Starting phenix.real_space_refine on Sat Jun 7 22:27:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9itx_60882/06_2025/9itx_60882.cif Found real_map, /net/cci-nas-00/data/ceres_data/9itx_60882/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9itx_60882/06_2025/9itx_60882.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9itx_60882/06_2025/9itx_60882.map" model { file = "/net/cci-nas-00/data/ceres_data/9itx_60882/06_2025/9itx_60882.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9itx_60882/06_2025/9itx_60882.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 1, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 7} 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: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 5} 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: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 3} 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: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 5} 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: {'GLN:plan1': 4, 'HIS:plan': 2, 'TYR:plan': 6, 'ASN:plan1': 12, 'TRP:plan': 2, 'ASP:plan': 3, 'PHE:plan': 30, 'GLU:plan': 7, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 369 Time building chain proxies: 7.24, per 1000 atoms: 0.80 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: 2.53 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 0.79 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: 2.62 Time building geometry restraints manager: 2.95 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: 16.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 25.860 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.050 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.007 0.001 TRP Z 122 HIS 0.002 0.001 HIS Z 170 PHE 0.020 0.001 PHE Z 276 TYR 0.007 0.001 TYR Z 296 ARG 0.001 0.000 ARG M 44 Details of bonding type rmsd hydrogen bonds : bond 0.11572 ( 899) hydrogen bonds : angle 4.37367 ( 2676) covalent geometry : bond 0.00314 ( 9204) covalent geometry : angle 0.54867 (12570) *********************** 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 : 1.027 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: 0.1720 time to fit residues: 104.2924 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 : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 110 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 66 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 102 optimal weight: 7.9990 chunk 39 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 118 optimal weight: 50.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 = 0.3498 r_free = 0.3498 target = 0.065985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.051960 restraints weight = 55274.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.053108 restraints weight = 42292.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.053946 restraints weight = 34200.020| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 9204 Z= 0.227 Angle : 0.606 6.197 12570 Z= 0.339 Chirality : 0.045 0.198 1596 Planarity : 0.005 0.058 1626 Dihedral : 3.799 21.475 1394 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.56 % Allowed : 4.51 % Favored : 94.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.23), residues: 1332 helix: 1.95 (0.15), residues: 1104 sheet: None (None), residues: 0 loop : -1.82 (0.42), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Z 208 HIS 0.006 0.003 HIS Z 31 PHE 0.026 0.002 PHE M 55 TYR 0.015 0.002 TYR O 48 ARG 0.009 0.001 ARG P 44 Details of bonding type rmsd hydrogen bonds : bond 0.04466 ( 899) hydrogen bonds : angle 4.10253 ( 2676) covalent geometry : bond 0.00472 ( 9204) covalent geometry : angle 0.60609 (12570) *********************** 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 359 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 355 time to evaluate : 1.173 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: 0.9366 (mt) cc_final: 0.8975 (mt) REVERT: H 48 TYR cc_start: 0.9145 (m-80) cc_final: 0.8945 (m-10) REVERT: H 49 MET cc_start: 0.9704 (ttp) cc_final: 0.9345 (tmm) REVERT: H 50 PHE cc_start: 0.9634 (m-80) cc_final: 0.9156 (m-80) REVERT: H 57 GLU cc_start: 0.9738 (tp30) cc_final: 0.9440 (tp30) REVERT: I 28 VAL cc_start: 0.9591 (t) cc_final: 0.9346 (m) REVERT: I 42 GLU cc_start: 0.9403 (tt0) cc_final: 0.9007 (tp30) REVERT: I 49 MET cc_start: 0.9426 (ttp) cc_final: 0.8976 (tmm) REVERT: I 55 PHE cc_start: 0.9489 (m-80) cc_final: 0.9129 (m-80) REVERT: J 1 MET cc_start: 0.8332 (mmt) cc_final: 0.7283 (mmt) REVERT: J 48 TYR cc_start: 0.9431 (m-80) cc_final: 0.8787 (m-80) REVERT: J 49 MET cc_start: 0.9576 (ttp) cc_final: 0.9359 (tmm) REVERT: J 53 ILE cc_start: 0.9654 (mt) cc_final: 0.9424 (mt) REVERT: K 15 LEU cc_start: 0.9797 (mt) cc_final: 0.9530 (tp) REVERT: K 18 ILE cc_start: 0.9508 (pt) cc_final: 0.9165 (tp) REVERT: K 33 GLN cc_start: 0.9489 (mt0) cc_final: 0.8970 (mm110) REVERT: K 44 ARG cc_start: 0.9436 (tpp80) cc_final: 0.9108 (tpp80) REVERT: K 48 TYR cc_start: 0.9596 (m-80) cc_final: 0.9146 (m-80) REVERT: K 55 PHE cc_start: 