allowed : 32.49 % Favored : 61.71 % 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: 1.83 (0.23), residues: 1342 helix: 1.90 (0.15), residues: 1093 sheet: None (None), residues: 0 loop : -2.00 (0.38), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 37 TYR 0.014 0.002 TYR Z 296 PHE 0.017 0.001 PHE T 114 TRP 0.021 0.002 TRP T 208 HIS 0.002 0.001 HIS T 136 Details of bonding type rmsd covalent geometry : bond 0.00350 (10164) covalent geometry : angle 0.52785 (13833) SS BOND : bond 0.00038 ( 1) SS BOND : angle 0.82540 ( 2) hydrogen bonds : bond 0.04030 ( 876) hydrogen bonds : angle 3.60472 ( 2604) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 291 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 2 GLU cc_start: 0.8706 (mm-30) cc_final: 0.8485 (mm-30) REVERT: I 5 ASN cc_start: 0.8763 (p0) cc_final: 0.8523 (p0) REVERT: I 38 ASN cc_start: 0.9053 (t0) cc_final: 0.8679 (t0) REVERT: I 48 TYR cc_start: 0.9248 (m-80) cc_final: 0.9042 (m-80) REVERT: J 4 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8715 (mp) REVERT: J 18 ILE cc_start: 0.9056 (OUTLIER) cc_final: 0.8844 (mp) REVERT: J 38 ASN cc_start: 0.9210 (t0) cc_final: 0.8915 (t0) REVERT: K 41 ILE cc_start: 0.9463 (OUTLIER) cc_final: 0.9231 (tp) REVERT: M 48 TYR cc_start: 0.9123 (m-80) cc_final: 0.8814 (m-80) REVERT: N 41 ILE cc_start: 0.9093 (tp) cc_final: 0.8778 (tp) REVERT: Q 37 ARG cc_start: 0.8542 (tpp80) cc_final: 0.8153 (mtm-85) REVERT: Q 38 ASN cc_start: 0.9044 (t0) cc_final: 0.8361 (t0) REVERT: Q 48 TYR cc_start: 0.8773 (m-80) cc_final: 0.8528 (m-80) REVERT: Z 23 PHE cc_start: 0.7551 (m-80) cc_final: 0.7241 (m-80) REVERT: Z 78 ARG cc_start: 0.4570 (tmt170) cc_final: 0.4283 (tmt170) REVERT: Z 101 LYS cc_start: 0.9316 (tttm) cc_final: 0.8929 (tttm) REVERT: Z 228 MET cc_start: 0.8473 (mmp) cc_final: 0.8067 (mmp) REVERT: Z 239 GLU cc_start: 0.9227 (tp30) cc_final: 0.8528 (tp30) REVERT: Z 242 LYS cc_start: 0.9137 (mttp) cc_final: 0.8570 (mtpp) REVERT: Y 31 ARG cc_start: 0.9054 (tpp-160) cc_final: 0.8670 (tpp80) REVERT: T 59 ASP cc_start: 0.5303 (OUTLIER) cc_final: 0.4873 (m-30) REVERT: T 136 HIS cc_start: 0.5746 (OUTLIER) cc_final: 0.5498 (m170) REVERT: T 239 GLU cc_start: 0.9060 (mm-30) cc_final: 0.8742 (mm-30) REVERT: T 253 ASN cc_start: 0.8651 (m-40) cc_final: 0.8343 (m-40) REVERT: T 254 ILE cc_start: 0.8966 (mm) cc_final: 0.8498 (tt) REVERT: T 264 MET cc_start: 0.5573 (tpp) cc_final: 0.5125 (tpp) REVERT: T 272 LEU cc_start: 0.7451 (tp) cc_final: 0.7003 (tt) REVERT: T 291 PHE cc_start: 0.9273 (t80) cc_final: 0.8977 (t80) outliers start: 55 outliers final: 43 residues processed: 323 average time/residue: 0.0792 time to fit residues: 37.0069 Evaluate side-chains 335 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 287 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain K residue 18 ILE Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain L residue 38 ASN Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 53 ILE Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 66 ILE Chi-restraints excluded: chain N residue 68 PHE Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 68 PHE Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 53 ILE Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 68 PHE Chi-restraints excluded: chain Z residue 26 TYR Chi-restraints excluded: chain Z residue 51 SER Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain Z residue 76 VAL Chi-restraints excluded: chain Z residue 80 LEU Chi-restraints excluded: chain Z residue 103 VAL Chi-restraints excluded: chain Z residue 126 LEU Chi-restraints excluded: chain Z residue 224 THR Chi-restraints