Starting phenix.real_space_refine on Wed Sep 17 14:08:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9itx_60882/09_2025/9itx_60882.cif Found real_map, /net/cci-nas-00/data/ceres_data/9itx_60882/09_2025/9itx_60882.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9itx_60882/09_2025/9itx_60882.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9itx_60882/09_2025/9itx_60882.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9itx_60882/09_2025/9itx_60882.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9itx_60882/09_2025/9itx_60882.map" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 24 5.16 5 C 5933 2.51 5 N 1518 2.21 5 O 1606 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9081 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: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 517 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "Q" Number of atoms: 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: 2021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2021 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 244} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "Y" Number of atoms: 253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 253 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 2, 'TRANS': 47} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 176 Unresolved non-hydrogen angles: 224 Unresolved non-hydrogen dihedrals: 139 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'PHE:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 3, 'ARG:plan': 7, 'TYR:plan': 1, 'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 96 Chain: "V" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 195 Classifications: {'peptide': 39} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 2, 'TRANS': 36} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 183 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'ASN:plan1': 4, 'PHE:plan': 3, 'GLN:plan1': 1, 'ARG:plan': 5, 'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 70 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: 1109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1109 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 184} Link IDs: {'PTRANS': 10, 'TRANS': 214} Chain breaks: 1 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 711 Unresolved non-hydrogen angles: 929 Unresolved non-hydrogen dihedrals: 600 Unresolved non-hydrogen chiralities: 83 Planarities with less than four sites: {'ASN:plan1': 12, 'PHE:plan': 30, 'ASP:plan': 3, 'ARG:plan': 6, 'GLN:plan1': 4, 'GLU:plan': 7, 'TYR:plan': 6, 'TRP:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 369 Time building chain proxies: 2.55, per 1000 atoms: 0.28 Number of scatterers: 9081 At special positions: 0 Unit cell: (86.49, 130.2, 90.21, 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 24 16.00 O 1606 8.00 N 1518 7.00 C 5933 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.98 Conformation dependent library (CDL) restraints added in 420.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2420 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 1 sheets defined 85.9% alpha, 0.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'H' and resid 3 through 38 removed outlier: 4.021A 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: 4.029A pdb=" N THR H 47 " --> pdb=" O ASN H 43 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE H 55 " --> pdb=" O ILE H 51 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU H 59 " --> pdb=" O PHE H 55 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ALA H 60 " --> pdb=" O THR H 56 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 17 Processing helix chain 'I' and resid 17 through 38 Processing helix chain 'I' and resid 41 through 72 removed outlier: 3.597A pdb=" N TYR I 48 " --> pdb=" O ARG I 44 " (cutoff:3.500A) Processing helix chain 'J' and resid 3 through 38 removed outlier: 3.627A 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 72 removed outlier: 3.761A pdb=" N TYR J 48 " --> pdb=" O ARG J 44 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU J 59 " --> pdb=" O PHE J 55 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA J 60 " --> pdb=" O THR J 56 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 38 removed outlier: 3.751A pdb=" N VAL K 7 " --> pdb=" O GLY K 3 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA K 17 " --> pdb=" O VAL K 13 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE K 18 " --> pdb=" O GLY K 14 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLY K 19 " --> pdb=" O LEU K 15 " (cutoff:3.500A) Proline residue: K 20 - end of helix Processing helix chain 'K' and resid 41 through 72 removed outlier: 3.680A pdb=" N THR K 47 " --> pdb=" O ASN K 43 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N TYR K 48 " --> pdb=" O ARG K 44 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE K 51 " --> pdb=" O THR K 47 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU K 59 " --> pdb=" O PHE K 55 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA K 60 " --> pdb=" O THR K 56 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 16 Processing helix chain 'L' and resid 17 through 38 removed outlier: 3.840A pdb=" N VAL L 22 " --> pdb=" O ILE L 18 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 72 removed outlier: 3.762A pdb=" N THR L 47 " --> pdb=" O ASN L 43 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N TYR L 48 " --> pdb=" O ARG L 44 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 38 removed outlier: 3.695A pdb=" N ALA M 17 " --> pdb=" O VAL M 13 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE M 18 " --> pdb=" O GLY M 14 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N GLY M 19 " --> pdb=" O LEU M 15 " (cutoff:3.500A) Proline residue: M 20 - end of helix Processing helix chain 'M' and resid 41 through 72 removed outlier: 3.741A pdb=" N GLY M 63 " --> pdb=" O LEU M 59 " (cutoff:3.500A) removed outlier: 3.546A 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: 5.627A pdb=" N ILE N 24 " --> pdb=" O PRO N 20 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLY N 25 " --> pdb=" O GLY N 21 " (cutoff:3.500A) Processing helix chain 'N' and resid 41 through 72 removed outlier: 3.671A pdb=" N LEU N 59 " --> pdb=" O PHE N 55 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 38 removed outlier: 3.672A pdb=" N VAL O 7 " --> pdb=" O GLY O 3 " (cutoff:3.500A) removed outlier: 4.612A 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: 4.973A pdb=" N TYR O 48 " --> pdb=" O ARG O 44 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE O 70 " --> pdb=" O ILE O 66 " (cutoff:3.500A) Processing helix chain 'P' and resid 3 through 15 removed outlier: 3.657A pdb=" N VAL P 13 " --> pdb=" O THR P 9 " (cutoff:3.500A) Processing helix chain 'P' and resid 17 through 38 Processing helix chain 'P' and resid 41 through 73 removed outlier: 5.159A pdb=" N THR P 47 " --> pdb=" O ASN P 43 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N TYR P 48 " --> pdb=" O ARG P 44 " (cutoff:3.500A) Processing helix chain 'Q' and resid 3 through 16 removed outlier: 3.809A pdb=" N VAL Q 7 " --> pdb=" O GLY Q 3 " (cutoff:3.500A) Processing helix chain 'Q' and resid 17 through 38 removed outlier: 3.841A pdb=" N VAL Q 22 " --> pdb=" O ILE Q 18 " (cutoff:3.500A) Processing helix chain 'Q' and resid 44 through 72 removed outlier: 3.548A pdb=" N TYR Q 48 " --> pdb=" O ARG Q 44 " (cutoff:3.500A) removed outlier: 3.686A 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 125 Proline residue: Z 108 - end of helix removed outlier: 3.653A pdb=" N LEU Z 125 " --> pdb=" O ASN Z 121 " (cutoff:3.500A) Processing helix chain 'Z' and resid 172 through 176 Processing helix chain 'Z' and resid 186 through 189 Processing helix chain 'Z' and resid 190 through 212 removed outlier: 3.588A pdb=" N ALA Z 196 " --> pdb=" O ASN Z 192 " (cutoff:3.500A) Processing helix chain 'Z' and resid 227 through 267 removed outlier: 3.700A pdb=" N ILE Z 233 " --> pdb=" O SER Z 229 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE Z 234 " --> pdb=" O PHE Z 230 " (cutoff:3.500A) Proline residue: Z 243 - end of helix removed outlier: 4.007A pdb=" N GLY Z 257 " --> pdb=" O ASN Z 253 " (cutoff:3.500A) Processing helix chain 'Z' and resid 273 through 304 removed outlier: 3.673A 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 44 removed outlier: 3.501A pdb=" N THR V 41 " --> pdb=" O LEU V 37 " (cutoff:3.500A) Processing helix chain 'X' and resid 7 through 40 removed outlier: 4.378A 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: 3.684A pdb=" N LEU U 28 " --> pdb=" O ILE U 24 " (cutoff:3.500A) Proline residue: U 32 - end of helix removed outlier: 4.202A pdb=" N GLU U 45 " --> pdb=" O THR U 41 " (cutoff:3.500A) Processing helix chain 'T' and resid 49 through 72 removed outlier: 3.873A pdb=" N VAL T 53 " --> pdb=" O THR T 49 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL T 54 " --> pdb=" O ASN T 50 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ASN T 72 " --> pdb=" O ALA T 68 " (cutoff:3.500A) Processing helix chain 'T' and resid 79 through 100 Processing helix chain 'T' and resid 106 through 126 removed outlier: 3.723A pdb=" N LEU T 125 " --> pdb=" O ASN T 121 " (cutoff:3.500A) Processing helix chain 'T' and resid 186 through 190 removed outlier: 3.627A pdb=" N ASP T 190 " --> pdb=" O PRO T 187 " (cutoff:3.500A) Processing helix chain 'T' and resid 192 through 212 removed outlier: 3.583A pdb=" N ALA T 196 " --> pdb=" O ASN T 192 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE T 197 " --> pdb=" O PHE T 193 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA T 198 " --> pdb=" O THR T 194 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA T 212 " --> pdb=" O TRP T 208 " (cutoff:3.500A) Processing helix chain 'T' and resid 213 through 217 Processing helix chain 'T' and resid 228 through 268 Proline residue: T 243 - end of helix Processing helix chain 'T' and resid 273 through 304 removed outlier: 3.752A pdb=" N PHE T 279 " --> pdb=" O PRO T 275 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL T 281 " --> pdb=" O TYR T 277 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE T 282 " --> pdb=" O GLY T 278 " (cutoff:3.500A) removed outlier: 3.571A 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 134 899 hydrogen bonds defined for protein. 