0.9610 (m-80) cc_final: 0.9302 (m-80) REVERT: K 68 PHE cc_start: 0.9591 (m-10) cc_final: 0.9299 (m-80) REVERT: L 1 MET cc_start: 0.8926 (mtp) cc_final: 0.8141 (mtt) REVERT: L 43 ASN cc_start: 0.9425 (m-40) cc_final: 0.9171 (p0) REVERT: L 49 MET cc_start: 0.9790 (ttp) cc_final: 0.9414 (tmm) REVERT: L 50 PHE cc_start: 0.9608 (m-80) cc_final: 0.9133 (m-80) REVERT: L 51 ILE cc_start: 0.9861 (mt) cc_final: 0.9618 (mt) REVERT: L 53 ILE cc_start: 0.9804 (tt) cc_final: 0.9422 (tp) REVERT: L 55 PHE cc_start: 0.9560 (m-80) cc_final: 0.9195 (m-80) REVERT: L 57 GLU cc_start: 0.9528 (tp30) cc_final: 0.9186 (pt0) REVERT: M 11 LEU cc_start: 0.9824 (mt) cc_final: 0.9577 (tt) REVERT: M 27 ILE cc_start: 0.9778 (mt) cc_final: 0.9385 (mt) REVERT: M 33 GLN cc_start: 0.9468 (pm20) cc_final: 0.9066 (pm20) REVERT: M 49 MET cc_start: 0.9546 (ttp) cc_final: 0.8856 (tpt) REVERT: M 50 PHE cc_start: 0.9386 (m-80) cc_final: 0.9120 (m-80) REVERT: M 59 LEU cc_start: 0.9467 (tp) cc_final: 0.9244 (mt) REVERT: N 11 LEU cc_start: 0.9809 (mm) cc_final: 0.9505 (mm) REVERT: N 32 VAL cc_start: 0.9785 (p) cc_final: 0.9389 (p) REVERT: N 40 GLU cc_start: 0.9361 (pt0) cc_final: 0.9152 (pp20) REVERT: N 64 LEU cc_start: 0.9676 (tp) cc_final: 0.9462 (mt) REVERT: O 29 SER cc_start: 0.9549 (t) cc_final: 0.9226 (p) REVERT: O 32 VAL cc_start: 0.9633 (p) cc_final: 0.9244 (m) REVERT: O 33 GLN cc_start: 0.9459 (mt0) cc_final: 0.9013 (mm110) REVERT: O 37 ARG cc_start: 0.9003 (mtt180) cc_final: 0.8491 (mtt180) REVERT: O 53 ILE cc_start: 0.9463 (tt) cc_final: 0.9248 (tp) REVERT: O 57 GLU cc_start: 0.9439 (mm-30) cc_final: 0.8852 (pt0) REVERT: O 62 PHE cc_start: 0.8734 (m-10) cc_final: 0.8511 (m-80) REVERT: O 64 LEU cc_start: 0.9736 (tt) cc_final: 0.9376 (mt) REVERT: P 33 GLN cc_start: 0.9544 (mt0) cc_final: 0.8932 (mt0) REVERT: P 49 MET cc_start: 0.9570 (ttp) cc_final: 0.9061 (tmm) REVERT: P 68 PHE cc_start: 0.9274 (m-80) cc_final: 0.8931 (m-80) REVERT: Q 18 ILE cc_start: 0.9509 (pt) cc_final: 0.9129 (mm) REVERT: Q 27 ILE cc_start: 0.9549 (mt) cc_final: 0.9334 (mt) REVERT: Q 33 GLN cc_start: 0.9128 (mm-40) cc_final: 0.8913 (mm110) REVERT: Q 37 ARG cc_start: 0.9241 (mtt180) cc_final: 0.8828 (mtt90) REVERT: Q 50 PHE cc_start: 0.9662 (m-80) cc_final: 0.9260 (m-80) REVERT: Q 55 PHE cc_start: 0.9476 (m-80) cc_final: 0.9242 (m-80) REVERT: Q 62 PHE cc_start: 0.9582 (m-10) cc_final: 0.9293 (m-80) REVERT: Z 95 PHE cc_start: 0.9582 (m-10) cc_final: 0.9132 (m-80) REVERT: Z 123 PHE cc_start: 0.9565 (t80) cc_final: 0.9243 (t80) REVERT: Z 191 LEU cc_start: 0.9463 (mt) cc_final: 0.9262 (pp) REVERT: Z 207 TYR cc_start: 0.8180 (t80) cc_final: 0.7789 (t80) REVERT: Z 228 MET cc_start: 0.9244 (ptt) cc_final: 0.9027 (ptt) REVERT: Z 248 PHE cc_start: 0.9589 (m-10) cc_final: 0.9123 (m-80) REVERT: Z 249 ARG cc_start: 0.9749 (ttm-80) cc_final: 0.9183 (ttm-80) REVERT: Z 260 LEU cc_start: 0.9823 (tt) cc_final: 0.9601 (pp) REVERT: Z 264 MET cc_start: 0.9139 (ttm) cc_final: 0.8815 (tpt) REVERT: Z 280 GLU cc_start: 0.9450 (mm-30) cc_final: 0.8996 (mm-30) REVERT: Z 282 PHE cc_start: 0.9642 (t80) cc_final: 0.9252 (t80) outliers start: 4 outliers final: 0 residues processed: 356 average time/residue: 0.1773 time to fit residues: 91.3848 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 : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 75 optimal weight: 0.7980 chunk 114 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 89 optimal weight: 0.0270 chunk 22 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 70 optimal weight: 0.0570 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 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 = 0.3532 r_free = 0.3532 target = 0.067501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.052859 restraints weight = 52507.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.054011 restraints weight = 40470.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.054830 restraints weight = 32876.810| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.3356 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= 0.148 Angle : 0.574 7.991 12570 Z= 0.309 Chirality : 0.044 0.241 1596 Planarity : 0.005 0.062 1626 Dihedral : 3.747 18.482 1394 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.56 % Allowed : 3.24 % Favored : 96.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.23), residues: 1332 helix: 1.91 (0.15), residues: 1103 sheet: None (None), residues: 0 loop : -1.83 (0.42), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Z 208 HIS 0.002 0.001 HIS Z 170 PHE 0.029 0.001 PHE M 55 TYR 0.016 0.001 TYR I 48 ARG 0.011 0.001 ARG P 44 Details of bonding type rmsd hydrogen bonds : bond 0.04236 ( 899) hydrogen bonds : angle 3.82715 ( 2676) covalent geometry : bond 0.00341 ( 9204) covalent geometry : angle 0.57446 (12570) *********************** 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 367 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 363 time to evaluate : 0.968 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: H 38 ASN cc_start: 0.9441 (t0) cc_final: 0.9051 (t0) REVERT: H 