excluded: chain Z residue 240 LEU Chi-restraints excluded: chain Z residue 254 ILE Chi-restraints excluded: chain Z residue 266 PHE Chi-restraints excluded: chain Z residue 286 ILE Chi-restraints excluded: chain Z residue 294 LEU Chi-restraints excluded: chain Y residue 20 LEU Chi-restraints excluded: chain Y residue 35 ASN Chi-restraints excluded: chain Y residue 56 GLU Chi-restraints excluded: chain V residue 25 LEU Chi-restraints excluded: chain V residue 36 LEU Chi-restraints excluded: chain T residue 59 ASP Chi-restraints excluded: chain T residue 84 MET Chi-restraints excluded: chain T residue 136 HIS Chi-restraints excluded: chain T residue 231 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 89 optimal weight: 0.6980 chunk 101 optimal weight: 0.0170 chunk 130 optimal weight: 0.4980 chunk 105 optimal weight: 8.9990 chunk 74 optimal weight: 0.9990 chunk 129 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 chunk 91 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 60 optimal weight: 0.0980 chunk 99 optimal weight: 0.9990 overall best weight: 0.3618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.124975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.089796 restraints weight = 19435.920| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.84 r_work: 0.3167 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10165 Z= 0.128 Angle : 0.525 8.079 13835 Z= 0.275 Chirality : 0.042 0.247 1716 Planarity : 0.005 0.063 1745 Dihedral : 3.578 20.270 1428 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 5.38 % Allowed : 32.91 % Favored : 61.71 % 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: 1.94 (0.23), residues: 1342 helix: 1.99 (0.15), residues: 1092 sheet: None (None), residues: 0 loop : -2.01 (0.38), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 37 TYR 0.015 0.001 TYR Z 296 PHE 0.009 0.001 PHE Z 276 TRP 0.020 0.002 TRP T 208 HIS 0.001 0.000 HIS T 136 Details of bonding type rmsd covalent geometry : bond 0.00290 (10164) covalent geometry : angle 0.52490 (13833) SS BOND : bond 0.00031 ( 1) SS BOND : angle 0.74648 ( 2) hydrogen bonds : bond 0.03900 ( 876) hydrogen bonds : angle 3.53901 ( 2604) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 303 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 2 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8459 (mm-30) REVERT: I 5 ASN cc_start: 0.8774 (p0) cc_final: 0.8561 (p0) REVERT: I 38 ASN cc_start: 0.8998 (t0) cc_final: 0.8612 (t0) REVERT: J 4 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8657 (mp) REVERT: J 38 ASN cc_start: 0.9175 (t0) cc_final: 0.8879 (t0) REVERT: K 41 ILE cc_start: 0.9421 (OUTLIER) cc_final: 0.9167 (tp) REVERT: M 48 TYR cc_start: 0.9112 (m-80) cc_final: 0.8762 (m-80) REVERT: N 41 ILE cc_start: 0.9067 (tp) cc_final: 0.8762 (tp) REVERT: Q 38 ASN cc_start: 0.9017 (t0) cc_final: 0.8361 (t0) REVERT: Q 44 ARG cc_start: 0.8188 (ttp80) cc_final: 0.7759 (tmm-80) REVERT: Q 48 TYR cc_start: 0.8773 (m-80) cc_final: 0.8451 (m-80) REVERT: Z 23 PHE cc_start: 0.7569 (m-80) cc_final: 0.7241 (m-80) REVERT: Z 78 ARG cc_start: 0.4662 (tmt170) cc_final: 0.4280 (tmt170) REVERT: Z 101 LYS cc_start: 0.9285 (tttm) cc_final: 0.8905 (tttm) REVERT: Z 228 MET cc_start: 0.8477 (mmp) cc_final: 0.8106 (mmp) REVERT: Z 239 GLU cc_start: 0.9245 (tp30) cc_final: 0.8732 (tp30) REVERT: Y 31 ARG cc_start: 0.9024 (tpp-160) cc_final: 0.8646 (tpp80) REVERT: Y 43 ARG cc_start: 0.7535 (tmm-80) cc_final: 0.7271 (ttp-170) REVERT: T 59 ASP cc_start: 0.5402 (OUTLIER) cc_final: 0.4982 (m-30) REVERT: T 136 HIS cc_start: 0.5731 (OUTLIER) cc_final: 0.5508 (m170) REVERT: T 239 GLU