2676 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: 1.77 Time building geometry restraints manager: 1.24 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: 3023 1.34 - 1.46: 1412 1.46 - 1.57: 4721 1.57 - 1.69: 0 1.69 - 1.80: 48 Bond restraints: 9204 Sorted by residual: bond pdb=" N ILE J 70 " pdb=" CA ILE J 70 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.21e-02 6.83e+03 8.91e+00 bond pdb=" N VAL T 303 " pdb=" CA VAL T 303 " ideal model delta sigma weight residual 1.461 1.495 -0.035 1.19e-02 7.06e+03 8.53e+00 bond pdb=" N ILE K 70 " pdb=" CA ILE K 70 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.23e-02 6.61e+03 8.46e+00 bond pdb=" N ILE N 70 " pdb=" CA ILE N 70 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.19e-02 7.06e+03 8.23e+00 bond pdb=" N ILE T 301 " pdb=" CA ILE T 301 " ideal model delta sigma weight residual 1.461 1.494 -0.034 1.19e-02 7.06e+03 8.10e+00 ... (remaining 9199 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 12110 1.30 - 2.60: 375 2.60 - 3.89: 73 3.89 - 5.19: 8 5.19 - 6.49: 4 Bond angle restraints: 12570 Sorted by residual: angle pdb=" C ASP Z 171 " pdb=" CA ASP Z 171 " pdb=" CB ASP Z 171 " ideal model delta sigma weight residual 116.54 110.05 6.49 1.15e+00 7.56e-01 3.18e+01 angle pdb=" N ILE N 41 " pdb=" CA ILE N 41 " pdb=" C ILE N 41 " ideal model delta sigma weight residual 111.91 108.03 3.88 8.90e-01 1.26e+00 1.90e+01 angle pdb=" CA ASP Z 171 " pdb=" C ASP Z 171 " pdb=" N THR Z 172 " ideal model delta sigma weight residual 119.52 116.87 2.65 7.90e-01 1.60e+00 1.13e+01 angle pdb=" N ILE O 70 " pdb=" CA ILE O 70 " pdb=" C ILE O 70 " ideal model delta sigma weight residual 110.72 107.54 3.18 1.01e+00 9.80e-01 9.91e+00 angle pdb=" C LYS T 178 " pdb=" N LYS T 179 " pdb=" CA LYS T 179 " ideal model delta sigma weight residual 121.54 127.16 -5.62 1.91e+00 2.74e-01 8.65e+00 ... (remaining 12565 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 4907 17.41 - 34.83: 309 34.83 - 52.24: 26 52.24 - 69.66: 8 69.66 - 87.07: 6 Dihedral angle restraints: 5256 sinusoidal: 1469 harmonic: 3787 Sorted by residual: dihedral pdb=" CA LEU Z 270 " pdb=" C LEU Z 270 " pdb=" N LEU Z 271 " pdb=" CA LEU Z 271 " ideal model delta harmonic sigma weight residual 180.00 162.96 17.04 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CB GLU Z 89 " pdb=" CG GLU Z 89 " pdb=" CD GLU Z 89 " pdb=" OE1 GLU Z 89 " ideal model delta sinusoidal sigma weight residual 0.00 -83.29 83.29 1 3.00e+01 1.11e-03 9.42e+00 dihedral pdb=" CB GLU Q 42 " pdb=" CG GLU Q 42 " pdb=" CD GLU Q 42 " pdb=" OE1 GLU Q 42 " ideal model delta sinusoidal sigma weight residual 0.00 83.12 -83.12 1 3.00e+01 1.11e-03 9.39e+00 ... (remaining 5253 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1218 0.047 - 0.094: 329 0.094 - 0.141: 38 0.141 - 0.189: 3 0.189 - 0.236: 8 Chirality restraints: 1596 Sorted by residual: 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 2.67 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CB ILE Q 41 " pdb=" CA ILE Q 41 " pdb=" CG1 ILE Q 41 " pdb=" CG2 ILE Q 41 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CA ILE T 301 " pdb=" N ILE T 301 " pdb=" C ILE T 301 " pdb=" CB ILE T 301 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 1593 not shown) Planarity restraints: 1626 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY N 19 " 0.036 5.00e-02 4.00e+02 5.49e-02 4.83e+00 pdb=" N PRO N 20 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO N 20 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO N 20 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY L 19 " 0.036 5.00e-02 4.00e+02 5.45e-02 4.75e+00 pdb=" N PRO L 20 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO L 20 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO L 20 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY O 19 " -0.035 5.00e-02 4.00e+02 5.32e-02 4.53e+00 pdb=" N PRO O 20 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO O 20 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO O 20 " -0.030 5.00e-02 4.00e+02 ... (remaining 1623 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 1867 2.78 - 3.31: 10103 3.31 - 3.84: 16051 3.84 - 4.37: 16396 4.37 - 4.90: 29318 Nonbonded interactions: 73735 Sorted by model distance: nonbonded pdb=" O ARG I 44 " pdb=" OG1 THR I 47 " model vdw 2.245 3.040 nonbonded pdb=" N MET K 1 " pdb=" O MET L 1 " model vdw 2.256 3.120 nonbonded pdb=" OH TYR I 48 " pdb=" OE2 GLU J 42 " model vdw 2.263 3.040 nonbonded pdb=" OH TYR H 48 " pdb=" OE2 GLU I 42 " model vdw 2.268 3.040 nonbonded pdb=" O ASN Z 223 " pdb=" OG SER Z 229 " model vdw 2.301 3.040 ... (remaining 73730 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' and resid 1 through 72) selection = chain 'Q' } ncs_group { reference = (chain 'T' and (resid 47 through 134 or resid 136 or resid 171 through 304)) selection = (chain 'Z' and ((resid 47 through 78 and (name N or name CA or name C or name O \ or name CB )) or resid 79 or (resid 80 through 119 and (name N or name CA or nam \ e C or name O or name CB )) or resid 120 or (resid 121 through 123 and (name N o \ r name CA or name C or name O or name CB )) or resid 124 or (resid 125 through 1 \ 27 and (name N or name CA or name C or name O or name CB )) or resid 128 or (res \ id 129 and (name N or name CA or name C or name O or name CB )) 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 170 through 176 and (name N or name CA or name C or name O or name \ CB )) or resid 177 or (resid 178 through 208 and (name N or name CA or name C o \ r name O or name CB )) or resid 209 or (resid 210 through 213 and (name N or nam \ e CA or name C or name O or name CB )) or resid 214 or (resid 215 and (name N or \ name CA or name C or name O or name CB )) or resid 216 or (resid 217 through 22 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 226 or (resi \ d 227 through 231 and (name N or name CA or name C or name O or name CB )) or re \ sid 232 or (resid 233 through 251 and (name N or name CA or name C or name O or \ name CB )) or resid 252 or (resid 253 through 256 and (name N or name CA or name \ C or name O or name CB )) or resid 257 or (resid 258 through 277 and (name N or \ name CA or name C or name O or name CB )) or resid 278 or (resid 279 through 28 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 284 or (resi \ d 285 through 304 and (name N or name CA or name C or name O or name CB )))) } ncs_group { reference = (chain 'U' and resid 8 through 40) selection = (chain 'V' and resid 8 through 40) selection = (chain 'X' and resid 8 through 40) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.140 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 11.130 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 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 : 0.003 0.036 9204 Z= 0.193 Angle : 0.549 6.490 12570 Z= 0.364 Chirality : 0.042 0.236 1596 Planarity : 0.004 0.055 1626 Dihedral : 11.863 87.072 2836 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.91 (0.23), residues: 1332 helix: 2.57 (0.15), residues: 1103 sheet: None (None), residues: 0 loop : -1.49 (0.42), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG M 44 TYR 0.007 0.001 TYR Z 296 PHE 0.020 0.001 PHE Z 276 TRP 0.007 0.001 TRP Z 122 HIS 0.002 0.001 HIS Z 170 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 9204) covalent geometry : angle 0.54867 (12570) hydrogen bonds : bond 0.11572 ( 899) hydrogen bonds : angle 4.37367 ( 2676) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 422 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 27 ILE cc_start: 0.9479 (mt) cc_final: 0.9132 (mt) REVERT: H 38 ASN cc_start: 0.9442 (t0) cc_final: 0.9083 (t0) REVERT: H 48 TYR cc_start: 0.9009 (m-80) cc_final: 0.8756 (m-80) REVERT: H 49 MET cc_start: 0.9581 (ttp) cc_final: 0.9277 (tmm) REVERT: H 50 PHE cc_start: 0.9535 (m-80) cc_final: 0.9218 (m-80) REVERT: H 57 GLU cc_start: 0.9705 (tp30) cc_final: 0.9385 (tp30) REVERT: I 7 VAL cc_start: 0.9780 (p) cc_final: 0.9579 (m) REVERT: I 15 LEU cc_start: 0.9405 (mt) cc_final: 0.9120 (tp) REVERT: I 27 ILE cc_start: 0.9659 (mt) cc_final: 0.9166 (mt) REVERT: I 28 VAL cc_start: 0.9640 (t) cc_final: 0.9376 (m) REVERT: I 35 ILE cc_start: 0.9485 (mm) cc_final: 0.9253 (tp) REVERT: I 49 MET cc_start: 0.9358 (ttp) cc_final: 0.8951 (tmm) REVERT: I 55 PHE cc_start: 0.9514 (m-80) cc_final: 0.9219 (m-80) REVERT: J 1 MET cc_start: 0.7389 (mmt) cc_final: 0.6327 (mmt) REVERT: J 18 ILE cc_start: 0.9302 (mt) cc_final: 0.8937 (mt) REVERT: J 27 ILE cc_start: 0.9456 (mt) cc_final: 0.8996 (mt) REVERT: J 48 TYR cc_start: 0.9263 (m-80) cc_final: 0.8628 (m-80) REVERT: J 49 MET cc_start: 0.9618 (ttp) cc_final: 0.9316 (tmm) REVERT: J 53 ILE cc_start: 0.9639 (mt) cc_final: 0.9364 (mm) REVERT: K 15 LEU cc_start: 0.9808 (mt) cc_final: 0.9540 (tp) REVERT: K 18 ILE cc_start: 0.9427 (pt) cc_final: 0.9181 (tp) REVERT: K 41 ILE cc_start: 0.9515 (tp) cc_final: 0.9277 (tp) REVERT: K 44 ARG cc_start: 0.9344 (tpp80) cc_final: 0.8822 (mmm-85) REVERT: K 48 TYR cc_start: 0.9366 (m-80) cc_final: 0.8875 (m-80) REVERT: K 55 PHE cc_start: 0.9616 (m-80) cc_final: 0.9212 (m-80) REVERT: K 68 PHE