49 MET cc_start: 0.9647 (ttp) cc_final: 0.9360 (tmm) REVERT: H 50 PHE cc_start: 0.9599 (m-80) cc_final: 0.9150 (m-80) REVERT: H 57 GLU cc_start: 0.9748 (tp30) cc_final: 0.9455 (tp30) REVERT: I 26 ILE cc_start: 0.9505 (tt) cc_final: 0.9236 (pt) REVERT: I 27 ILE cc_start: 0.9578 (OUTLIER) cc_final: 0.9372 (mt) REVERT: I 49 MET cc_start: 0.9422 (ttp) cc_final: 0.8934 (tmm) REVERT: I 55 PHE cc_start: 0.9512 (m-80) cc_final: 0.9167 (m-80) REVERT: J 48 TYR cc_start: 0.9409 (m-80) cc_final: 0.8719 (m-80) REVERT: J 53 ILE cc_start: 0.9683 (mt) cc_final: 0.9440 (mt) REVERT: K 15 LEU cc_start: 0.9770 (mt) cc_final: 0.9500 (tp) REVERT: K 18 ILE cc_start: 0.9467 (pt) cc_final: 0.9154 (tp) REVERT: K 27 ILE cc_start: 0.9564 (mt) cc_final: 0.9258 (mt) REVERT: K 33 GLN cc_start: 0.9491 (mt0) cc_final: 0.8973 (mm110) REVERT: K 44 ARG cc_start: 0.9456 (tpp80) cc_final: 0.8891 (mmm-85) REVERT: K 48 TYR cc_start: 0.9617 (m-80) cc_final: 0.8940 (m-80) REVERT: K 49 MET cc_start: 0.9621 (ttp) cc_final: 0.9391 (ppp) REVERT: K 55 PHE cc_start: 0.9627 (m-80) cc_final: 0.9291 (m-80) REVERT: K 68 PHE cc_start: 0.9561 (m-10) cc_final: 0.9245 (m-80) REVERT: L 1 MET cc_start: 0.8884 (mtp) cc_final: 0.8276 (mtt) REVERT: L 33 GLN cc_start: 0.9356 (pt0) cc_final: 0.9069 (pt0) REVERT: L 50 PHE cc_start: 0.9629 (m-80) cc_final: 0.9309 (m-10) REVERT: L 51 ILE cc_start: 0.9839 (mt) cc_final: 0.9527 (mt) REVERT: L 53 ILE cc_start: 0.9788 (tt) cc_final: 0.9455 (tp) REVERT: L 55 PHE cc_start: 0.9517 (m-80) cc_final: 0.9054 (m-80) REVERT: L 57 GLU cc_start: 0.9525 (tp30) cc_final: 0.9148 (pt0) REVERT: M 11 LEU cc_start: 0.9828 (mt) cc_final: 0.9563 (tt) REVERT: M 27 ILE cc_start: 0.9735 (mt) cc_final: 0.9505 (mt) REVERT: M 50 PHE cc_start: 0.9356 (m-80) cc_final: 0.8649 (m-80) REVERT: M 62 PHE cc_start: 0.8981 (m-80) cc_final: 0.8744 (m-80) REVERT: N 1 MET cc_start: 0.6467 (tpt) cc_final: 0.5692 (tpt) REVERT: N 11 LEU cc_start: 0.9809 (mm) cc_final: 0.9511 (mm) REVERT: N 55 PHE cc_start: 0.9624 (m-80) cc_final: 0.9120 (m-80) REVERT: O 29 SER cc_start: 0.9504 (t) cc_final: 0.9184 (p) REVERT: O 32 VAL cc_start: 0.9565 (p) cc_final: 0.9232 (m) REVERT: O 33 GLN cc_start: 0.9422 (mt0) cc_final: 0.9019 (mm-40) REVERT: O 37 ARG cc_start: 0.9004 (mtt180) cc_final: 0.8555 (mtm180) REVERT: O 50 PHE cc_start: 0.9429 (m-80) cc_final: 0.9206 (m-80) REVERT: O 57 GLU cc_start: 0.9348 (mm-30) cc_final: 0.8764 (pt0) REVERT: O 62 PHE cc_start: 0.8670 (m-10) cc_final: 0.8467 (m-80) REVERT: O 64 LEU cc_start: 0.9654 (tt) cc_final: 0.9392 (mt) REVERT: P 1 MET cc_start: 0.6712 (mtm) cc_final: 0.6014 (mtt) REVERT: P 33 GLN cc_start: 0.9493 (mt0) cc_final: 0.9158 (mm110) REVERT: P 49 MET cc_start: 0.9420 (ttp) cc_final: 0.9008 (tmm) REVERT: P 68 PHE cc_start: 0.9226 (m-80) cc_final: 0.8866 (m-80) REVERT: Q 18 ILE cc_start: 0.9473 (pt) cc_final: 0.9142 (mm) REVERT: Q 33 GLN cc_start: 0.8929 (mm-40) cc_final: 0.8561 (mm110) REVERT: Q 37 ARG cc_start: 0.9160 (mtt180) cc_final: 0.7927 (ttm110) REVERT: Q 49 MET cc_start: 0.9497 (ppp) cc_final: 0.9224 (ppp) REVERT: Q 50 PHE cc_start: 0.9624 (m-80) cc_final: 0.9212 (m-80) REVERT: Q 55 PHE cc_start: 0.9468 (m-80) cc_final: 0.9211 (m-80) REVERT: Q 62 PHE cc_start: 0.9427 (m-10) cc_final: 0.9219 (m-80) REVERT: Z 95 PHE cc_start: 0.9559 (m-10) cc_final: 0.9162 (m-80) REVERT: Z 123 PHE cc_start: 0.9526 (t80) cc_final: 0.9147 (t80) REVERT: Z 132 ILE cc_start: 0.9213 (mt) cc_final: 0.8931 (mm) REVERT: Z 207 TYR cc_start: 0.8174 (t80) cc_final: 0.7760 (t80) REVERT: Z 228 MET cc_start: 0.9175 (ptt) cc_final: 0.8970 (ptt) REVERT: Z 248 PHE cc_start: 0.9565 (m-10) cc_final: 0.9112 (m-80) REVERT: Z 264 MET cc_start: 0.9195 (ttm) cc_final: 0.8849 (tpt) REVERT: Z 272 LEU cc_start: 0.9513 (tt) cc_final: 0.9285 (tt) REVERT: Z 280 GLU cc_start: 0.9419 (mm-30) cc_final: 0.9202 (mm-30) REVERT: Z 282 PHE cc_start: 0.9576 (t80) cc_final: 0.9172 (t80) REVERT: Z 287 GLN cc_start: 0.9570 (mm110) cc_final: 0.9130 (mm-40) REVERT: Z 289 LEU cc_start: 0.9754 (mt) cc_final: 0.9526 (mt) outliers start: 4 outliers final: 1 residues processed: 364 average time/residue: 0.1638 time to fit residues: 86.3236 Evaluate side-chains 296 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 294 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 125 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 107 optimal weight: 30.0000 chunk 100 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 93 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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** Q 33 GLN ** 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 = 0.3531 r_free = 0.3531 target = 0.067654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.053062 restraints weight = 52827.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.054173 restraints weight = 40469.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.054900 restraints weight = 32890.412| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9204 Z= 0.151 Angle : 0.581 8.096 12570 Z= 0.309 Chirality : 0.044 0.251 1596 Planarity : 0.005 0.069 1626 Dihedral : 3.743 19.921 1394 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.56 % Allowed : 2.96 % Favored : 96.