cc_start: 0.9022 (mm-30) cc_final: 0.8709 (mm-30) REVERT: T 253 ASN cc_start: 0.8703 (m-40) cc_final: 0.8274 (m110) REVERT: T 254 ILE cc_start: 0.8940 (mm) cc_final: 0.8527 (tt) REVERT: T 264 MET cc_start: 0.5607 (tpp) cc_final: 0.5162 (tpp) REVERT: T 272 LEU cc_start: 0.7535 (tp) cc_final: 0.7048 (tt) REVERT: T 291 PHE cc_start: 0.9235 (t80) cc_final: 0.8970 (t80) outliers start: 51 outliers final: 41 residues processed: 331 average time/residue: 0.0808 time to fit residues: 38.4540 Evaluate side-chains 332 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 287 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain K residue 18 ILE Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain L residue 38 ASN Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 66 ILE Chi-restraints excluded: chain N residue 68 PHE Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 66 ILE Chi-restraints excluded: chain O residue 68 PHE Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 64 LEU Chi-restraints excluded: chain Q residue 68 PHE Chi-restraints excluded: chain Z residue 26 TYR Chi-restraints excluded: chain Z residue 51 SER Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain Z residue 76 VAL Chi-restraints excluded: chain Z residue 103 VAL Chi-restraints excluded: chain Z residue 126 LEU Chi-restraints excluded: chain Z residue 224 THR Chi-restraints excluded: chain Z residue 240 LEU Chi-restraints excluded: chain Z residue 254 ILE Chi-restraints excluded: chain Z residue 266 PHE Chi-restraints excluded: chain Z residue 283 VAL Chi-restraints excluded: chain Z residue 286 ILE Chi-restraints excluded: chain Z residue 294 LEU Chi-restraints excluded: chain Y residue 20 LEU Chi-restraints excluded: chain Y residue 35 ASN Chi-restraints excluded: chain Y residue 56 GLU Chi-restraints excluded: chain V residue 25 LEU Chi-restraints excluded: chain V residue 36 LEU Chi-restraints excluded: chain T residue 59 ASP Chi-restraints excluded: chain T residue 84 MET Chi-restraints excluded: chain T residue 136 HIS Chi-restraints excluded: chain T residue 231 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 13 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 chunk 115 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 126 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.122990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.087664 restraints weight = 19577.510| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.89 r_work: 0.3142 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 10165 Z= 0.164 Angle : 0.575 7.088 13835 Z= 0.300 Chirality : 0.044 0.296 1716 Planarity : 0.005 0.064 1745 Dihedral : 3.595 20.610 1428 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 4.96 % Allowed : 33.97 % Favored : 61.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.87 (0.23), residues: 1342 helix: 1.92 (0.15), residues: 1093 sheet: None (None), residues: 0 loop : -1.95 (0.38), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 37 TYR 0.015 0.002 TYR T 277 PHE 0.018 0.001 PHE T 202 TRP 0.018 0.002 TRP T 208 HIS 0.001 0.000 HIS Z 170 Details of bonding type rmsd covalent geometry : bond 0.00391 (10164) covalent geometry : angle 0.57540 (13833) SS BOND : bond 0.00058 ( 1) SS BOND : angle 0.73183 ( 2) hydrogen bonds : bond 0.04114 ( 876) hydrogen bonds : angle 3.63142 ( 2604) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 282 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 2 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8450 (mm-30) REVERT: I 5 ASN cc_start: 0.8797 (p0) cc_final: 0.8548 (p0) REVERT: I 38 ASN cc_start: 0.9056 (t0) cc_final: 0.8679 (t0) REVERT: J 4 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8708 (mp) REVERT: J 38 ASN cc_start: 0.9223 (t0) cc_final: 0.8935 (t0) REVERT: K 41 ILE cc_start: 0.9467 (OUTLIER) cc_final: 0.9249 (tp) REVERT: N 41 ILE cc_start: 0.9101 (tp) cc_final: 0.8795 (tp) REVERT: Q 37 ARG cc_start: 0.8786 (tpp80) cc_final: 0.8533 (ttm-80) REVERT: Q 38 ASN cc_start: 0.9013 (t0) cc_final: 0.8344 (t0) REVERT: Q 44 ARG cc_start: 0.8296 (ttp80) cc_final: 0.7909 (tmm-80) REVERT: Q 48 TYR cc_start: 0.8798 (m-80) cc_final: 0.8456 (m-80) REVERT: Z 23 PHE cc_start: 0.7570 (m-80) cc_final: 0.7245 (m-80) REVERT: Z 78 ARG cc_start: 0.4699 (tmt170) cc_final: 0.4272 (tmt170) REVERT: Z 201 SER cc_start: 0.9045 (t) cc_final: 0.8807 (t) REVERT: Z 239 GLU cc_start: 0.9226 (tp30) cc_final: 0.8528 (tp30) REVERT: Z 242 LYS cc_start: 0.9166 (mttt) cc_final: 0.8791 (mttt) REVERT: Y 31 ARG cc_start: 0.9076 (tpp-160) cc_final: 0.8712 (tpp80) REVERT: T 59 ASP cc_start: 0.5334 (OUTLIER) cc_final: 0.4899 (m-30) REVERT: T 239 GLU cc_start: 0.9022 (mm-30) cc_final: 0.8756 (mm-30) REVERT: T 253 ASN cc_start: 0.8664 (m-40) cc_final: 0.8220 (m110) REVERT: T 254 ILE cc_start: 0.8963 (mm) cc_final: 0.8547 (tt) REVERT: T 264 MET cc_start: 0.5645 (tpp) cc_final: 0.5195 (tpp) REVERT: T 272 LEU cc_start: 0.7517 (tp) cc_final: 0.7022 (tt) REVERT: T 291 PHE cc_start: 0.9269 (t80) cc_final: 0.8960 (t80) outliers start: 47 outliers final: 38 residues processed: 312 average time/residue: 0.0736 time to fit residues: 33.1505 Evaluate side-chains 316 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 275 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain K residue 18 ILE Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain L residue 38 ASN Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 53 ILE Chi-restraints excluded: chain N residue 66 ILE Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 68 PHE Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain Q residue 68 PHE Chi-restraints excluded: chain Z residue 26 TYR Chi-restraints excluded: chain Z residue 51 SER Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain Z residue 76 VAL Chi-restraints excluded: chain Z residue 80 LEU Chi-restraints excluded: chain Z residue 103 VAL Chi-restraints excluded: chain Z residue 126 LEU Chi-restraints excluded: chain Z residue 224 THR Chi-restraints excluded: chain Z residue 240 LEU Chi-restraints excluded: chain Z residue 254 ILE Chi-restraints excluded: chain Z residue 266 PHE Chi-restraints excluded: chain Z residue 283 VAL Chi-restraints excluded: chain Z residue 286 ILE Chi-restraints excluded: chain Y residue 20 LEU Chi-restraints excluded: chain Y residue 35 ASN Chi-restraints excluded: chain Y residue 56 GLU Chi-restraints excluded: chain V residue 25 LEU Chi-restraints excluded: chain V residue 36 LEU Chi-restraints excluded: chain T residue 59 ASP Chi-restraints excluded: chain T residue 84 MET Chi-restraints excluded: chain T residue 118 LEU Chi-restraints excluded: chain T residue 231 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 114 optimal weight: 0.0000 chunk 42 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 86 optimal weight: 0.0980 chunk 109 optimal weight: 20.0000 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.123990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.090089 restraints weight = 19330.639| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.77 r_work: 0.3159 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 10165 Z= 0.150 Angle : 0.583 8.548 13835 Z= 0.303 Chirality : 0.044 0.317 1716 Planarity : 0.005 0.064 1745 Dihedral : 3.631 20.558 1428 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.64 % Allowed : 33.86 % Favored : 61.