cc_start: 0.9735 (m-10) cc_final: 0.9348 (m-80) REVERT: L 1 MET cc_start: 0.9026 (mtp) cc_final: 0.7944 (mtt) REVERT: L 27 ILE cc_start: 0.9691 (mt) cc_final: 0.9224 (mt) REVERT: L 43 ASN cc_start: 0.9488 (m-40) cc_final: 0.9130 (p0) REVERT: L 49 MET cc_start: 0.9763 (ttp) cc_final: 0.9412 (tmm) REVERT: L 50 PHE cc_start: 0.9651 (m-80) cc_final: 0.9126 (m-80) REVERT: L 57 GLU cc_start: 0.9547 (tp30) cc_final: 0.9221 (pt0) REVERT: M 4 LEU cc_start: 0.9571 (tp) cc_final: 0.9357 (tp) REVERT: M 41 ILE cc_start: 0.9308 (tp) cc_final: 0.8755 (tp) REVERT: M 49 MET cc_start: 0.9664 (ttp) cc_final: 0.9183 (tpt) REVERT: N 15 LEU cc_start: 0.9651 (mt) cc_final: 0.9374 (tp) REVERT: N 24 ILE cc_start: 0.9398 (mt) cc_final: 0.9101 (tt) REVERT: N 33 GLN cc_start: 0.9708 (mt0) cc_final: 0.9354 (mt0) REVERT: N 40 GLU cc_start: 0.9449 (pt0) cc_final: 0.9198 (pp20) REVERT: N 51 ILE cc_start: 0.8933 (mm) cc_final: 0.8509 (mt) REVERT: N 55 PHE cc_start: 0.9698 (m-80) cc_final: 0.9149 (m-80) REVERT: N 57 GLU cc_start: 0.9510 (mm-30) cc_final: 0.9177 (pt0) REVERT: N 64 LEU cc_start: 0.9691 (tp) cc_final: 0.9470 (mt) REVERT: O 1 MET cc_start: 0.7082 (mpp) cc_final: 0.6727 (mmt) REVERT: O 4 LEU cc_start: 0.9703 (tp) cc_final: 0.9501 (tp) REVERT: O 29 SER cc_start: 0.9526 (t) cc_final: 0.9165 (m) REVERT: O 32 VAL cc_start: 0.9677 (p) cc_final: 0.9239 (m) REVERT: O 33 GLN cc_start: 0.9485 (mt0) cc_final: 0.9050 (mm110) REVERT: O 37 ARG cc_start: 0.9042 (mtt180) cc_final: 0.8663 (mtt180) REVERT: O 50 PHE cc_start: 0.9413 (m-80) cc_final: 0.9148 (m-80) REVERT: O 56 THR cc_start: 0.9238 (m) cc_final: 0.9022 (t) REVERT: O 57 GLU cc_start: 0.9462 (mm-30) cc_final: 0.8824 (pt0) REVERT: O 62 PHE cc_start: 0.8733 (m-10) cc_final: 0.8346 (m-80) REVERT: O 64 LEU cc_start: 0.9680 (tt) cc_final: 0.9371 (mt) REVERT: P 49 MET cc_start: 0.9339 (ttp) cc_final: 0.8970 (tmm) REVERT: P 61 ILE cc_start: 0.9427 (mm) cc_final: 0.9192 (mm) REVERT: P 68 PHE cc_start: 0.9198 (m-80) cc_final: 0.8938 (m-80) REVERT: Q 4 LEU cc_start: 0.9682 (tp) cc_final: 0.9467 (tt) REVERT: Q 18 ILE cc_start: 0.9612 (pt) cc_final: 0.9145 (mm) REVERT: Q 27 ILE cc_start: 0.9691 (mt) cc_final: 0.9480 (mt) REVERT: Q 50 PHE cc_start: 0.9656 (m-80) cc_final: 0.9337 (m-80) REVERT: Q 62 PHE cc_start: 0.9589 (m-10) cc_final: 0.9359 (m-80) REVERT: Z 84 MET cc_start: 0.9357 (mmt) cc_final: 0.9111 (mmm) REVERT: Z 95 PHE cc_start: 0.9543 (m-10) cc_final: 0.9198 (m-80) REVERT: Z 123 PHE cc_start: 0.9602 (t80) cc_final: 0.9172 (t80) REVERT: Z 132 ILE cc_start: 0.9181 (mt) cc_final: 0.8909 (mm) REVERT: Z 191 LEU cc_start: 0.9538 (mt) cc_final: 0.9310 (pp) REVERT: Z 207 TYR cc_start: 0.8116 (t80) cc_final: 0.7717 (t80) REVERT: Z 248 PHE cc_start: 0.9640 (m-10) cc_final: 0.9221 (m-80) REVERT: Z 249 ARG cc_start: 0.9699 (ttm-80) cc_final: 0.9013 (ttm-80) REVERT: Z 253 ASN cc_start: 0.9427 (t0) cc_final: 0.9088 (m-40) REVERT: Z 258 GLU cc_start: 0.9482 (tt0) cc_final: 0.9153 (tm-30) REVERT: Z 264 MET cc_start: 0.9187 (ttm) cc_final: 0.8945 (tpt) REVERT: Z 280 GLU cc_start: 0.9489 (mm-30) cc_final: 0.9230 (mm-30) REVERT: Z 282 PHE cc_start: 0.9602 (t80) cc_final: 0.9225 (t80) outliers start: 0 outliers final: 0 residues processed: 422 average time/residue: 0.0827 time to fit residues: 50.9143 Evaluate side-chains 312 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 312 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 30.0000 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 33 GLN ** N 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 33 GLN ** Z 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.067813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.053253 restraints weight = 53484.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.054459 restraints weight = 40988.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.055319 restraints weight = 33184.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.055862 restraints weight = 28148.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.056403 restraints weight = 25102.479| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9204 Z= 0.176 Angle : 0.578 6.678 12570 Z= 0.316 Chirality : 0.045 0.238 1596 Planarity : 0.005 0.060 1626 Dihedral : 3.667 19.811 1394 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.42 % Allowed : 4.23 % Favored : 95.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.24 (0.23), residues: 1332 helix: 2.12 (0.15), residues: 1105 sheet: None (None), residues: 0 loop : -1.84 (0.42), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG P 44 TYR 0.014 0.001 TYR O 48 PHE 0.026 0.002 PHE M 55 TRP 0.006 0.001 TRP Z 208 HIS 0.003 0.002 HIS Z 31 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 9204) covalent geometry : angle 0.57848 (12570) hydrogen bonds : bond 0.04327 ( 899) hydrogen bonds : angle 3.93314 ( 2676) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 365 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 27 ILE cc_start: 0.9368 (mt) cc_final: 0.8945 (mt) REVERT: H 38 ASN cc_start: 0.9348 (t0) cc_final: 0.9082 (t0) REVERT: H 48 TYR cc_start: 0.9163 (m-80) cc_final: 0.8639 (m-80) REVERT: H 49 MET cc_start: 0.9691 (ttp) cc_final: 0.9411 (tmm) REVERT: H 50 PHE cc_start: 0.9639 (m-80) cc_final: 0.9163 (m-80) REVERT: H 57 GLU cc_start: 0.9748 (tp30) cc_final: 0.9434 (tp30) REVERT: H 64 LEU cc_start: 0.9772 (mm) cc_final: 0.9552 (mt) REVERT: I 28 VAL cc_start: 0.9576 (t) cc_final: 0.9336 (m) REVERT: I 42 GLU cc_start: 0.9384 (tt0) cc_final: 0.8988 (tp30) REVERT: I 49 MET cc_start: 0.9367 (ttp) cc_final: 0.8927 (tmm) REVERT: I 55 PHE cc_start: 0.9476 (m-80) cc_final: 0.9090 (m-80) REVERT: J 1 MET cc_start: 0.8299 (mmt) cc_final: 0.7166 (mmt) REVERT: J 48 TYR cc_start: 0.9407 (m-80) cc_final: 0.8790 (m-80) REVERT: J 53 ILE cc_start: 0.9626 (mt) cc_final: 0.9377 (mt) REVERT: K 15 LEU cc_start: 0.9794 (mt) cc_final: 0.9507 (tp) REVERT: K 18 ILE cc_start: 0.9450 (pt) cc_final: 0.9121 (tp) REVERT: K 33 GLN cc_start: 0.9496 (mt0) cc_final: 0.8978 (mm110) REVERT: K 44 ARG cc_start: 0.9495 (tpp80) cc_final: 0.9137 (tpp80) REVERT: K 48 TYR cc_start: 0.9588 (m-80) cc_final: 0.9150 (m-80) REVERT: K 49 MET cc_start: 0.9650 (ttp) cc_final: 0.9406 (ptt) REVERT: K 55 PHE cc_start: 0.9607 (m-80) cc_final: 0.9285 (m-80) REVERT: K 68 PHE cc_start: 0.9572 (m-10) cc_final: 0.9255 (m-80) REVERT: L 1 MET cc_start: 0.8861 (mtp) cc_final: 0.8094 (mtt) REVERT: L 43 ASN cc_start: 0.9408 (m-40) cc_final: 0.9070 (p0) REVERT: L 49 MET cc_start: 0.9791 (ttp) cc_final: 0.9382 (tmm) REVERT: L 50 PHE cc_start: 0.9612 (m-80) cc_final: 0.9148 (m-80) REVERT: L 51 ILE cc_start: 0.9865 (mt) cc_final: 0.9590 (mt) REVERT: L 53 ILE cc_start: 0.9805 (tt) cc_final: 0.9489 (tt) REVERT: L 55 PHE cc_start: 0.9542 (m-80) cc_final: 0.9129 (m-80) REVERT: L 57 GLU cc_start: 0.9503 (tp30) cc_final: 0.9134 (pt0) REVERT: M 11 LEU cc_start: 0.9815 (mt) cc_final: 0.9542 (tt) REVERT: M 15 LEU cc_start: 0.9563 (mt) cc_final: 0.9362 (mt) REVERT: M 27 ILE cc_start: 0.9788 (mt) cc_final: 0.9570 (mt) REVERT: M 33 GLN cc_start: 0.9433 (pm20) cc_final: 0.9058 (pm20) REVERT: M 49 MET cc_start: 0.9534 (ttp) cc_final: 0.9308 (tmm) REVERT: M 50 PHE cc_start: 0.9383 (m-80) cc_final: 0.8698 (m-80) REVERT: M 59 LEU cc_start: 0.9413 (tp) cc_final: 0.9107 (mt) REVERT: N 11 LEU cc_start: 0.9792 (mm) cc_final: 0.9521 (mm) REVERT: N 32 VAL cc_start: 0.9765 (p) cc_final: 0.9316 (p) REVERT: O 4 LEU cc_start: 0.9739 (tp) cc_final: 0.9523 (tp) REVERT: O 29 SER cc_start: 0.9486 (t) cc_final: 0.9097 (p) REVERT: O 32 VAL cc_start: 0.9586 (p) cc_final: 0.9150 (m) REVERT: O 33 GLN cc_start: 0.9421 (mt0) cc_final: 0.8988 (mm110) REVERT: O 37 ARG cc_start: 0.8973 (mtt180) cc_final: 0.8593 (mtt180) REVERT: O 53 ILE cc_start: 0.9484 (tt) cc_final: 0.9236 (tp) REVERT: O 56 THR cc_start: 0.9269 (m) cc_final: 0.9062 (p) REVERT: O 57 GLU cc_start: 0.9422 (mm-30) cc_final: 0.8813 (pt0) REVERT: O 62 PHE cc_start: 0.8685 (m-10) cc_final: 0.8372 (m-80) REVERT: O 64 LEU cc_start: 0.9742 (tt) cc_final: 0.9386 (mt) REVERT: P 33 GLN cc_start: 0.9525 (mt0) cc_final: 0.9203 (mt0) REVERT: P 49 MET cc_start: 0.9527 (ttp) cc_final: 0.9000 (tmm) REVERT: P 61 ILE cc_start: 0.9440 (mm) cc_final: 0.9131 (mm) REVERT: P 68 PHE cc_start: 0.9243 (m-80) cc_final: 0.8934 (m-80) REVERT: Q 18 ILE cc_start: 0.9508 (pt) cc_final: 0.9102 (mm) REVERT: Q 33 GLN cc_start: 0.9130 (mm-40) cc_final: 0.8652 (mm110) REVERT: Q 37 ARG cc_start: 0.9245 (mtt180) cc_final: 0.7989 (ttm110) REVERT: Q 50 PHE cc_start: 0.9625 (m-80) cc_final: 0.9307 (m-80) REVERT: Q 61 ILE cc_start: 0.9591 (mm) cc_final: 0.9382 (mm) REVERT: Q 62 PHE cc_start: 0.9577 (m-10) cc_final: 0.9303 (m-80) REVERT: Z 84 MET cc_start: 0.9326 (mmt) cc_final: 0.9091 (mmm) REVERT: Z 95 PHE cc_start: 0.9556 (m-10) cc_final: 0.9220 (m-80) REVERT: Z 123 PHE cc_start: 0.9550 (t80) cc_final: 0.9205 (t80) REVERT: Z 132 ILE cc_start: 0.9203 (mt) cc_final: 0.8940 (mm) REVERT: Z 191 LEU cc_start: 0.9422 (mt) cc_final: 0.9211 (pp) REVERT: Z 207 TYR cc_start: 0.8137 (t80) cc_final: 0.7751 (t80) REVERT: Z 228 MET cc_start: 0.9232 (ptt) cc_final: 0.8998 (ptt) REVERT: Z 248 PHE cc_start: 0.9543 (m-10) cc_final: 0.9186 (m-80) REVERT: Z 249 ARG cc_start: 0.9732 (ttm-80) cc_final: 0.8976 (ttm-80) REVERT: Z 253 ASN cc_start: 0.9396 (t0) cc_final: 0.9115 (m110) REVERT: Z 280 GLU cc_start: 0.9416 (mm-30) cc_final: 0.8953 (mm-30) REVERT: Z 282 PHE cc_start: 0.9604 (t80) cc_final: 0.9191 (t80) REVERT: Z 289 LEU cc_start: 0.9770 (mt) cc_final: 0.9559 (mt) outliers start: 3 outliers final: 1 residues processed: 366 average time/residue: 0.0787 time to fit residues: 42.3380 Evaluate side-chains 298 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 297 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 97 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 114 optimal weight: 20.0000 chunk 57 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 121 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 287 GLN ** 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 = 0.3498 r_free = 0.3498 target = 0.066519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.052304 restraints weight = 54146.