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.23), residues: 1332 helix: 1.87 (0.15), residues: 1102 sheet: None (None), residues: 0 loop : -1.83 (0.41), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Z 208 HIS 0.002 0.001 HIS Z 170 PHE 0.025 0.001 PHE I 62 TYR 0.020 0.001 TYR I 48 ARG 0.004 0.000 ARG Q 37 Details of bonding type rmsd hydrogen bonds : bond 0.04081 ( 899) hydrogen bonds : angle 3.87412 ( 2676) covalent geometry : bond 0.00345 ( 9204) covalent geometry : angle 0.58148 (12570) *********************** 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: 4 poor density : 344 time to evaluate : 1.260 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: 0.9455 (t0) cc_final: 0.9073 (t0) REVERT: H 49 MET cc_start: 0.9650 (ttp) cc_final: 0.9376 (tmm) REVERT: H 50 PHE cc_start: 0.9608 (m-80) cc_final: 0.9148 (m-80) REVERT: H 57 GLU cc_start: 0.9757 (tp30) cc_final: 0.9464 (tp30) REVERT: H 64 LEU cc_start: 0.9748 (mm) cc_final: 0.9543 (mm) REVERT: H 68 PHE cc_start: 0.9405 (m-10) cc_final: 0.9192 (m-80) REVERT: I 27 ILE cc_start: 0.9559 (OUTLIER) cc_final: 0.9355 (mt) REVERT: I 49 MET cc_start: 0.9442 (ttp) cc_final: 0.8889 (tmm) REVERT: I 55 PHE cc_start: 0.9505 (m-80) cc_final: 0.9235 (m-80) REVERT: J 48 TYR cc_start: 0.9369 (m-80) cc_final: 0.8681 (m-80) REVERT: J 49 MET cc_start: 0.9469 (tmm) cc_final: 0.9208 (tmm) REVERT: K 1 MET cc_start: 0.5044 (mmt) cc_final: 0.4749 (tpp) REVERT: K 15 LEU cc_start: 0.9767 (mt) cc_final: 0.9489 (tp) REVERT: K 18 ILE cc_start: 0.9450 (pt) cc_final: 0.9108 (tp) REVERT: K 22 VAL cc_start: 0.9197 (p) cc_final: 0.8970 (p) REVERT: K 27 ILE cc_start: 0.9563 (mt) cc_final: 0.9320 (mt) REVERT: K 44 ARG cc_start: 0.9491 (tpp80) cc_final: 0.8944 (tpp80) REVERT: K 48 TYR cc_start: 0.9602 (m-80) cc_final: 0.9023 (m-80) REVERT: K 49 MET cc_start: 0.9634 (ttp) cc_final: 0.9373 (ppp) REVERT: K 55 PHE cc_start: 0.9612 (m-80) cc_final: 0.9191 (m-80) REVERT: K 59 LEU cc_start: 0.9602 (mt) cc_final: 0.9395 (mt) REVERT: K 65 VAL cc_start: 0.9748 (p) cc_final: 0.9488 (p) REVERT: K 68 PHE cc_start: 0.9496 (m-10) cc_final: 0.9205 (m-80) REVERT: L 1 MET cc_start: 0.8894 (mtp) cc_final: 0.8453 (mtt) REVERT: L 24 ILE cc_start: 0.9830 (mt) cc_final: 0.9576 (mt) REVERT: L 33 GLN cc_start: 0.9360 (pt0) cc_final: 0.9015 (pt0) REVERT: L 50 PHE cc_start: 0.9629 (m-80) cc_final: 0.9332 (m-10) REVERT: L 51 ILE cc_start: 0.9844 (mt) cc_final: 0.9525 (mt) REVERT: L 53 ILE cc_start: 0.9789 (tt) cc_final: 0.9518 (tp) REVERT: L 55 PHE cc_start: 0.9546 (m-80) cc_final: 0.8982 (m-80) REVERT: M 11 LEU cc_start: 0.9822 (mt) cc_final: 0.9600 (tt) REVERT: M 27 ILE cc_start: 0.9744 (mt) cc_final: 0.9279 (mt) REVERT: M 49 MET cc_start: 0.8984 (tmm) cc_final: 0.8571 (tpt) REVERT: N 1 MET cc_start: 0.6275 (tpt) cc_final: 0.5755 (tpt) REVERT: N 11 LEU cc_start: 0.9806 (mm) cc_final: 0.9532 (mm) REVERT: N 55 PHE cc_start: 0.9649 (m-80) cc_final: 0.9169 (m-80) REVERT: O 29 SER cc_start: 0.9507 (t) cc_final: 0.9136 (p) REVERT: O 32 VAL cc_start: 0.9599 (p) cc_final: 0.9170 (m) REVERT: O 33 GLN cc_start: 0.9441 (mt0) cc_final: 0.9052 (mm110) REVERT: O 37 ARG cc_start: 0.9074 (mtt180) cc_final: 0.8515 (mtm180) REVERT: O 57 GLU cc_start: 0.9338 (mm-30) cc_final: 0.8769 (pt0) REVERT: O 62 PHE cc_start: 0.8661 (m-10) cc_final: 0.8361 (m-80) REVERT: O 64 LEU cc_start: 0.9754 (tt) cc_final: 0.9452 (mt) REVERT: P 33 GLN cc_start: 0.9616 (mt0) cc_final: 0.9256 (mm-40) REVERT: P 49 MET cc_start: 0.9510 (ttp) cc_final: 0.9060 (tmm) REVERT: P 55 PHE cc_start: 0.9182 (m-80) cc_final: 0.8651 (m-80) REVERT: P 68 PHE cc_start: 0.9224 (m-80) cc_final: 0.8888 (m-80) REVERT: Q 18 ILE cc_start: 0.9422 (pt) cc_final: 0.9091 (mm) REVERT: Q 27 ILE cc_start: 0.9463 (mt) cc_final: 0.9259 (mt) REVERT: Q 33 GLN cc_start: 0.9179 (mm110) cc_final: 0.8943 (mm110) REVERT: Q 49 MET cc_start: 0.9423 (ppp) cc_final: 0.9156 (ppp) REVERT: Q 50 PHE cc_start: 0.9629 (m-80) cc_final: 0.9189 (m-80) REVERT: Q 57 GLU cc_start: 0.9368 (mt-10) cc_final: 0.8744 (mt-10) REVERT: Z 74 GLN cc_start: 0.9520 (mm110) cc_final: 0.9284 (mm110) REVERT: Z 80 LEU cc_start: 0.9223 (mm) cc_final: 0.8936 (pt) REVERT: Z 95 PHE cc_start: 0.9576 (m-10) cc_final: 0.9175 (m-80) REVERT: Z 123 PHE cc_start: 0.9545 (t80) cc_final: 0.9132 (t80) REVERT: Z 132 ILE cc_start: 0.9230 (mt) cc_final: 0.8924 (mm) REVERT: Z 207 TYR cc_start: 0.8123 (t80) cc_final: 0.7724 (t80) REVERT: Z 228 MET cc_start: 0.9184 (ptt) cc_final: 0.8964 (ptt) REVERT: Z 248 PHE cc_start: 0.9492 (m-10) cc_final: 0.9160 (m-80) REVERT: Z 249 ARG cc_start: 0.9376 (mtp180) cc_final: 0.8891 (ptp-110) REVERT: Z 264 MET cc_start: 0.9238 (ttm) cc_final: 0.8847 (tpp) REVERT: Z 280 GLU cc_start: 0.9468 (mm-30) cc_final: 0.9203 (mm-30) REVERT: Z 282 PHE cc_start: 0.9548 (t80) cc_final: 0.9152 (t80) REVERT: Z 287 GLN cc_start: 0.9545 (mm110) cc_final: 0.9124 (mm110) REVERT: Z 289 LEU cc_start: 0.9754 (mt) cc_final: 0.9537 (mt) outliers start: 4 outliers