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.85 (0.23), residues: 1342 helix: 1.92 (0.15), residues: 1093 sheet: None (None), residues: 0 loop : -1.97 (0.38), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG K 37 TYR 0.016 0.002 TYR M 48 PHE 0.014 0.001 PHE M 62 TRP 0.018 0.002 TRP T 208 HIS 0.001 0.000 HIS Z 170 Details of bonding type rmsd covalent geometry : bond 0.00357 (10164) covalent geometry : angle 0.58253 (13833) SS BOND : bond 0.00028 ( 1) SS BOND : angle 0.73695 ( 2) hydrogen bonds : bond 0.04029 ( 876) hydrogen bonds : angle 3.63211 ( 2604) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 287 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 2 GLU cc_start: 0.8668 (mm-30) cc_final: 0.8438 (mm-30) REVERT: I 5 ASN cc_start: 0.8791 (p0) cc_final: 0.8558 (p0) REVERT: I 38 ASN cc_start: 0.9039 (t0) cc_final: 0.8651 (t0) REVERT: J 4 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8695 (mp) REVERT: J 37 ARG cc_start: 0.8610 (mtt180) cc_final: 0.8327 (mtm-85) REVERT: J 38 ASN cc_start: 0.9231 (t0) cc_final: 0.8917 (t0) REVERT: K 41 ILE cc_start: 0.9455 (OUTLIER) cc_final: 0.9221 (tp) REVERT: N 41 ILE cc_start: 0.9084 (tp) cc_final: 0.8786 (tp) REVERT: Q 37 ARG cc_start: 0.8775 (tpp80) cc_final: 0.8489 (ttm-80) REVERT: Q 38 ASN cc_start: 0.9012 (t0) cc_final: 0.8349 (t0) REVERT: Q 44 ARG cc_start: 0.8239 (ttp80) cc_final: 0.7851 (tmm-80) REVERT: Q 48 TYR cc_start: 0.8752 (m-80) cc_final: 0.8406 (m-80) REVERT: Z 23 PHE cc_start: 0.7598 (m-80) cc_final: 0.7305 (m-80) REVERT: Z 71 ARG cc_start: 0.7925 (ttt90) cc_final: 0.7569 (ttm-80) REVERT: Z 78 ARG cc_start: 0.4773 (tmt170) cc_final: 0.4336 (tmt170) REVERT: Z 201 SER cc_start: 0.9035 (t) cc_final: 0.8792 (t) REVERT: Z 228 MET cc_start: 0.8455 (mmp) cc_final: 0.8166 (mmp) REVERT: Z 239 GLU cc_start: 0.9229 (tp30) cc_final: 0.8682 (tp30) REVERT: Z 242 LYS cc_start: 0.9154 (mttt) cc_final: 0.8693 (mttt) REVERT: Y 31 ARG cc_start: 0.9049 (tpp-160) cc_final: 0.8686 (tpp80) REVERT: T 59 ASP cc_start: 0.5312 (OUTLIER) cc_final: 0.4815 (m-30) REVERT: T 239 GLU cc_start: 0.9052 (mm-30) cc_final: 0.8785 (mm-30) REVERT: T 253 ASN cc_start: 0.8709 (m-40) cc_final: 0.8258 (m110) REVERT: T 254 ILE cc_start: 0.8944 (mm) cc_final: 0.8549 (tt) REVERT: T 264 MET cc_start: 0.5665 (tpp) cc_final: 0.5361 (tpp) REVERT: T 272 LEU cc_start: 0.7531 (tp) cc_final: 0.7045 (tt) REVERT: T 287 GLN cc_start: 0.7521 (mt0) cc_final: 0.7186 (mt0) REVERT: T 291 PHE cc_start: 0.9241 (t80) cc_final: 0.8917 (t80) outliers start: 44 outliers final: 40 residues processed: 313 average time/residue: 0.0755 time to fit residues: 33.9580 Evaluate side-chains 322 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 279 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain K residue 18 ILE Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain L residue 38 ASN Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 53 ILE Chi-restraints excluded: chain N residue 66 ILE Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 66 ILE Chi-restraints excluded: chain O residue 68 PHE Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 68 PHE Chi-restraints excluded: chain Z residue 26 TYR Chi-restraints excluded: chain Z residue 51 SER Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain Z residue 76 VAL Chi-restraints excluded: chain Z residue 80 LEU Chi-restraints excluded: chain Z residue 103 VAL Chi-restraints excluded: chain Z residue 126 LEU Chi-restraints excluded: chain Z residue 224 THR