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.053456 restraints weight = 41338.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.054287 restraints weight = 33425.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.054798 restraints weight = 28465.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.055286 restraints weight = 25434.663| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9204 Z= 0.200 Angle : 0.584 6.451 12570 Z= 0.323 Chirality : 0.044 0.168 1596 Planarity : 0.005 0.063 1626 Dihedral : 3.801 19.357 1394 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.42 % Allowed : 3.80 % Favored : 95.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.91 (0.23), residues: 1332 helix: 1.88 (0.15), residues: 1101 sheet: None (None), residues: 0 loop : -1.79 (0.42), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 37 TYR 0.018 0.002 TYR I 48 PHE 0.030 0.002 PHE M 55 TRP 0.008 0.001 TRP Z 208 HIS 0.004 0.002 HIS Z 31 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 9204) covalent geometry : angle 0.58385 (12570) hydrogen bonds : bond 0.04274 ( 899) hydrogen bonds : angle 4.02493 ( 2676) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 353 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 27 ILE cc_start: 0.9374 (mt) cc_final: 0.8999 (mt) REVERT: H 48 TYR cc_start: 0.9135 (m-80) cc_final: 0.8892 (m-10) REVERT: H 49 MET cc_start: 0.9730 (ttp) cc_final: 0.9390 (tmm) REVERT: H 50 PHE cc_start: 0.9610 (m-80) cc_final: 0.9157 (m-80) REVERT: H 57 GLU cc_start: 0.9728 (tp30) cc_final: 0.9470 (tp30) REVERT: H 64 LEU cc_start: 0.9776 (mm) cc_final: 0.9510 (mt) REVERT: I 28 VAL cc_start: 0.9554 (t) cc_final: 0.9350 (m) REVERT: I 49 MET cc_start: 0.9431 (ttp) cc_final: 0.8921 (tmm) REVERT: I 55 PHE cc_start: 0.9500 (m-80) cc_final: 0.9179 (m-80) REVERT: J 18 ILE cc_start: 0.9356 (mt) cc_final: 0.8997 (mt) REVERT: J 48 TYR cc_start: 0.9425 (m-80) cc_final: 0.8807 (m-80) REVERT: J 49 MET cc_start: 0.9559 (tmm) cc_final: 0.9231 (tmm) REVERT: K 15 LEU cc_start: 0.9795 (mt) cc_final: 0.9554 (tp) REVERT: K 22 VAL cc_start: 0.9259 (p) cc_final: 0.9056 (p) REVERT: K 44 ARG cc_start: 0.9475 (tpp80) cc_final: 0.8912 (tpp80) REVERT: K 48 TYR cc_start: 0.9642 (m-80) cc_final: 0.8957 (m-80) REVERT: K 55 PHE cc_start: 0.9621 (m-80) cc_final: 0.9316 (m-80) REVERT: K 68 PHE cc_start: 0.9457 (m-10) cc_final: 0.9174 (m-80) REVERT: L 1 MET cc_start: 0.9020 (mtp) cc_final: 0.8329 (mtt) REVERT: L 33 GLN cc_start: 0.9339 (pt0) cc_final: 0.9027 (pt0) REVERT: L 50 PHE cc_start: 0.9631 (m-80) cc_final: 0.9299 (m-10) REVERT: L 51 ILE cc_start: 0.9862 (mt) cc_final: 0.9571 (mt) REVERT: L 53 ILE cc_start: 0.9808 (tt) cc_final: 0.9431 (tp) REVERT: L 55 PHE cc_start: 0.9527 (m-80) cc_final: 0.9062 (m-80) REVERT: L 57 GLU cc_start: 0.9550 (tp30) cc_final: 0.9179 (pt0) REVERT: N 1 MET cc_start: 0.6516 (tpt) cc_final: 0.5733 (tpt) REVERT: N 11 LEU cc_start: 0.9824 (mm) cc_final: 0.9529 (mm) REVERT: N 32 VAL cc_start: 0.9740 (p) cc_final: 0.9531 (p) REVERT: N 33 GLN cc_start: 0.9138 (mp10) cc_final: 0.8923 (mp10) REVERT: N 55 PHE cc_start: 0.9640 (m-80) cc_final: 0.9172 (m-80) REVERT: O 20 PRO cc_start: 0.9063 (Cg_exo) cc_final: 0.8858 (Cg_endo) REVERT: O 29 SER cc_start: 0.9514 (t) cc_final: 0.9152 (p) REVERT: O 32 VAL cc_start: 0.9619 (p) cc_final: 0.9175 (m) REVERT: O 33 GLN cc_start: 0.9447 (mt0) cc_final: 0.9008 (mm-40) REVERT: O 57 GLU cc_start: 0.9408 (mm-30) cc_final: 0.8838 (pt0) REVERT: O 62 PHE cc_start: 0.8706 (m-10) cc_final: 0.8488 (m-80) REVERT: O 64 LEU cc_start: 0.9676 (tt) cc_final: 0.9407 (mt) REVERT: P 33 GLN cc_start: 0.9628 (mt0) cc_final: 0.9410 (mm-40) REVERT: P 49 MET cc_start: 0.9500 (ttp) cc_final: 0.9055 (tmm) REVERT: P 68 PHE cc_start: 0.9239 (m-80) cc_final: 0.8907 (m-80) REVERT: Q 18 ILE cc_start: 0.9485 (pt) cc_final: 0.9085 (mm) REVERT: Q 27 ILE cc_start: 0.9546 (mt) cc_final: 0.9307 (mt) REVERT: Q 33 GLN cc_start: 0.9282 (mm-40) cc_final: 0.8927 (mm110) REVERT: Q 49 MET cc_start: 0.9410 (ttp) cc_final: 0.9178 (tmm) REVERT: Q 50 PHE cc_start: 0.9647 (m-80) cc_final: 0.9163 (m-80) REVERT: Q 57 GLU cc_start: 0.9397 (mt-10) cc_final: 0.8914 (mt-10) REVERT: Q 62 PHE cc_start: 0.9529 (m-10) cc_final: 0.9271 (m-80) REVERT: Z 84 MET cc_start: 0.9346 (mmt) cc_final: 0.9113 (mmm) REVERT: Z 95 PHE cc_start: 0.9578 (m-10) cc_final: 0.9158 (m-80) REVERT: Z 123 PHE cc_start: 0.9578 (t80) cc_final: 0.9253 (t80) REVERT: Z 132 ILE cc_start: 0.9184 (mt) cc_final: 0.8917 (mm) REVERT: Z 207 TYR cc_start: 0.8098 (t80) cc_final: 0.7713 (t80) REVERT: Z 228 MET cc_start: 0.9198 (ptt) cc_final: 0.8956 (ptt) REVERT: Z 248 PHE cc_start: 0.9610 (m-10) cc_final: 0.9108 (m-80) REVERT: Z 249 ARG cc_start: 0.9733 (ttm170) cc_final: 0.9336 (ttt180) REVERT: Z 258 GLU cc_start: 0.9304 (tm-30) cc_final: 0.8907 (tm-30) REVERT: Z 282 PHE cc_start: 0.9611 (t80) cc_final: 0.9236 (t80) REVERT: Z 287 GLN cc_start: 0.9648 (mm110) cc_final: 0.9238 (mm110) REVERT: Z 289 LEU cc_start: 0.9797 (mt) cc_final: 0.9562 (mt) outliers start: 3 outliers final: 0 residues processed: 353 average time/residue: 0.0739 time to fit residues: 38.9202 Evaluate side-chains 293 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 293 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 121 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 109 optimal weight: 30.0000 chunk 30 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 253 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 = 0.3508 r_free = 0.3508 target = 0.066490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.051932 restraints weight = 54629.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.053099 restraints weight = 41645.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.053933 restraints weight = 33577.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.054553 restraints weight = 28539.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.055067 restraints weight = 25136.139| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9204 Z= 0.156 Angle : 0.589 8.173 12570 Z= 0.313 Chirality : 0.044 0.181 1596 Planarity : 0.005 0.068 1626 Dihedral : 3.758 19.194 1394 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.42 % Allowed : 4.37 % Favored : 95.21 % 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: 1.88 (0.23), residues: 1332 helix: 1.86 (0.15), residues: 1101 sheet: None (None), residues: 0 loop : -1.77 (0.41), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG P 44 TYR 0.019 0.002 TYR I 48 PHE 0.027 0.001 PHE H 62 TRP 0.007 0.001 TRP Z 208 HIS 0.002 0.002 HIS Z 170 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 9204) covalent geometry : angle 0.58880 (12570) hydrogen bonds : bond 0.04129 ( 899) hydrogen bonds : angle 3.94226 ( 2676) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 345 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 38 ASN cc_start: 0.9398 (t0) cc_final: 0.8974 (t0) REVERT: H 48 TYR cc_start: 0.9157 (m-80) cc_final: 0.8917 (m-10) REVERT: H 49 MET cc_start: 0.9700 (ttp) cc_final: 0.9395 (tmm) REVERT: H 50 PHE cc_start: 0.9583 (m-80) cc_final: 0.9145 (m-80) REVERT: H 57 GLU cc_start: 0.9757 (tp30) cc_final: 0.9335 (tp30) REVERT: I 35 ILE cc_start: 0.9371 (mm) cc_final: 0.9138 (tp) REVERT: I 42 GLU cc_start: 0.9465 (tt0) cc_final: 0.9231 (tt0) REVERT: I 49 MET cc_start: 0.9437 (ttp) cc_final: 0.8917 (tmm) REVERT: I 55 PHE cc_start: 0.9498 (m-80) cc_final: 0.9161 (m-80) REVERT: J 48 TYR cc_start: 0.9357 (m-80) cc_final: 0.8745 (m-80) REVERT: J 49 MET cc_start: 0.9475 (tmm) cc_final: 0.9164 (tmm) REVERT: K 15 LEU cc_start: 0.9814 (mt) cc_final: 0.9522 (tp) REVERT: K 18 ILE cc_start: 0.9480 (pt) cc_final: 0.9191 (tp) REVERT: K 22 VAL cc_start: 0.9226 (p) cc_final: 0.9008 (p) REVERT: K 33 GLN cc_start: 0.9488 (mt0) cc_final: 0.8992 (mm110) REVERT: K 44 ARG cc_start: 0.9424 (tpp80) cc_final: 0.9150 (tpp80) REVERT: K 55 PHE cc_start: 0.9604 (m-80) cc_final: 0.9186 (m-80) REVERT: K 68 PHE cc_start: 0.9454 (m-10) cc_final: 0.9174 (m-80) REVERT: L 24 ILE cc_start: 0.9829 (mt) cc_final: 0.9599 (mt) REVERT: L 50 PHE cc_start: 0.9603 (m-80) cc_final: 0.9316 (m-10) REVERT: L 51 ILE cc_start: 0.9848 (mt) cc_final: 0.9556 (mt) REVERT: L 53 ILE cc_start: 0.9790 (tt) cc_final: 0.9511 (tp) REVERT: L 55 PHE cc_start: 0.9529 (m-80) cc_final: 0.8998 (m-80) REVERT: M 27 ILE cc_start: 0.9731 (mt) cc_final: 0.9474 (mt) REVERT: M 50 PHE cc_start: 0.9555 (m-80) cc_final: 0.9024 (m-80) REVERT: M 59 LEU cc_start: 0.9395 (mt) cc_final: 0.9177 (mt) REVERT: N 1 MET cc_start: 0.6189 (tpt) cc_final: 0.5814 (tpt) REVERT: N 55 PHE cc_start: 0.9631 (m-80) cc_final: 0.9074 (m-80) REVERT: O 29 SER cc_start: 0.9533 (t) cc_final: 0.9213 (p) REVERT: O 32 VAL cc_start: 0.9639 (p) cc_final: 0.9239 (m) REVERT: O 33 GLN cc_start: 0.9468 (mt0) cc_final: 0.9087 (mm-40) REVERT: O 37 ARG cc_start: 0.9088 (mtt180) cc_final: 0.8633 (mtm180) REVERT: O 57 GLU cc_start: 0.9348 (mm-30) cc_final: 0.8774 (pt0) REVERT: O 62 PHE cc_start: 0.8683 (m-10) cc_final: 0.8333 (m-80) REVERT: O 64 LEU cc_start: 0.9744 (tt) cc_final: 0.9406 (mt) REVERT: P 33 GLN cc_start: 0.9616 (mt0) cc_final: 0.9170 (mm110) REVERT: P 49 MET cc_start: 0.9502 (ttp) cc_final: 0.9045 (tmm) REVERT: P 68 PHE cc_start: 0.9184 (m-80) cc_final: 0.8811 (m-80) REVERT: Q 18 ILE cc_start: 0.9482 (pt) cc_final: 0.9187 (mm) REVERT: Q 27 ILE cc_start: 