final: 0 residues processed: 344 average time/residue: 0.2127 time to fit residues: 106.7115 Evaluate side-chains 280 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 279 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 42 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 126 optimal weight: 6.9990 chunk 17 optimal weight: 0.0170 chunk 113 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 120 optimal weight: 0.1980 overall best weight: 0.4818 ------------------------------------------------------------------------------- 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 ** 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 = 0.3540 r_free = 0.3540 target = 0.068618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.053725 restraints weight = 51593.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.054839 restraints weight = 40055.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.055683 restraints weight = 32847.242| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.4065 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= 0.143 Angle : 0.582 7.823 12570 Z= 0.310 Chirality : 0.044 0.177 1596 Planarity : 0.005 0.070 1626 Dihedral : 3.777 21.933 1394 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.70 % Allowed : 2.82 % Favored : 96.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.23), residues: 1332 helix: 1.86 (0.15), residues: 1103 sheet: None (None), residues: 0 loop : -1.91 (0.41), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Z 208 HIS 0.001 0.001 HIS Z 170 PHE 0.026 0.001 PHE K 62 TYR 0.021 0.002 TYR Z 277 ARG 0.002 0.000 ARG Q 44 Details of bonding type rmsd hydrogen bonds : bond 0.04015 ( 899) hydrogen bonds : angle 3.84928 ( 2676) covalent geometry : bond 0.00330 ( 9204) covalent geometry : angle 0.58173 (12570) *********************** 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 353 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 348 time to evaluate : 1.136 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: 0.9139 (t0) cc_final: 0.8748 (t0) REVERT: H 49 MET cc_start: 0.9674 (ttp) cc_final: 0.9423 (tmm) REVERT: H 50 PHE cc_start: 0.9624 (m-80) cc_final: 0.9183 (m-80) REVERT: H 57 GLU cc_start: 0.9786 (tp30) cc_final: 0.9474 (tp30) REVERT: H 64 LEU cc_start: 0.9741 (mm) cc_final: 0.9533 (mt) REVERT: H 68 PHE cc_start: 0.9407 (m-10) cc_final: 0.9190 (m-80) REVERT: I 27 ILE cc_start: 0.9549 (OUTLIER) cc_final: 0.9246 (mp) REVERT: I 35 ILE cc_start: 0.9210 (mm) cc_final: 0.8918 (tp) REVERT: I 51 ILE cc_start: 0.9694 (mt) cc_final: 0.9431 (mt) REVERT: I 55 PHE cc_start: 0.9507 (m-80) cc_final: 0.9159 (m-80) REVERT: I 68 PHE cc_start: 0.9371 (m-80) cc_final: 0.8970 (m-80) REVERT: J 1 MET cc_start: 0.8317 (mmp) cc_final: 0.8048 (mmp) REVERT: J 15 LEU cc_start: 0.9574 (mp) cc_final: 0.9279 (tp) REVERT: J 48 TYR cc_start: 0.9389 (m-80) cc_final: 0.8698 (m-80) REVERT: J 49 MET cc_start: 0.9626 (tmm) cc_final: 0.9213 (tmm) REVERT: K 1 MET cc_start: 0.4998 (mmt) cc_final: 0.4781 (tpp) REVERT: K 15 LEU cc_start: 0.9785 (mt) cc_final: 0.9498 (tp) REVERT: K 18 ILE cc_start: 0.9419 (pt) cc_final: 0.8969 (tp) REVERT: K 22 VAL cc_start: 0.9150 (p) cc_final: 0.8946 (p) REVERT: K 44 ARG cc_start: 0.9454 (tpp80) cc_final: 0.9178 (tpp80) REVERT: K 49 MET cc_start: 0.9603 (ttp) cc_final: 0.9382 (ppp) REVERT: K 55 PHE cc_start: 0.9569 (m-80) cc_final: 0.9335 (m-80) REVERT: K 65 VAL cc_start: 0.9755 (p) cc_final: 0.9405 (p) REVERT: K 68 PHE cc_start: 0.9464 (m-10) cc_final: 0.9168 (m-80) REVERT: L 1 MET cc_start: 0.9106 (mtp) cc_final: 0.8835 (mtt) REVERT: L 43 ASN cc_start: 0.9376 (p0) cc_final: 0.9047 (m-40) REVERT: L 50 PHE cc_start: 0.9626 (m-80) cc_final: 0.9303 (m-10) REVERT: L 51 ILE cc_start: 0.9847 (mt) cc_final: 0.9512 (mt) REVERT: L 53 ILE cc_start: 0.9822 (tt) cc_final: 0.9454 (tp) REVERT: L 55 PHE cc_start: 0.9452 (m-80) cc_final: 0.8951 (m-80) REVERT: L 57 GLU cc_start: 0.9481 (mm-30) cc_final: 0.8916 (mt-10) REVERT: M 26 ILE cc_start: 0.9748 (OUTLIER) cc_final: 0.9477 (tp) REVERT: M 27 ILE cc_start: 0.9691 (mt) cc_final: 0.9358 (mt) REVERT: M 50 PHE cc_start: 0.9546 (m-80) cc_final: 0.9223 (m-10) REVERT: M 59 LEU cc_start: 0.9389 (mt) cc_final: 0.9188 (mt) REVERT: N 1 MET cc_start: 0.6578 (tpt) cc_final: 0.5785 (mmm) REVERT: N 11 LEU cc_start: 0.9809 (mm) cc_final: 0.9522 (mm) REVERT: N 33 GLN cc_start: 0.9257 (mp10) cc_final: 0.8997 (mp10) REVERT: N 55 PHE cc_start: 0.9652 (m-80) cc_final: 0.9149 (m-80) REVERT: O 1 MET cc_start: 0.6784 (mmt) cc_final: 0.6039 (mmt) REVERT: O 29 SER cc_start: 0.9515 (t) cc_final: 0.9174 (p) REVERT: O 32 VAL cc_start: 0.9612 (p) cc_final: 0.9213 (m) REVERT: O 33 GLN cc_start: 0.9411 (mt0) cc_final: 0.9058 (mm-40) REVERT: O 37 ARG cc_start: 0.9089 (mtt180) cc_final: 0.8605 (mtm180) REVERT: O 57 GLU cc_start: 0.9304 (mm-30) cc_final: 0.8737 (pt0) REVERT: O 64 LEU cc_start: 0.9713 (tt) cc_final: 0.9327 (mt) REVERT: O 66 ILE cc_start: 0.9539 (tp) cc_final: 0.9315 (tp) REVERT: P 33 GLN cc_start: 0.9595 (mt0) cc_final: 0.9287 (mm110) REVERT: P 49 MET cc_start: 0.9411 (ttp) cc_final: 0.8351 (tpp) REVERT: P 68 PHE cc_start: 0.9229 (m-80) cc_final: 0.8847 (m-80) REVERT: Q 18 ILE cc_start: 0.9432 (pt) cc_final: 0.9075 (mm) REVERT: Q 33 GLN cc_start: 0.9124 (mm110) cc_final: 0.8879 (mm110) REVERT: Q 50 PHE cc_start: 0.9653 (m-80) cc_final: 0.9252 (m-80) REVERT: Z 74 GLN cc_start: 0.9482 (mm110) cc_final: 0.9264 (mm110) REVERT: Z 84 MET cc_start: 0.9211 (mmp) cc_final: 0.9006 (mmm) REVERT: Z 95 PHE cc_start: 0.9520 (m-10) cc_final: 0.9163 (m-80) REVERT: Z 123 PHE cc_start: 0.9525 (t80) cc_final: 0.9124 (t80) REVERT: Z 132 ILE cc_start: 0.9199 (mt) cc_final: 0.8871 (mm) REVERT: Z 207 TYR cc_start: 0.8044 (t80) cc_final: 0.7666 (t80) REVERT: Z 228 MET cc_start: 0.9202 (ptt) cc_final: 0.8966 (ptt) REVERT: Z 248 PHE cc_start: 0.9506 (m-10) cc_final: 0.9106 (m-80) REVERT: Z 249 ARG cc_start: 0.9389 (mtp180) cc_final: 0.9188 (ttm-80) REVERT: Z 264 MET cc_start: 0.9263 (ttm) cc_final: 0.8896 (ttm) REVERT: Z 280 GLU cc_start: 0.9461 (mm-30) cc_final: 0.9222 (mm-30) REVERT: Z 282 PHE cc_start: 0.9519 (t80) cc_final: 0.9144 (t80) REVERT: Z 287 GLN cc_start: 0.9537 (mm110) cc_final: 0.9230 (mm110) outliers start: 5 outliers final: 0 residues processed: 348 average time/residue: 0.2042 time to fit residues: 105.3198 Evaluate side-chains 296 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 294 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 114 optimal weight: 0.0870 chunk 110 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 76 optimal weight: 0.1980 chunk 35 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 75 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 overall best weight: 0.9960 ------------------------------------------------------------------------------- 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 = 0.3535 r_free = 0.3535 target = 0.068275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.053297 restraints weight = 50535.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.054219 restraints weight = 39595.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.055080 restraints weight = 33035.643| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.4332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 9204 Z= 0.156 Angle : 0.592 7.217 12570 Z= 0.316 Chirality : 0.044 0.206 1596 Planarity : 0.005 0.072 1626 Dihedral : 3.800 22.287 1394 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.23), residues: 1332 helix: 1.85 (0.15), residues: 1104 sheet: None (None), residues: 0 loop : -1.85 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Z 208 HIS 0.002 0.001 HIS Z 170 PHE 0.030 0.001 PHE H 62 TYR 0.022 0.002 TYR I 48 ARG 0.013 0.001 ARG I 37 Details of bonding type rmsd hydrogen bonds : bond 0.04054 ( 899) hydrogen bonds : angle 3.86151 ( 2676) covalent geometry : bond 0.00368 ( 9204) covalent geometry : angle 0.59156 (12570) *********************** 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 338 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 338 time to evaluate : 1.036 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 38 ASN cc_start: 0.9074 (t0) cc_final: 0.8857 (t0) REVERT: H 49 MET cc_start: 0.9661 (ttp) cc_final: 0.9402 (tmm) REVERT: H 50 PHE cc_start: 0.9614 (m-80) cc_final: 0.9164 (m-80) REVERT: H 57 GLU cc_start: 0.9791 (tp30) cc_final: 0.9403 (tp30) REVERT: H 64 LEU cc_start: 0.9770 (mm) cc_final: 0.9489 (mt) REVERT: H 68 PHE cc_start: 0.9389 (m-10) cc_final: 0.9174 (m-80) REVERT: I 35 ILE cc_start: 0.9269 (mm) cc_final: 0.8954 (tp) REVERT: I 49 MET cc_start: 0.9554 (ptt) cc_final: 0.9127 (ppp) REVERT: I 51 ILE cc_start: 0.9685 (mt) cc_final: 0.9454 (mt) REVERT: I 55 PHE cc_start: 0.9541 (m-80) cc_final: 0.9186 (m-80) REVERT: J 1 MET cc_start: 0.8449 (mmp) cc_final: 0.8132 (mmp) REVERT: J 15 LEU cc_start: 0.9571 (mp) cc_final: 0.9260 (tp) REVERT: J 48 TYR cc_start: 0.9350 (m-80) cc_final: 0.8736 (m-80) REVERT: J 49 MET cc_start: 0.9604 (tmm) cc_final: 0.9239 (tmm) REVERT: J 53 ILE cc_start: 0.9743 (mt) cc_final: 0.9519 (mt) REVERT: K 15 LEU cc_start: 0.9790 (mt) cc_final: 0.9564 (tp) REVERT: K 18 ILE cc_start: 0.9410 (pt) cc_final: 0.8934 (tp) REVERT: K 22 VAL cc_start: 0.9099 (p) cc_final: 0.8881 (p) REVERT: K 44 ARG cc_start: 0.9405 (tpp80) cc_final: 0.8809 (tpp80) REVERT: K 48 TYR cc_start: 0.9564 (m-10) cc_final: 0.9267 (m-80) REVERT: K 55 PHE cc_start: 0.9574 (m-80) cc_final: 0.9220 (m-80) REVERT: K 65 VAL cc_start: 0.9698 (p) cc_final: 0.9401 (p) REVERT: K 68 PHE cc_start: 0.9436 (m-10) cc_final: 0.9164 (m-80) REVERT: L 1 MET cc_start: 0.9072 (mtp) cc_final: 0.8825 (mtt) REVERT: L 50 PHE cc_start: 0.9639 (m-80) cc_final: 0.9318 (m-10) REVERT: L 51 ILE cc_start: 0.9843 (mt) cc_final: 0.9521 (mt) REVERT: L 55 PHE cc_start: 0.9433 (m-80) cc_final: 0.8971 (m-80) REVERT: L 57 GLU cc_start: 0.9465 (mm-30) cc_final: 0.9108 (mm-30) REVERT: M 50 PHE cc_start: 0.9546 (m-80) cc_final: 0.9226 (m-80) REVERT: M 68 PHE cc_start: 0.9464 (t80) cc_final: 0.9212 (t80) REVERT: N 1 MET cc_start: 0.6344 (tpt) cc_final: 0.5657 (mmm) REVERT: N 55 PHE cc_start: 0.9637 (m-80) cc_final: 