Chi-restraints excluded: chain Z residue 240 LEU Chi-restraints excluded: chain Z residue 254 ILE Chi-restraints excluded: chain Z residue 266 PHE Chi-restraints excluded: chain Z residue 286 ILE Chi-restraints excluded: chain Y residue 20 LEU Chi-restraints excluded: chain Y residue 35 ASN Chi-restraints excluded: chain Y residue 56 GLU Chi-restraints excluded: chain V residue 25 LEU Chi-restraints excluded: chain V residue 36 LEU Chi-restraints excluded: chain T residue 59 ASP Chi-restraints excluded: chain T residue 84 MET Chi-restraints excluded: chain T residue 118 LEU Chi-restraints excluded: chain T residue 231 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 11 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 92 optimal weight: 0.1980 chunk 98 optimal weight: 0.8980 chunk 106 optimal weight: 6.9990 chunk 16 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 300 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.123490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.088770 restraints weight = 19234.419| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.83 r_work: 0.3162 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 10165 Z= 0.150 Angle : 0.605 12.924 13835 Z= 0.310 Chirality : 0.046 0.446 1716 Planarity : 0.005 0.064 1745 Dihedral : 3.641 20.429 1428 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 4.64 % Allowed : 34.07 % Favored : 61.29 % 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: 1.77 (0.23), residues: 1342 helix: 1.85 (0.15), residues: 1093 sheet: None (None), residues: 0 loop : -1.95 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 37 TYR 0.015 0.002 TYR Z 296 PHE 0.037 0.001 PHE M 62 TRP 0.018 0.002 TRP T 208 HIS 0.001 0.000 HIS Z 170 Details of bonding type rmsd covalent geometry : bond 0.00355 (10164) covalent geometry : angle 0.60542 (13833) SS BOND : bond 0.00037 ( 1) SS BOND : angle 0.73348 ( 2) hydrogen bonds : bond 0.04060 ( 876) hydrogen bonds : angle 3.65148 ( 2604) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 282 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 2 GLU cc_start: 0.8669 (mm-30) cc_final: 0.8426 (mm-30) REVERT: I 5 ASN cc_start: 0.8801 (p0) cc_final: 0.8573 (p0) REVERT: I 38 ASN cc_start: 0.9047 (t0) cc_final: 0.8658 (t0) REVERT: J 4 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8705 (mp) REVERT: J 38 ASN cc_start: 0.9265 (t0) cc_final: 0.8943 (t0) REVERT: J 57 GLU cc_start: 0.8803 (tp30) cc_final: 0.8561 (tp30) REVERT: K 41 ILE cc_start: 0.9436 (OUTLIER) cc_final: 0.9193 (tp) REVERT: M 48 TYR cc_start: 0.9153 (m-80) cc_final: 0.8757 (m-80) REVERT: N 41 ILE cc_start: 0.9094 (tp) cc_final: 0.8817 (tp) REVERT: O 40 GLU cc_start: 0.8528 (mm-30) cc_final: 0.8312 (mp0) REVERT: P 1 MET cc_start: 0.5737 (mmt) cc_final: 0.5241 (mmt) REVERT: Q 37 ARG cc_start: 0.8752 (tpp80) cc_final: 0.8452 (ttm-80) REVERT: Q 38 ASN cc_start: 0.9011 (t0) cc_final: 0.8334 (t0) REVERT: Q 44 ARG cc_start: 0.8268 (ttp80) cc_final: 0.7864 (tmm-80) REVERT: Q 48 TYR cc_start: 0.8744 (m-80) cc_final: 0.8411 (m-80) REVERT: Z 23 PHE cc_start: 0.7618 (m-80) cc_final: 0.7330 (m-80) REVERT: Z 71 ARG cc_start: 0.7935 (ttt90) cc_final: 0.7589 (ttm-80) REVERT: Z 78 ARG cc_start: 0.4704 (tmt170) cc_final: 0.4279 (tmt170) REVERT: Z 201 SER cc_start: 0.9027 (t) cc_final: 0.8777 (t) REVERT: Z 228 MET cc_start: 0.8444 (mmp) cc_final: 0.8158 (mmp) REVERT: Z 239 GLU cc_start: 0.9227 (tp30) cc_final: 0.8678 (tp30) REVERT: Z 242 LYS cc_start: 0.9170 (mttt) cc_final: 0.8611 (mttm) REVERT: Z 272 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8245 (tt) REVERT: Y 31 ARG cc_start: 0.9059 (tpp-160) cc_final: 0.8694 (tpp80) REVERT: T 239 GLU cc_start: 0.9074 (mm-30) cc_final: 0.8796 (mm-30) REVERT: T 253 ASN cc_start: 0.8750 (m-40) cc_final: 0.8317 (m110) REVERT: T 254 ILE cc_start: 0.8945 (mm) cc_final: 0.8546 (tt) REVERT: T 264 MET cc_start: 0.5864 (tpp) cc_final: 0.5453 (tpp) REVERT: T 272 LEU cc_start: 0.7507 (tp) cc_final: 0.7035 (tt) REVERT: T 287 GLN cc_start: 0.7542 (mt0) cc_final: 0.7211 (mt0) REVERT: T 291 PHE cc_start: 0.9237 (t80) cc_final: 0.8915 (t80) outliers start: 44 outliers final: 38 residues processed: 309 average time/residue: 0.0752 time to fit residues: 33.2599 Evaluate side-chains 319 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 278 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain K residue 18 ILE Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain L residue 38 ASN Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 53 ILE Chi-restraints excluded: chain N residue 66 ILE Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 66 ILE Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain Q residue 68 PHE Chi-restraints excluded: chain Z residue 26 TYR Chi-restraints excluded: chain Z residue 51 SER Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain Z residue 76 VAL Chi-restraints excluded: chain Z residue 80 LEU Chi-restraints excluded: chain Z residue 103 VAL Chi-restraints excluded: chain Z residue 126 LEU Chi-restraints excluded: chain Z residue 224 THR Chi-restraints excluded: chain Z residue 240 LEU Chi-restraints excluded: chain Z residue 254 ILE Chi-restraints excluded: chain Z residue 266 PHE Chi-restraints excluded: chain Z residue 272 LEU Chi-restraints excluded: chain Z residue 286 ILE Chi-restraints excluded: chain Y residue 20 LEU Chi-restraints excluded: chain Y residue 35 ASN Chi-restraints excluded: chain Y residue 56 GLU Chi-restraints excluded: chain V residue 25 LEU Chi-restraints excluded: chain V residue 36 LEU Chi-restraints excluded: chain T residue 84 MET Chi-restraints excluded: chain T residue 118 LEU Chi-restraints excluded: chain T residue 231 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 46 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 25 optimal weight: 0.0010 chunk 92 optimal weight: 0.0770 chunk 13 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 2 optimal weight: 0.5980 overall best weight: 0.4944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 97 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.124822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.090000 restraints weight = 19467.675| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.79 r_work: 0.3179 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 10165 Z= 0.142 Angle : 0.608 13.334 13835 Z= 0.309 Chirality : 0.046 0.465 1716 Planarity : 0.005 0.063 1745 Dihedral : 3.638 20.518 1428 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 4.64 % Allowed : 34.28 % Favored : 61.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.82 (0.23), residues: 1342 helix: 1.89 (0.15), residues: 1093 sheet: None (None), residues: 0 loop : -1.95 (0.38), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 37 TYR 0.015 0.002 TYR T 277 PHE 0.019 0.001 PHE O 55 TRP 0.019 0.002 TRP T 208 HIS 0.001 0.000 HIS Z 170 Details of bonding type rmsd covalent geometry : bond 0.00333 (10164) covalent geometry : angle 0.60758 (13833) SS BOND : bond 0.00015 ( 1) SS BOND : angle 0.74484 ( 2) hydrogen bonds : bond 0.03977 ( 876) hydrogen bonds : angle 3.62244 ( 2604) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2135.90 seconds wall clock time: 37 minutes 8.29 seconds (2228.29 seconds total)