0.9563 (mt) cc_final: 0.9321 (mt) REVERT: Q 33 GLN cc_start: 0.9284 (mm-40) cc_final: 0.8921 (mm110) REVERT: Q 49 MET cc_start: 0.9311 (ttp) cc_final: 0.9107 (tmm) REVERT: Q 50 PHE cc_start: 0.9630 (m-80) cc_final: 0.9175 (m-80) REVERT: Q 55 PHE cc_start: 0.9551 (m-80) cc_final: 0.9157 (m-80) REVERT: Q 62 PHE cc_start: 0.9567 (m-10) cc_final: 0.9295 (m-80) REVERT: Z 80 LEU cc_start: 0.9197 (mm) cc_final: 0.8976 (pt) REVERT: Z 84 MET cc_start: 0.9267 (mmt) cc_final: 0.9059 (mmm) REVERT: Z 95 PHE cc_start: 0.9533 (m-10) cc_final: 0.9159 (m-80) REVERT: Z 123 PHE cc_start: 0.9534 (t80) cc_final: 0.9177 (t80) REVERT: Z 132 ILE cc_start: 0.9134 (mt) cc_final: 0.8860 (mm) REVERT: Z 207 TYR cc_start: 0.8068 (t80) cc_final: 0.7687 (t80) REVERT: Z 228 MET cc_start: 0.9205 (ptt) cc_final: 0.8983 (ptt) REVERT: Z 248 PHE cc_start: 0.9575 (m-10) cc_final: 0.9179 (m-80) REVERT: Z 249 ARG cc_start: 0.9641 (ttm170) cc_final: 0.9346 (ttm-80) REVERT: Z 258 GLU cc_start: 0.9269 (tm-30) cc_final: 0.8841 (tm-30) REVERT: Z 259 VAL cc_start: 0.9793 (t) cc_final: 0.9448 (m) REVERT: Z 280 GLU cc_start: 0.9592 (tm-30) cc_final: 0.9280 (mm-30) REVERT: Z 282 PHE cc_start: 0.9559 (t80) cc_final: 0.9113 (t80) REVERT: Z 287 GLN cc_start: 0.9603 (mm110) cc_final: 0.9192 (mm110) REVERT: Z 289 LEU cc_start: 0.9800 (mt) cc_final: 0.9578 (mt) outliers start: 3 outliers final: 0 residues processed: 345 average time/residue: 0.0754 time to fit residues: 39.0316 Evaluate side-chains 297 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 16 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 118 optimal weight: 50.0000 chunk 98 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 107 optimal weight: 30.0000 chunk 117 optimal weight: 0.0570 chunk 66 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 33 GLN ** 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 = 0.3542 r_free = 0.3542 target = 0.068051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.053200 restraints weight = 54300.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.054275 restraints weight = 42701.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.055079 restraints weight = 35342.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.055611 restraints weight = 30416.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.056143 restraints weight = 27382.318| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.4039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9204 Z= 0.147 Angle : 0.583 7.207 12570 Z= 0.313 Chirality : 0.044 0.253 1596 Planarity : 0.005 0.068 1626 Dihedral : 3.764 20.271 1394 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.28 % Allowed : 1.97 % Favored : 97.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.86 (0.23), residues: 1332 helix: 1.84 (0.15), residues: 1102 sheet: None (None), residues: 0 loop : -1.78 (0.41), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 44 TYR 0.018 0.001 TYR Z 277 PHE 0.038 0.001 PHE P 55 TRP 0.008 0.001 TRP Z 208 HIS 0.002 0.001 HIS Z 170 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 9204) covalent geometry : angle 0.58349 (12570) hydrogen bonds : bond 0.04067 ( 899) hydrogen bonds : angle 3.92744 ( 2676) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 344 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 38 ASN cc_start: 0.9261 (t0) cc_final: 0.8949 (t0) REVERT: H 48 TYR cc_start: 0.9152 (m-80) cc_final: 0.8867 (m-10) REVERT: H 49 MET cc_start: 0.9683 (ttp) cc_final: 0.9397 (tmm) REVERT: H 50 PHE cc_start: 0.9597 (m-80) cc_final: 0.9153 (m-80) REVERT: H 57 GLU cc_start: 0.9772 (tp30) cc_final: 0.9362 (tp30) REVERT: H 64 LEU cc_start: 0.9818 (mt) cc_final: 0.9571 (mm) REVERT: H 68 PHE cc_start: 0.9394 (m-10) cc_final: 0.9155 (m-80) REVERT: I 27 ILE cc_start: 0.9486 (mt) cc_final: 0.9207 (mt) REVERT: I 42 GLU cc_start: 0.9463 (tt0) cc_final: 0.9205 (tt0) REVERT: I 55 PHE cc_start: 0.9520 (m-80) cc_final: 0.9230 (m-80) REVERT: I 68 PHE cc_start: 0.9374 (m-80) cc_final: 0.9006 (m-80) REVERT: J 48 TYR cc_start: 0.9346 (m-80) cc_final: 0.8662 (m-80) REVERT: J 49 MET cc_start: 0.9593 (tmm) cc_final: 0.9176 (tmm) REVERT: K 15 LEU cc_start: 0.9805 (mt) cc_final: 0.9464 (tp) REVERT: K 18 ILE cc_start: 0.9441 (pt) cc_final: 0.9162 (tp) REVERT: K 22 VAL cc_start: 0.9249 (p) cc_final: 0.9032 (p) REVERT: K 27 ILE cc_start: 0.9573 (mt) cc_final: 0.9265 (mt) REVERT: K 43 ASN cc_start: 0.9132 (t0) cc_final: 0.8928 (t0) REVERT: K 44 ARG cc_start: 0.9417 (tpp80) cc_final: 0.8803 (tpp80) REVERT: K 48 TYR cc_start: 0.9563 (m-10) cc_final: 0.9269 (m-80) REVERT: K 49 MET cc_start: 0.9616 (ttp) cc_final: 0.9371 (ppp) REVERT: K 55 PHE cc_start: 0.9559 (m-80) cc_final: 0.9314 (m-80) REVERT: K 68 PHE cc_start: 0.9451 (m-10) cc_final: 0.9175 (m-80) REVERT: L 1 MET cc_start: 0.8927 (mtp) cc_final: 0.8440 (mtt) REVERT: L 43 ASN cc_start: 0.9312 (p0) cc_final: 0.9019 (m-40) REVERT: L 50 PHE cc_start: 0.9640 (m-80) cc_final: 0.9325 (m-10) REVERT: L 51 ILE cc_start: 0.9843 (mt) cc_final: 0.9523 (mt) REVERT: L 53 ILE cc_start: 0.9817 (tt) cc_final: 0.9441 (tp) REVERT: L 55 PHE cc_start: 0.9458 (m-80) cc_final: 0.8969 (m-80) REVERT: L 57 GLU cc_start: 0.9448 (mm-30) cc_final: 0.8914 (mt-10) REVERT: M 27 ILE cc_start: 0.9723 (mt) cc_final: 0.9318 (mt) REVERT: M 59 LEU cc_start: 0.9367 (mt) cc_final: 0.9041 (mt) REVERT: N 1 MET cc_start: 0.6298 (tpt) cc_final: 0.5614 (tpt) REVERT: N 55 PHE cc_start: 0.9648 (m-80) cc_final: 0.9151 (m-80) REVERT: O 29 SER cc_start: 0.9531 (t) cc_final: 0.9205 (p) REVERT: O 32 VAL cc_start: 0.9643 (p) cc_final: 0.9264 (m) REVERT: O 33 GLN cc_start: 0.9435 (mt0) cc_final: 0.9083 (mm-40) REVERT: O 37 ARG cc_start: 0.9082 (mtt180) cc_final: 0.8605 (mtm180) REVERT: O 55 PHE cc_start: 0.8798 (m-10) cc_final: 0.8448 (m-10) REVERT: O 57 GLU cc_start: 0.9343 (mm-30) cc_final: 0.8800 (pt0) REVERT: O 62 PHE cc_start: 0.8681 (m-10) cc_final: 0.8327 (m-80) REVERT: O 64 LEU cc_start: 0.9719 (tt) cc_final: 0.9305 (mt) REVERT: P 33 GLN cc_start: 0.9627 (mt0) cc_final: 0.9210 (mm110) REVERT: P 49 MET cc_start: 0.9490 (ttp) cc_final: 0.9003 (tmm) REVERT: P 68 PHE cc_start: 0.9245 (m-80) cc_final: 0.8875 (m-80) REVERT: Q 18 ILE cc_start: 0.9459 (pt) cc_final: 0.9124 (mm) REVERT: Q 33 GLN cc_start: 0.9288 (mm-40) cc_final: 0.8941 (mm110) REVERT: Q 50 PHE cc_start: 0.9630 (m-80) cc_final: 0.9281 (m-80) REVERT: Q 55 PHE cc_start: 0.9606 (m-80) cc_final: 0.9213 (m-80) REVERT: Q 62 PHE cc_start: 0.9475 (m-10) cc_final: 0.9262 (m-80) REVERT: Z 80 LEU cc_start: 0.9120 (mm) cc_final: 0.8912 (pt) REVERT: Z 84 MET cc_start: 0.9286 (mmt) cc_final: 0.9085 (mmm) REVERT: Z 95 PHE cc_start: 0.9519 (m-10) cc_final: 0.9042 (m-80) REVERT: Z 123 PHE cc_start: 0.9513 (t80) cc_final: 0.9184 (t80) REVERT: Z 132 ILE cc_start: 0.9120 (mt) cc_final: 0.8813 (mm) REVERT: Z 207 TYR cc_start: 0.8077 (t80) cc_final: 0.7692 (t80) REVERT: Z 228 MET cc_start: 0.9198 (ptt) cc_final: 0.8919 (ptt) REVERT: Z 248 PHE cc_start: 0.9610 (m-10) cc_final: 0.9247 (m-80) REVERT: Z 249 ARG cc_start: 0.9692 (ttm170) cc_final: 0.9400 (ttm-80) REVERT: Z 258 GLU cc_start: 0.9233 (tm-30) cc_final: 0.8764 (tm-30) REVERT: Z 259 VAL cc_start: 0.9798 (t) cc_final: 0.9447 (m) REVERT: Z 280 GLU cc_start: 0.9584 (tm-30) cc_final: 0.9288 (mm-30) REVERT: Z 282 PHE cc_start: 0.9510 (t80) cc_final: 0.9010 (t80) REVERT: Z 287 GLN cc_start: 0.9602 (mm110) cc_final: 0.9170 (mm110) REVERT: Z 289 LEU cc_start: 0.9801 (mt) cc_final: 0.9568 (mt) outliers start: 2 outliers final: 0 residues processed: 344 average time/residue: 0.0747 time to fit residues: 38.6310 Evaluate side-chains 295 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 295 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 42 optimal weight: 0.6980 chunk 111 optimal weight: 40.0000 chunk 48 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 33 GLN ** L 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.067815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.052732 restraints weight = 51720.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.053778 restraints weight = 41100.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.054524 restraints weight = 34253.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.054939 restraints weight = 29893.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.055456 restraints weight = 27377.992| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.4306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9204 Z= 0.149 Angle : 0.597 9.656 12570 Z= 0.317 Chirality : 0.044 0.256 1596 Planarity : 0.005 0.070 1626 Dihedral : 3.804 20.796 1394 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.14 % Allowed : 2.39 % Favored : 97.