0.9147 (m-80) REVERT: O 1 MET cc_start: 0.6882 (mmt) cc_final: 0.6434 (mmt) REVERT: O 29 SER cc_start: 0.9507 (t) cc_final: 0.9125 (p) REVERT: O 32 VAL cc_start: 0.9629 (p) cc_final: 0.9160 (m) REVERT: O 33 GLN cc_start: 0.9439 (mt0) cc_final: 0.9111 (mm110) REVERT: O 37 ARG cc_start: 0.9082 (mtt180) cc_final: 0.8591 (mtm180) REVERT: O 57 GLU cc_start: 0.9416 (mm-30) cc_final: 0.8906 (pt0) REVERT: O 64 LEU cc_start: 0.9764 (tt) cc_final: 0.9460 (mt) REVERT: P 33 GLN cc_start: 0.9619 (mt0) cc_final: 0.9279 (mm110) REVERT: P 49 MET cc_start: 0.9447 (ttp) cc_final: 0.8438 (tpp) REVERT: P 68 PHE cc_start: 0.9249 (m-80) cc_final: 0.8895 (m-80) REVERT: Q 18 ILE cc_start: 0.9416 (pt) cc_final: 0.9066 (mm) REVERT: Q 33 GLN cc_start: 0.9089 (mm110) cc_final: 0.8851 (mm110) REVERT: Q 49 MET cc_start: 0.9377 (ppp) cc_final: 0.9107 (ppp) REVERT: Q 50 PHE cc_start: 0.9639 (m-80) cc_final: 0.9249 (m-80) REVERT: Q 55 PHE cc_start: 0.9517 (m-80) cc_final: 0.9200 (m-80) REVERT: Z 84 MET cc_start: 0.9205 (mmp) cc_final: 0.8991 (mmm) REVERT: Z 95 PHE cc_start: 0.9543 (m-10) cc_final: 0.9124 (m-80) REVERT: Z 123 PHE cc_start: 0.9535 (t80) cc_final: 0.9218 (t80) REVERT: Z 207 TYR cc_start: 0.8100 (t80) cc_final: 0.7697 (t80) REVERT: Z 248 PHE cc_start: 0.9485 (m-10) cc_final: 0.9117 (m-80) REVERT: Z 258 GLU cc_start: 0.9068 (pp20) cc_final: 0.8768 (pp20) REVERT: Z 264 MET cc_start: 0.9255 (ttm) cc_final: 0.8965 (ttm) REVERT: Z 280 GLU cc_start: 0.9461 (mm-30) cc_final: 0.9214 (mm-30) REVERT: Z 282 PHE cc_start: 0.9543 (t80) cc_final: 0.9211 (t80) REVERT: Z 287 GLN cc_start: 0.9528 (mm110) cc_final: 0.9007 (mm110) REVERT: Z 290 ILE cc_start: 0.9728 (pt) cc_final: 0.9416 (pt) outliers start: 0 outliers final: 0 residues processed: 338 average time/residue: 0.1491 time to fit residues: 75.2898 Evaluate side-chains 285 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 285 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 20 optimal weight: 1.9990 chunk 127 optimal weight: 6.9990 chunk 1 optimal weight: 0.4980 chunk 71 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 118 optimal weight: 50.0000 chunk 66 optimal weight: 7.9990 chunk 110 optimal weight: 8.9990 chunk 115 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 = 0.3507 r_free = 0.3507 target = 0.066935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.052214 restraints weight = 53074.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.053263 restraints weight = 41786.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.053893 restraints weight = 34685.310| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.4619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 9204 Z= 0.187 Angle : 0.632 7.549 12570 Z= 0.341 Chirality : 0.045 0.265 1596 Planarity : 0.005 0.072 1626 Dihedral : 3.893 22.746 1394 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.23), residues: 1332 helix: 1.70 (0.15), residues: 1111 sheet: None (None), residues: 0 loop : -1.73 (0.42), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP Z 208 HIS 0.003 0.002 HIS Z 170 PHE 0.030 0.002 PHE Q 62 TYR 0.019 0.002 TYR O 48 ARG 0.011 0.001 ARG I 37 Details of bonding type rmsd hydrogen bonds : bond 0.04228 ( 899) hydrogen bonds : angle 4.04697 ( 2676) covalent geometry : bond 0.00419 ( 9204) covalent geometry : angle 0.63190 (12570) *********************** 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 340 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 340 time to evaluate : 1.461 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: 0.9533 (mm) cc_final: 0.9179 (mm) REVERT: H 38 ASN cc_start: 0.9273 (t0) cc_final: 0.8957 (t0) REVERT: H 49 MET cc_start: 0.9687 (ttp) cc_final: 0.9343 (tmm) REVERT: H 50 PHE cc_start: 0.9582 (m-80) cc_final: 0.9139 (m-80) REVERT: H 57 GLU cc_start: 0.9803 (tp30) cc_final: 0.9333 (tp30) REVERT: H 64 LEU cc_start: 0.9815 (mm) cc_final: 0.9542 (mt) REVERT: H 68 PHE cc_start: 0.9417 (m-10) cc_final: 0.9199 (m-80) REVERT: I 35 ILE cc_start: 0.9362 (mm) cc_final: 0.9159 (tp) REVERT: I 49 MET cc_start: 0.9535 (ptt) cc_final: 0.9012 (ppp) REVERT: I 51 ILE cc_start: 0.9712 (mt) cc_final: 0.9505 (mt) REVERT: I 55 PHE cc_start: 0.9531 (m-80) cc_final: 0.9058 (m-10) REVERT: I 68 PHE cc_start: 0.9410 (m-80) cc_final: 0.9010 (m-80) REVERT: J 15 LEU cc_start: 0.9601 (mp) cc_final: 0.9224 (tp) REVERT: J 48 TYR cc_start: 0.9371 (m-80) cc_final: 0.8753 (m-80) REVERT: J 49 MET cc_start: 0.9700 (tmm) cc_final: 0.9247 (tmm) REVERT: K 15 LEU cc_start: 0.9792 (mt) cc_final: 0.9580 (tp) REVERT: K 18 ILE cc_start: 0.9446 (pt) cc_final: 0.8975 (tp) REVERT: K 27 ILE cc_start: 0.9571 (mt) cc_final: 0.9356 (mt) REVERT: K 44 ARG cc_start: 0.9424 (tpp80) cc_final: 0.8850 (tpp80) REVERT: K 49 MET cc_start: 0.9702 (ttp) cc_final: 0.9316 (tmm) REVERT: K 55 PHE cc_start: 0.9574 (m-80) cc_final: 0.9328 (m-80) REVERT: K 65 VAL cc_start: 0.9708 (p) cc_final: 0.9470 (p) REVERT: K 68 PHE cc_start: 0.9445 (m-10) cc_final: 0.9142 (m-80) REVERT: L 1 MET cc_start: 0.9107 (mtp) cc_final: 0.8755 (mtt) REVERT: L 50 PHE cc_start: 0.9643 (m-80) cc_final: 