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.86 (0.23), residues: 1332 helix: 1.83 (0.15), residues: 1103 sheet: None (None), residues: 0 loop : -1.77 (0.41), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 37 TYR 0.023 0.001 TYR I 48 PHE 0.039 0.002 PHE M 62 TRP 0.008 0.001 TRP Z 208 HIS 0.002 0.001 HIS Z 170 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 9204) covalent geometry : angle 0.59739 (12570) hydrogen bonds : bond 0.04060 ( 899) hydrogen bonds : angle 3.90433 ( 2676) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 349 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 38 ASN cc_start: 0.9267 (t0) cc_final: 0.8942 (t0) REVERT: H 50 PHE cc_start: 0.9584 (m-80) cc_final: 0.8964 (m-80) REVERT: H 57 GLU cc_start: 0.9772 (tp30) cc_final: 0.9459 (tp30) REVERT: H 64 LEU cc_start: 0.9808 (mt) cc_final: 0.9559 (mm) REVERT: H 68 PHE cc_start: 0.9370 (m-10) cc_final: 0.9136 (m-80) REVERT: I 42 GLU cc_start: 0.9447 (tt0) cc_final: 0.9139 (tp30) REVERT: I 49 MET cc_start: 0.9560 (ptt) cc_final: 0.9041 (ppp) REVERT: I 51 ILE cc_start: 0.9706 (mt) cc_final: 0.9430 (mt) REVERT: I 55 PHE cc_start: 0.9517 (m-80) cc_final: 0.9215 (m-80) REVERT: J 48 TYR cc_start: 0.9333 (m-80) cc_final: 0.8735 (m-80) REVERT: J 49 MET cc_start: 0.9499 (tmm) cc_final: 0.9165 (tmm) REVERT: J 53 ILE cc_start: 0.9679 (mm) cc_final: 0.9436 (mm) REVERT: K 18 ILE cc_start: 0.9430 (pt) cc_final: 0.9071 (tp) REVERT: K 22 VAL cc_start: 0.9169 (p) cc_final: 0.8920 (p) REVERT: K 44 ARG cc_start: 0.9383 (tpp80) cc_final: 0.8762 (tpp80) REVERT: K 48 TYR cc_start: 0.9530 (m-10) cc_final: 0.9206 (m-80) REVERT: K 55 PHE cc_start: 0.9555 (m-80) cc_final: 0.9307 (m-80) REVERT: K 66 ILE cc_start: 0.9605 (mm) cc_final: 0.9305 (tp) REVERT: K 68 PHE cc_start: 0.9446 (m-10) cc_final: 0.9140 (m-80) REVERT: L 1 MET cc_start: 0.8852 (mtp) cc_final: 0.8388 (mtt) REVERT: L 15 LEU cc_start: 0.9554 (tp) cc_final: 0.9234 (tp) REVERT: L 33 GLN cc_start: 0.9358 (pt0) cc_final: 0.9053 (pt0) REVERT: L 43 ASN cc_start: 0.9334 (p0) cc_final: 0.9033 (m-40) REVERT: L 50 PHE cc_start: 0.9608 (m-80) cc_final: 0.9299 (m-10) REVERT: L 51 ILE cc_start: 0.9835 (mt) cc_final: 0.9523 (mt) REVERT: L 53 ILE cc_start: 0.9811 (tt) cc_final: 0.9421 (tp) REVERT: L 55 PHE cc_start: 0.9454 (m-80) cc_final: 0.8984 (m-80) REVERT: L 57 GLU cc_start: 0.9455 (mm-30) cc_final: 0.8897 (mt-10) REVERT: M 50 PHE cc_start: 0.9409 (m-80) cc_final: 0.9049 (m-10) REVERT: N 1 MET cc_start: 0.6324 (tpt) cc_final: 0.5549 (mmm) REVERT: N 55 PHE cc_start: 0.9650 (m-80) cc_final: 0.9113 (m-80) REVERT: O 1 MET cc_start: 0.6862 (mmt) cc_final: 0.6406 (mmt) REVERT: O 29 SER cc_start: 0.9523 (t) cc_final: 0.9150 (p) REVERT: O 32 VAL cc_start: 0.9646 (p) cc_final: 0.9181 (m) REVERT: O 33 GLN cc_start: 0.9423 (mt0) cc_final: 0.9098 (mm110) REVERT: O 37 ARG cc_start: 0.9086 (mtt180) cc_final: 0.8612 (mtm180) REVERT: O 55 PHE cc_start: 0.8697 (m-10) cc_final: 0.8472 (m-10) REVERT: O 57 GLU cc_start: 0.9391 (mm-30) cc_final: 0.8905 (pt0) REVERT: O 62 PHE cc_start: 0.8586 (m-10) cc_final: 0.8243 (m-80) REVERT: O 64 LEU cc_start: 0.9747 (tt) cc_final: 0.9411 (mt) REVERT: P 33 GLN cc_start: 0.9613 (mt0) cc_final: 0.9236 (mm110) REVERT: P 49 MET cc_start: 0.9375 (ttp) cc_final: 0.9061 (tmm) REVERT: P 68 PHE cc_start: 0.9245 (m-80) cc_final: 0.8858 (m-80) REVERT: Q 18 ILE cc_start: 0.9437 (pt) cc_final: 0.9100 (mm) REVERT: Q 27 ILE cc_start: 0.9547 (mt) cc_final: 0.9263 (mt) REVERT: Q 33 GLN cc_start: 0.9265 (mm-40) cc_final: 0.8944 (mm110) REVERT: Q 50 PHE cc_start: 0.9626 (m-80) cc_final: 0.9060 (m-80) REVERT: Q 55 PHE cc_start: 0.9625 (m-80) cc_final: 0.9256 (m-80) REVERT: Z 80 LEU cc_start: 0.9012 (mm) cc_final: 0.8582 (tt) REVERT: Z 84 MET cc_start: 0.9244 (mmt) cc_final: 0.8964 (mmm) REVERT: Z 95 PHE cc_start: 0.9507 (m-10) cc_final: 0.9109 (m-80) REVERT: Z 123 PHE cc_start: 0.9482 (t80) cc_final: 0.9163 (t80) REVERT: Z 132 ILE cc_start: 0.9143 (mt) cc_final: 0.8729 (tp) REVERT: Z 228 MET cc_start: 0.9125 (ptt) cc_final: 0.8838 (ptt) REVERT: Z 235 GLU cc_start: 0.9660 (pt0) cc_final: 0.9239 (tm-30) REVERT: Z 248 PHE cc_start: 0.9607 (m-10) cc_final: 0.9383 (m-80) REVERT: Z 249 ARG cc_start: 0.9691 (ttm170) cc_final: 0.9357 (ttm170) REVERT: Z 258 GLU cc_start: 0.9209 (tm-30) cc_final: 0.8821 (tm-30) REVERT: Z 259 VAL cc_start: 0.9783 (t) cc_final: 0.9472 (m) REVERT: Z 280 GLU cc_start: 0.9582 (tm-30) cc_final: 0.9258 (mm-30) REVERT: Z 282 PHE cc_start: 0.9489 (t80) cc_final: 0.9037 (t80) REVERT: Z 287 GLN cc_start: 0.9557 (mm110) cc_final: 0.9165 (mm110) REVERT: Z 289 LEU cc_start: 0.9805 (mt) cc_final: 0.9556 (mt) outliers start: 1 outliers final: 0 residues processed: 350 average time/residue: 0.0732 time to fit residues: 38.7578 Evaluate side-chains 294 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 294 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 73 optimal weight: 9.9990 chunk 88 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 0.9980 chunk 120 optimal weight: 0.3980 chunk 108 optimal weight: 8.9990 chunk 72 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 109 optimal weight: 30.0000 chunk 121 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 253 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 = 0.3526 r_free = 0.3526 target = 0.067235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.052367 restraints weight = 52952.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.053395 restraints weight = 41712.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.054175 restraints weight = 34685.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.054538 restraints weight = 30454.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.054962 restraints weight = 28104.420| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.4628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 9204 Z= 0.168 Angle : 0.632 8.120 12570 Z= 0.337 Chirality : 0.045 0.205 1596 Planarity : 0.005 0.070 1626 Dihedral : 3.859 22.420 1394 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % 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: 1332 helix: 1.75 (0.15), residues: 1107 sheet: None (None), residues: 0 loop : -1.73 (0.42), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 37 TYR 0.015 0.001 TYR Z 277 PHE 0.048 0.002 PHE Q 62 TRP 0.009 0.001 TRP Z 208 HIS 0.002 0.001 HIS Z 170 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 9204) covalent geometry : angle 0.63177 (12570) hydrogen bonds : bond 0.04117 ( 899) hydrogen bonds : angle 4.01782 ( 2676) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 341 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 38 ASN cc_start: 0.9357 (t0) cc_final: 0.9053 (t0) REVERT: H 57 GLU cc_start: 0.9803 (tp30) cc_final: 0.9453 (tp30) REVERT: H 64 LEU cc_start: 0.9800 (mt) cc_final: 0.9591 (mt) REVERT: H 68 PHE cc_start: 0.9387 (m-10) cc_final: 0.9151 (m-80) REVERT: I 42 GLU cc_start: 0.9434 (tt0) cc_final: 0.9186 (tp30) REVERT: I 49 MET cc_start: 0.9522 (ptt) cc_final: 0.9125 (ppp) REVERT: I 51 ILE cc_start: 0.9690 (mt) cc_final: 0.9438 (mt) REVERT: I 55 PHE cc_start: 0.9513 (m-80) cc_final: 0.9172 (m-80) REVERT: I 68 PHE cc_start: 0.9367 (m-80) cc_final: 0.8970 (m-80) REVERT: J 48 TYR cc_start: 0.9356 (m-80) cc_final: 0.8735 (m-80) REVERT: J 49 MET cc_start: 0.9569 (tmm) cc_final: 0.9159 (tmm) REVERT: J 53 ILE cc_start: 0.9674 (mm) cc_final: 0.9465 (mm) REVERT: K 18 ILE cc_start: 0.9444 (pt) cc_final: 0.9096 (tp) REVERT: K 22 VAL cc_start: 0.9199 (p) cc_final: 0.8975 (p) REVERT: K 33 GLN cc_start: 0.9513 (mt0) cc_final: 0.9040 (mm110) REVERT: K 44 ARG cc_start: 0.9414 (tpp80) cc_final: 0.8563 (tpp80) REVERT: K 48 TYR cc_start: 0.9513 (m-10) cc_final: 0.8968 (m-80) REVERT: K 55 PHE cc_start: 0.9574 (m-80) cc_final: 0.9214 (m-80) REVERT: K 66 ILE cc_start: 0.9608 (mm) cc_final: 0.9350 (tp) REVERT: K 68 PHE cc_start: 0.9428 (m-10) cc_final: 0.9097 (m-80) REVERT: L 1 MET cc_start: 0.8985 (mtp) cc_final: 0.8577 (mtt) REVERT: L 43 ASN cc_start: 0.9343 (p0) cc_final: 0.9037 (m-40) REVERT: L 50 PHE cc_start: 0.9602 (m-80) cc_final: 0.9309 (m-10) REVERT: L 51 ILE cc_start: 0.9833 (mt) cc_final: 0.9514 (mt) REVERT: L 53 ILE cc_start: 0.9800 (tt) cc_final: 0.9508 (tp) REVERT: L 55 PHE cc_start: 0.9451 (m-80) cc_final: 0.8992 (m-80) REVERT: L 57 GLU cc_start: 0.9471 (mm-30) cc_final: 0.9083 (mm-30) REVERT: M 50 PHE cc_start: 0.9370 (m-80) cc_final: 0.9107 (m-80) REVERT: N 1 MET cc_start: 0.6131 (tpt) cc_final: 0.5867 (mmt) REVERT: N 33 GLN cc_start: 0.9237 (mp10) cc_final: 0.9034 (mp10) REVERT: N 55 PHE cc_start: 0.9645 (m-80) cc_final: 0.9156 (m-80) REVERT: O 15 LEU cc_start: 0.9741 (mp) cc_final: 0.9365 (tp) REVERT: O 29 SER cc_start: 0.9544 (t) cc_final: 0.9217 (p) REVERT: O 32 VAL cc_start: 0.9683 (p) cc_final: 0.9269 (m) REVERT: O 33 GLN cc_start: 0.9458 (mt0) cc_final: 0.9112 (mm110) REVERT: O 37 ARG cc_start: 0.9094 (mtt180) cc_final: 0.8602 (mtm180) REVERT: O 55 PHE cc_start: 0.8778 (m-10) cc_final: 0.8543 (m-10) REVERT: O 57 GLU cc_start: 0.9361 (mm-30) cc_final: 0.8937 (pt0) REVERT: O 62 PHE cc_start: 0.8689 (m-10) cc_final: 0.8466 (m-80) REVERT: O 64 LEU cc_start: 0.9716 (tt) cc_final: 0.9333 (mt) REVERT: P 33 GLN cc_start: 0.9620 (mt0) cc_final: 0.9230 (mm110) REVERT: P 49 MET cc_start: 0.9515 (ttp) cc_final: 0.9121 (tmm) REVERT: P 68 PHE cc_start: 0.9260 (m-80) cc_final: 0.8892 (m-80) REVERT: Q 18 ILE cc_start: 0.9408 (pt) cc_final: 0.9076 (mm) REVERT: Q 33 GLN cc_start: 0.9254 (mm-40) cc_final: 0.8934 (mm110) REVERT: Q 50 PHE cc_start: 0.9639 (m-80) cc_final: 0.9268 (m-80) REVERT: Q 55 PHE cc_start: 0.9673 (m-80) cc_final: 0.9271 (m-80) REVERT: Z 84 MET cc_start: 0.9274 (mmt) cc_final: 0.9052 (mmm) REVERT: Z 95 PHE cc_start: 0.9528 (m-10) cc_final: 0.9046 (m-80) REVERT: Z 123 PHE cc_start: 0.9517 (t80) cc_final: 0.9217 (t80) REVERT: Z 207 TYR cc_start: 0.8190 (t80) cc_final: 0.7809 (t80) REVERT: Z 228 MET cc_start: 0.9188 (ptt) cc_final: 0.8907 (ptt) REVERT: Z 235 GLU cc_start: 0.9642 (pt0) cc_final: 0.9064 (tm-30) REVERT: Z 248 PHE cc_start: 0.9611 (m-10) cc_final: 0.9283 (m-10) REVERT: Z 249 ARG cc_start: 0.9689 (ttm170) cc_final: 0.9289 (ttm-80) REVERT: Z 258 GLU cc_start: 0.9273 (tm-30) cc_final: 0.8772 (tm-30) REVERT: Z 282 PHE cc_start: 0.9505 (t80) cc_final: 0.9079 (t80) REVERT: Z 287 GLN cc_start: 0.9568 (mm110) cc_final: 0.9153 (mm110) REVERT: Z 289 LEU cc_start: 0.9800 (mt) cc_final: 0.9546 (mt) outliers start: 0 outliers final: 0 residues processed: 341 average time/residue: 0.0747 time to fit residues: 38.4702 Evaluate side-chains 294 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 294 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 11 optimal weight: 2.9990 chunk 114 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 121 optimal weight: 10.0000 chunk 82 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 109 optimal weight: 40.0000 chunk 65 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 33 GLN ** 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 = 0.3560 r_free = 0.3560 target = 0.068561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.053910 restraints weight = 55519.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.055067 restraints weight = 43696.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.055832 restraints weight = 35761.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.056365 restraints weight = 30981.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.056675 restraints weight = 27688.440| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.4842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 9204 Z= 0.160 Angle : 0.653 10.303 12570 Z= 0.345 Chirality : 0.046 0.229 1596 Planarity : 0.005 0.073 1626 Dihedral : 3.876 22.494 1394 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 18.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % 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: 1.72 (0.23), residues: 1332 helix: 1.71 (0.15), residues: 1108 sheet: None (None), residues: 0 loop : -1.74 (0.41), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 37 TYR 0.020 0.001 TYR I 48 PHE 0.037 0.002 PHE H 62 TRP 0.010 0.001 TRP Z 208 HIS 0.002 0.001 HIS Z 170 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 9204) covalent geometry : angle 0.65313 (12570) hydrogen bonds : bond 0.04104 ( 899) hydrogen bonds : angle 3.99691 ( 2676) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 338 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 15 LEU cc_start: 0.9601 (mp) cc_final: 0.9101 (tp) REVERT: H 38 ASN cc_start: 0.9285 (t0) cc_final: 0.9039 (t0) REVERT: H 57 GLU cc_start: 0.9809 (tp30) cc_final: 0.9390 (tp30) REVERT: H 64 LEU cc_start: 0.9853 (mt) cc_final: 0.9582 (mt) REVERT: H 68 PHE cc_start: 0.9417 (m-10) cc_final: 0.9176 (m-80) REVERT: I 24 ILE cc_start: 0.9138 (pt) cc_final: 0.8913 (pt) REVERT: I 42 GLU cc_start: 0.9437 (tt0) cc_final: 0.9185 (tp30) REVERT: I 49 MET cc_start: 0.9505 (ptt) cc_final: 0.9180 (ppp) REVERT: I 51 ILE cc_start: 0.9666 (mt) cc_final: 0.9421 (mt) REVERT: I 55 PHE cc_start: 0.9535 (m-80) cc_final: 0.9131 (m-80) REVERT: I 68 PHE cc_start: 0.9389 (m-80) cc_final: 0.8957 (m-80) REVERT: J 48 TYR cc_start: 0.9351 (m-80) cc_final: 0.8732 (m-80) REVERT: J 49 MET cc_start: 0.9491 (tmm) cc_final: 0.9161 (tmm) REVERT: K 18 ILE cc_start: 0.9438 (pt) cc_final: 0.9121 (tp) REVERT: K 22 VAL cc_start: 0.9169 (p) cc_final: 0.8947 (p) REVERT: K 33 GLN cc_start: 0.9519 (mt0) cc_final: 0.9051 (mm110) REVERT: K 44 ARG cc_start: 0.9438 (tpp80) cc_final: 0.8921 (tpp80) REVERT: K 55 PHE cc_start: 0.9578 (m-80) cc_final: 0.9246 (m-80) REVERT: K 68 PHE cc_start: 0.9421 (m-10) cc_final: 0.9065 (m-80) REVERT: L 50 PHE cc_start: 0.9622 (m-80) cc_final: 0.9318 (m-10) REVERT: L 51 ILE cc_start: 0.9831 (mt) cc_final: 0.9512 (mt) REVERT: L 53 ILE cc_start: 0.9806 (tt) cc_final: 0.9507 (tp) REVERT: L 55 PHE cc_start: 0.9465 (m-80) cc_final: 0.9118 (m-80) REVERT: L 57 GLU cc_start: 0.9472 (mm-30) cc_final: 0.9170 (mm-30) REVERT: M 27 ILE cc_start: 0.9757 (tt) cc_final: 0.9434 (tt) REVERT: M 49 MET cc_start: 0.9227 (tpt) cc_final: 0.8892 (tpp) REVERT: M 50 PHE cc_start: 0.9308 (m-80) cc_final: 0.9042 (m-80) REVERT: M 68 PHE cc_start: 0.9457 (t80) cc_final: 0.9217 (t80) REVERT: N 1 MET cc_start: 0.6430 (tpt) cc_final: 0.5881 (mmm) REVERT: N 11 LEU cc_start: 0.9842 (mm) cc_final: 0.9637 (mm) REVERT: N 55 PHE cc_start: 0.9647 (m-80) cc_final: 0.9142 (m-80) REVERT: O 1 MET cc_start: 0.6526 (mmt) cc_final: 0.6208 (mmt) REVERT: O 11 LEU cc_start: 0.9561 (mt) cc_final: 0.9335 (mt) REVERT: O 15 LEU cc_start: 0.9734 (mp) cc_final: 0.9342 (tp) REVERT: O 29 SER cc_start: 0.9563 (t) cc_final: 0.9228 (p) REVERT: O 32 VAL cc_start: 0.9676 (p) cc_final: 0.9280 (m) REVERT: O 33 GLN cc_start: 0.9429 (mt0) cc_final: 0.9104 (mm110) REVERT: O 37 ARG cc_start: 0.9081 (mtt180) cc_final: 0.8582 (mtm180) REVERT: O 55 PHE cc_start: 0.8791 (m-10) cc_final: 0.8494 (m-10) REVERT: O 57 GLU cc_start: 0.9386 (mm-30) cc_final: 0.8909 (pt0) REVERT: O 62 PHE cc_start: 0.8657 (m-10) cc_final: 0.8368 (m-80) REVERT: O 64 LEU cc_start: 0.9731 (tt) cc_final: 0.9410 (mt) REVERT: P 33 GLN cc_start: 0.9621 (mt0) cc_final: 0.9239 (mm110) REVERT: P 37 ARG cc_start: 0.9126 (ptm160) cc_final: 0.8897 (ptm-80) REVERT: P 49 MET cc_start: 0.9499 (ttp) cc_final: 0.9081 (tmm) REVERT: P 68 PHE cc_start: 0.9316 (m-80) cc_final: 0.8969 (m-80) REVERT: Q 15 LEU cc_start: 0.9152 (mm) cc_final: 0.8736 (tp) REVERT: Q 18 ILE cc_start: 0.9418 (pt) cc_final: 0.8987 (mm) REVERT: Q 33 GLN cc_start: 0.9246 (mm-40) cc_final: 0.8874 (mm110) REVERT: Q 49 MET cc_start: 0.9353 (ppp) cc_final: 0.9058 (ppp) REVERT: Q 50 PHE cc_start: 0.9602 (m-80) cc_final: 0.9217 (m-80) REVERT: Q 55 PHE cc_start: 0.9644 (m-80) cc_final: 0.9398 (m-80) REVERT: Q 62 PHE cc_start: 0.9547 (m-80) cc_final: 0.9296 (m-80) REVERT: Z 84 MET cc_start: 0.9269 (mmt) cc_final: 0.9036 (mmm) REVERT: Z 95 PHE cc_start: 0.9536 (m-10) cc_final: 0.9062 (m-80) REVERT: Z 123 PHE cc_start: 0.9549 (t80) cc_final: 0.9268 (t80) REVERT: Z 207 TYR cc_start: 0.8201 (t80) cc_final: 0.7816 (t80) REVERT: Z 228 MET cc_start: 0.9180 (ptt) cc_final: 0.8937 (ptt) REVERT: Z 235 GLU cc_start: 0.9638 (pt0) cc_final: 0.9274 (tm-30) REVERT: Z 248 PHE cc_start: 0.9594 (m-10) cc_final: 0.9288 (m-10) REVERT: Z 249 ARG cc_start: 0.9685 (ttm170) cc_final: 0.9351 (ttm-80) REVERT: Z 258 GLU cc_start: 0.9245 (tm-30) cc_final: 0.8794 (tm-30) REVERT: Z 282 PHE cc_start: 0.9508 (t80) cc_final: 0.9062 (t80) REVERT: Z 287 GLN cc_start: 0.9585 (mm110) cc_final: 0.9194 (mm110) REVERT: Z 289 LEU cc_start: 0.9800 (mt) cc_final: 0.9558 (mt) outliers start: 0 outliers final: 0 residues processed: 338 average time/residue: 0.0739 time to fit residues: 37.8997 Evaluate side-chains 291 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 291 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 43 optimal weight: 0.9980 chunk 114 optimal weight: 6.9990 chunk 16 optimal weight: 0.7980 chunk 85 optimal weight: 0.8980 chunk 76 optimal weight: 6.9990 chunk 129 optimal weight: 1.9990 chunk 104 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 121 optimal weight: 10.0000 chunk 90 optimal weight: 0.4980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 33 GLN ** 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 = 0.3544 r_free = 0.3544 target = 0.068379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.053561 restraints weight = 51922.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.054546 restraints weight = 41359.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.055300 restraints weight = 34927.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.055874 restraints weight = 30597.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.056321 restraints weight = 27568.322| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.5035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 9204 Z= 0.158 Angle : 0.660 9.244 12570 Z= 0.348 Chirality : 0.047 0.397 1596 Planarity : 0.005 0.071 1626 Dihedral : 3.926 21.821 1394 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 18.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.68 (0.23), residues: 1332 helix: 1.69 (0.15), residues: 1109 sheet: None (None), residues: 0 loop : -1.87 (0.40), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 37 TYR 0.010 0.001 TYR Z 296 PHE 0.035 0.002 PHE P 55 TRP 0.010 0.001 TRP Z 208 HIS 0.002 0.001 HIS Z 170 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 9204) covalent geometry : angle 0.65994 (12570) hydrogen bonds : bond 0.04110 ( 899) hydrogen bonds : angle 3.99509 ( 2676) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 327 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 38 ASN cc_start: 0.9339 (t0) cc_final: 0.8987 (t0) REVERT: H 40 GLU cc_start: 0.9363 (tm-30) cc_final: 0.8963 (mp0) REVERT: H 49 MET cc_start: 0.9633 (ppp) cc_final: 0.9301 (ppp) REVERT: H 50 PHE cc_start: 0.9558 (m-80) cc_final: 0.9106 (m-80) REVERT: H 57 GLU cc_start: 0.9792 (tp30) cc_final: 0.9390 (tp30) REVERT: H 64 LEU cc_start: 0.9854 (mt) cc_final: 0.9595 (mt) REVERT: H 68 PHE cc_start: 0.9398 (m-10) cc_final: 0.9166 (m-80) REVERT: I 49 MET cc_start: 0.9483 (ptt) cc_final: 0.9159 (ppp) REVERT: I 51 ILE cc_start: 0.9656 (mt) cc_final: 0.9435 (mt) REVERT: I 55 PHE cc_start: 0.9343 (m-80) cc_final: 0.9070 (m-10) REVERT: I 68 PHE cc_start: 0.9377 (m-80) cc_final: 0.8902 (m-80) REVERT: J 48 TYR cc_start: 0.9330 (m-80) cc_final: 0.8747 (m-80) REVERT: J 49 MET cc_start: 0.9549 (tmm) cc_final: 0.9147 (tmm) REVERT: J 64 LEU cc_start: 0.9616 (mt) cc_final: 0.9320 (pp) REVERT: K 18 ILE cc_start: 0.9412 (pt) cc_final: 0.9098 (tp) REVERT: K 33 GLN cc_start: 0.9525 (mt0) cc_final: 0.9071 (mm110) REVERT: K 44 ARG cc_start: 0.9389 (tpp80) cc_final: 0.8914 (tpp80) REVERT: K 55 PHE cc_start: 0.9536 (m-80) cc_final: 0.9332 (m-80) REVERT: K 66 ILE cc_start: 0.9601 (mm) cc_final: 0.9358 (tp) REVERT: K 68 PHE cc_start: 0.9420 (m-10) cc_final: 0.9114 (m-80) REVERT: L 43 ASN cc_start: 0.9312 (p0) cc_final: 0.9029 (m-40) REVERT: L 50 PHE cc_start: 0.9614 (m-80) cc_final: 0.9308 (m-10) REVERT: L 51 ILE cc_start: 0.9830 (mt) cc_final: 0.9530 (mt) REVERT: L 53 ILE cc_start: 0.9814 (tt) cc_final: 0.9421 (tp) REVERT: L 55 PHE cc_start: 0.9501 (m-80) cc_final: 0.9081 (m-80) REVERT: L 57 GLU cc_start: 0.9511 (mm-30) cc_final: 0.9047 (mt-10) REVERT: M 27 ILE cc_start: 0.9780 (tt) cc_final: 0.9500 (tt) REVERT: M 48 TYR cc_start: 0.9092 (m-80) cc_final: 0.8847 (m-80) REVERT: M 68 PHE cc_start: 0.9432 (t80) cc_final: 0.9196 (t80) REVERT: N 55 PHE cc_start: 0.9624 (m-80) cc_final: 0.9136 (m-80) REVERT: O 29 SER cc_start: 0.9589 (t) cc_final: 0.9241 (p) REVERT: O 32 VAL cc_start: 0.9713 (p) cc_final: 0.9303 (m) REVERT: O 33 GLN cc_start: 0.9461 (mt0) cc_final: 0.9109 (mm110) REVERT: O 37 ARG cc_start: 0.9128 (mtt180) cc_final: 0.8623 (mtm180) REVERT: O 57 GLU cc_start: 0.9372 (mm-30) cc_final: 0.8889 (pt0) REVERT: O 62 PHE cc_start: 0.8635 (m-10) cc_final: 0.8422 (m-80) REVERT: O 64 LEU cc_start: 0.9697 (tt) cc_final: 0.9355 (mt) REVERT: P 33 GLN cc_start: 0.9605 (mt0) cc_final: 0.9241 (mm110) REVERT: P 37 ARG cc_start: 0.9106 (ptm160) cc_final: 0.8889 (ptm-80) REVERT: P 49 MET cc_start: 0.9373 (ttp) cc_final: 0.9078 (tmm) REVERT: P 68 PHE cc_start: 0.9214 (m-80) cc_final: 0.8838 (m-80) REVERT: Q 18 ILE cc_start: 0.9451 (pt) cc_final: 0.9052 (mm) REVERT: Q 27 ILE cc_start: 0.9426 (mt) cc_final: 0.9219 (mt) REVERT: Q 33 GLN cc_start: 0.9274 (mm-40) cc_final: 0.8896 (mm110) REVERT: Q 49 MET cc_start: 0.9355 (ppp) cc_final: 0.9046 (ppp) REVERT: Q 50 PHE cc_start: 0.9602 (m-80) cc_final: 0.9126 (m-80) REVERT: Q 55 PHE cc_start: 0.9632 (m-80) cc_final: 0.9406 (m-80) REVERT: Q 62 PHE cc_start: 0.9584 (m-80) cc_final: 0.9197 (m-80) REVERT: Z 84 MET cc_start: 0.9242 (mmt) cc_final: 0.9033 (mmm) REVERT: Z 95 PHE cc_start: 0.9527 (m-10) cc_final: 0.9063 (m-80) REVERT: Z 123 PHE cc_start: 0.9505 (t80) cc_final: 0.9300 (t80) REVERT: Z 207 TYR cc_start: 0.8118 (t80) cc_final: 0.7750 (t80) REVERT: Z 228 MET cc_start: 0.9156 (ptt) cc_final: 0.8915 (ptt) REVERT: Z 235 GLU cc_start: 0.9619 (pt0) cc_final: 0.9204 (tm-30) REVERT: Z 248 PHE cc_start: 0.9594 (m-10) cc_final: 0.9295 (m-10) REVERT: Z 249 ARG cc_start: 0.9663 (ttm170) cc_final: 0.9259 (ttm170) REVERT: Z 258 GLU cc_start: 0.9219 (tm-30) cc_final: 0.8723 (tm-30) REVERT: Z 259 VAL cc_start: 0.9745 (t) cc_final: 0.9380 (m) REVERT: Z 287 GLN cc_start: 0.9583 (mm110) cc_final: 0.9188 (mm110) REVERT: Z 289 LEU cc_start: 0.9790 (mt) cc_final: 0.9534 (mt) outliers start: 0 outliers final: 0 residues processed: 327 average time/residue: 0.0741 time to fit residues: 36.5682 Evaluate side-chains 284 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 82 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 119 optimal weight: 50.0000 chunk 92 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 121 optimal weight: 6.9990 chunk 37 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 253 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 = 0.3546 r_free = 0.3546 target = 0.067814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.053487 restraints weight = 56293.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.054514 restraints weight = 44521.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 16)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.055178 restraints weight = 36806.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.055766 restraints weight = 32292.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.056177 restraints weight = 28811.025| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.5204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 9204 Z= 0.177 Angle : 0.665 10.110 12570 Z= 0.357 Chirality : 0.047 0.382 1596 Planarity : 0.005 0.071 1626 Dihedral : 3.923 22.376 1394 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 18.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % 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: 1.68 (0.23), residues: 1332 helix: 1.69 (0.15), residues: 1109 sheet: None (None), residues: 0 loop : -1.78 (0.41), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 37 TYR 0.019 0.002 TYR M 48 PHE 0.034 0.002 PHE M 55 TRP 0.011 0.001 TRP Z 208 HIS 0.002 0.002 HIS Z 31 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 9204) covalent geometry : angle 0.66506 (12570) hydrogen bonds : bond 0.04216 ( 899) hydrogen bonds : angle 4.08307 ( 2676) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 331 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 38 ASN cc_start: 0.9349 (t0) cc_final: 0.8888 (t0) REVERT: H 40 GLU cc_start: 0.9429 (tm-30) cc_final: 0.8990 (mp0) REVERT: H 48 TYR cc_start: 0.9281 (m-10) cc_final: 0.8723 (m-80) REVERT: H 49 MET cc_start: 0.9645 (ppp) cc_final: 0.9342 (ppp) REVERT: H 50 PHE cc_start: 0.9562 (m-80) cc_final: 0.9135 (m-80) REVERT: H 57 GLU cc_start: 0.9811 (tp30) cc_final: 0.9413 (tp30) REVERT: H 64 LEU cc_start: 0.9856 (mt) cc_final: 0.9640 (mt) REVERT: H 68 PHE cc_start: 0.9433 (m-10) cc_final: 0.9190 (m-80) REVERT: I 24 ILE cc_start: 0.9048 (pt) cc_final: 0.8794 (pt) REVERT: I 49 MET cc_start: 0.9464 (ptt) cc_final: 0.9128 (ppp) REVERT: I 51 ILE cc_start: 0.9646 (mt) cc_final: 0.9421 (mt) REVERT: I 55 PHE cc_start: 0.9346 (m-80) cc_final: 0.9073 (m-10) REVERT: I 68 PHE cc_start: 0.9428 (m-80) cc_final: 0.8960 (m-80) REVERT: J 1 MET cc_start: 0.9157 (mmm) cc_final: 0.8908 (tpp) REVERT: J 48 TYR cc_start: 0.9348 (m-80) cc_final: 0.8768 (m-80) REVERT: J 49 MET cc_start: 0.9629 (tmm) cc_final: 0.9189 (tmm) REVERT: J 64 LEU cc_start: 0.9632 (mt) cc_final: 0.9325 (pp) REVERT: K 18 ILE cc_start: 0.9495 (pt) cc_final: 0.9210 (tp) REVERT: K 33 GLN cc_start: 0.9523 (mt0) cc_final: 0.9051 (mm-40) REVERT: K 44 ARG cc_start: 0.9424 (tpp80) cc_final: 0.8929 (tpp80) REVERT: K 55 PHE cc_start: 0.9538 (m-80) cc_final: 0.9318 (m-80) REVERT: K 66 ILE cc_start: 0.9661 (mm) cc_final: 0.9404 (tp) REVERT: K 68 PHE cc_start: 0.9461 (m-10) cc_final: 0.9147 (m-80) REVERT: L 50 PHE cc_start: 0.9646 (m-80) cc_final: 0.9263 (m-10) REVERT: L 51 ILE cc_start: 0.9841 (mt) cc_final: 0.9557 (mt) REVERT: L 53 ILE cc_start: 0.9826 (tt) cc_final: 0.9420 (tp) REVERT: L 55 PHE cc_start: 0.9518 (m-80) cc_final: 0.9101 (m-80) REVERT: L 57 GLU cc_start: 0.9485 (mm-30) cc_final: 0.8989 (pt0) REVERT: M 27 ILE cc_start: 0.9752 (tt) cc_final: 0.9538 (tt) REVERT: M 68 PHE cc_start: 0.9492 (t80) cc_final: 0.9265 (t80) REVERT: N 33 GLN cc_start: 0.9286 (mp10) cc_final: 0.9053 (mp10) REVERT: N 55 PHE cc_start: 0.9634 (m-80) cc_final: 0.9163 (m-80) REVERT: O 29 SER cc_start: 0.9606 (t) cc_final: 0.9288 (p) REVERT: O 32 VAL cc_start: 0.9725 (p) cc_final: 0.9334 (m) REVERT: O 33 GLN cc_start: 0.9485 (mt0) cc_final: 0.9145 (mm110) REVERT: O 37 ARG cc_start: 0.9107 (mtt180) cc_final: 0.8573 (mtm180) REVERT: O 57 GLU cc_start: 0.9365 (mm-30) cc_final: 0.8916 (pt0) REVERT: O 62 PHE cc_start: 0.8675 (m-10) cc_final: 0.8463 (m-80) REVERT: O 64 LEU cc_start: 0.9746 (tt) cc_final: 0.9436 (mt) REVERT: P 33 GLN cc_start: 0.9618 (mt0) cc_final: 0.9251 (mm110) REVERT: P 37 ARG cc_start: 0.9136 (ptm160) cc_final: 0.8927 (ptm-80) REVERT: P 49 MET cc_start: 0.9422 (ttp) cc_final: 0.9069 (tmm) REVERT: P 68 PHE cc_start: 0.9255 (m-80) cc_final: 0.8901 (m-80) REVERT: Q 27 ILE cc_start: 0.9435 (mt) cc_final: 0.9217 (mt) REVERT: Q 33 GLN cc_start: 0.9285 (mm-40) cc_final: 0.8884 (mm110) REVERT: Q 49 MET cc_start: 0.9342 (ppp) cc_final: 0.9038 (ppp) REVERT: Q 50 PHE cc_start: 0.9625 (m-80) cc_final: 0.9174 (m-80) REVERT: Q 55 PHE cc_start: 0.9646 (m-80) cc_final: 0.9390 (m-80) REVERT: Q 57 GLU cc_start: 0.9262 (mt-10) cc_final: 0.9049 (mt-10) REVERT: Q 62 PHE cc_start: 0.9561 (m-80) cc_final: 0.9238 (m-80) REVERT: Z 95 PHE cc_start: 0.9556 (m-10) cc_final: 0.9113 (m-80) REVERT: Z 207 TYR cc_start: 0.8203 (t80) cc_final: 0.7833 (t80) REVERT: Z 228 MET cc_start: 0.9261 (ptt) cc_final: 0.9027 (ptt) REVERT: Z 235 GLU cc_start: 0.9616 (pt0) cc_final: 0.9150 (tm-30) REVERT: Z 248 PHE cc_start: 0.9638 (m-10) cc_final: 0.9311 (m-10) REVERT: Z 249 ARG cc_start: 0.9693 (ttm170) cc_final: 0.9358 (ttm-80) REVERT: Z 258 GLU cc_start: 0.9121 (tm-30) cc_final: 0.8868 (tp30) REVERT: Z 289 LEU cc_start: 0.9799 (mt) cc_final: 0.9545 (mt) outliers start: 0 outliers final: 0 residues processed: 331 average time/residue: 0.0735 time to fit residues: 36.9528 Evaluate side-chains 288 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 288 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 87 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 108 optimal weight: 7.9990 chunk 85 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 78 optimal weight: 0.0060 chunk 59 optimal weight: 0.5980 chunk 94 optimal weight: 0.6980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 33 GLN ** 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 = 0.3563 r_free = 0.3563 target = 0.068740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.053561 restraints weight = 52801.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.054723 restraints weight = 42514.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.055429 restraints weight = 35173.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.055822 restraints weight = 30935.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.056327 restraints weight = 28430.101| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.5328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 9204 Z= 0.151 Angle : 0.661 9.833 12570 Z= 0.348 Chirality : 0.046 0.321 1596 Planarity : 0.005 0.071 1626 Dihedral : 3.897 21.883 1394 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % 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: 1.63 (0.23), residues: 1332 helix: 1.65 (0.15), residues: 1115 sheet: None (None), residues: 0 loop : -1.92 (0.40), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 37 TYR 0.016 0.002 TYR H 48 PHE 0.032 0.002 PHE P 55 TRP 0.007 0.001 TRP Z 208 HIS 0.001 0.001 HIS Z 170 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 9204) covalent geometry : angle 0.66108 (12570) hydrogen bonds : bond 0.04126 ( 899) hydrogen bonds : angle 3.97221 ( 2676) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1745.66 seconds wall clock time: 30 minutes 50.50 seconds (1850.50 seconds total)