0.9296 (m-10) REVERT: L 51 ILE cc_start: 0.9839 (mt) cc_final: 0.9533 (mt) REVERT: L 53 ILE cc_start: 0.9784 (tt) cc_final: 0.9355 (tp) REVERT: L 55 PHE cc_start: 0.9443 (m-80) cc_final: 0.8944 (m-80) REVERT: L 57 GLU cc_start: 0.9494 (mm-30) cc_final: 0.8953 (mt-10) REVERT: M 68 PHE cc_start: 0.9444 (t80) cc_final: 0.9199 (t80) REVERT: N 1 MET cc_start: 0.6308 (tpt) cc_final: 0.5751 (mmm) REVERT: N 11 LEU cc_start: 0.9844 (mm) cc_final: 0.9634 (mm) REVERT: N 33 GLN cc_start: 0.9355 (mp10) cc_final: 0.8967 (mp10) REVERT: N 55 PHE cc_start: 0.9637 (m-80) cc_final: 0.9201 (m-80) REVERT: O 1 MET cc_start: 0.6635 (mmt) cc_final: 0.6297 (mmt) REVERT: O 29 SER cc_start: 0.9545 (t) cc_final: 0.9156 (p) REVERT: O 32 VAL cc_start: 0.9687 (p) cc_final: 0.9188 (m) REVERT: O 33 GLN cc_start: 0.9460 (mt0) cc_final: 0.9076 (mm110) REVERT: O 37 ARG cc_start: 0.9093 (mtt180) cc_final: 0.8555 (mtm180) REVERT: O 57 GLU cc_start: 0.9376 (mm-30) cc_final: 0.8929 (pt0) REVERT: O 62 PHE cc_start: 0.9166 (m-80) cc_final: 0.8817 (m-80) REVERT: O 64 LEU cc_start: 0.9746 (tt) cc_final: 0.9388 (mt) REVERT: P 33 GLN cc_start: 0.9621 (mt0) cc_final: 0.9274 (mm-40) REVERT: P 49 MET cc_start: 0.9524 (ttp) cc_final: 0.8654 (tpp) REVERT: P 55 PHE cc_start: 0.9256 (m-80) cc_final: 0.8307 (m-80) REVERT: P 68 PHE cc_start: 0.9240 (m-80) cc_final: 0.8829 (m-80) REVERT: Q 18 ILE cc_start: 0.9433 (pt) cc_final: 0.9087 (mm) REVERT: Q 27 ILE cc_start: 0.9427 (mt) cc_final: 0.9187 (mt) REVERT: Q 33 GLN cc_start: 0.9149 (mm110) cc_final: 0.8863 (mm110) REVERT: Q 49 MET cc_start: 0.9290 (ppp) cc_final: 0.9031 (ppp) REVERT: Q 50 PHE cc_start: 0.9673 (m-80) cc_final: 0.9335 (m-80) REVERT: Q 55 PHE cc_start: 0.9580 (m-80) cc_final: 0.9175 (m-80) REVERT: Q 57 GLU cc_start: 0.9511 (mt-10) cc_final: 0.8874 (mp0) REVERT: Q 62 PHE cc_start: 0.9704 (m-80) cc_final: 0.9349 (m-80) REVERT: Z 80 LEU cc_start: 0.9207 (mm) cc_final: 0.8952 (pt) REVERT: Z 84 MET cc_start: 0.9192 (mmp) cc_final: 0.8972 (mmm) REVERT: Z 95 PHE cc_start: 0.9548 (m-10) cc_final: 0.9095 (m-80) REVERT: Z 123 PHE cc_start: 0.9570 (t80) cc_final: 0.9270 (t80) REVERT: Z 207 TYR cc_start: 0.8117 (t80) cc_final: 0.7688 (t80) REVERT: Z 228 MET cc_start: 0.9223 (ptt) cc_final: 0.8896 (ptt) REVERT: Z 239 GLU cc_start: 0.9294 (mp0) cc_final: 0.9068 (mp0) REVERT: Z 248 PHE cc_start: 0.9580 (m-10) cc_final: 0.9144 (m-80) REVERT: Z 249 ARG cc_start: 0.9038 (mtt180) cc_final: 0.8677 (ttm110) REVERT: Z 255 PHE cc_start: 0.9048 (t80) cc_final: 0.8805 (t80) REVERT: Z 258 GLU cc_start: 0.9029 (pp20) cc_final: 0.8753 (pp20) REVERT: Z 277 TYR cc_start: 0.9221 (m-80) cc_final: 0.8876 (m-80) REVERT: Z 280 GLU cc_start: 0.9461 (mm-30) cc_final: 0.9234 (mm-30) REVERT: Z 282 PHE cc_start: 0.9612 (t80) cc_final: 0.9209 (t80) REVERT: Z 287 GLN cc_start: 0.9538 (mm110) cc_final: 0.9133 (mm110) REVERT: Z 290 ILE cc_start: 0.9664 (pt) cc_final: 0.9418 (pt) outliers start: 0 outliers final: 0 residues processed: 340 average time/residue: 0.1979 time to fit residues: 99.8758 Evaluate side-chains 289 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 38 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 43 optimal weight: 3.9990 chunk 25 optimal weight: 0.4980 chunk 128 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 73 optimal weight: 7.9990 chunk 87 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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** ** 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 = 0.3527 r_free = 0.3527 target = 0.068410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.053518 restraints weight = 51816.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.054582 restraints weight = 39904.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.055230 restraints weight = 32766.371| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.4822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 9204 Z= 0.164 Angle : 0.635 7.432 12570 Z= 0.337 Chirality : 0.045 0.207 1596 Planarity : 0.005 0.074 1626 Dihedral : 3.876 21.264 1394 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.23), residues: 1332 helix: 1.66 (0.15), residues: 1113 sheet: None (None), residues: 0 loop : -1.75 (0.42), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Z 208 HIS 0.002 0.001 HIS Z 170 PHE 0.031 0.002 PHE K 62 TYR 0.012 0.001 TYR O 48 ARG 0.014 0.001 ARG I 37 Details of bonding type rmsd hydrogen bonds : bond 0.04151 ( 899) hydrogen bonds : angle 3.96346 ( 2676) covalent geometry : bond 0.00398 ( 9204) covalent geometry : angle 0.63524 (12570) *********************** 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 341 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 341 time to evaluate : 0.990 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 15 LEU cc_start: 0.9598 (mp) cc_final: 0.9191 (tp) REVERT: H 38 ASN cc_start: 0.9304 (t0) cc_final: 0.8985 (t0) REVERT: H 49 MET cc_start: 0.9608 (ttp) cc_final: 0.9341 (tmm) REVERT: H 50 PHE cc_start: 0.9573 (m-80) cc_final: 0.9194 (m-80) REVERT: H 57 GLU cc_start: 0.9790 (tp30) cc_final: 0.9502 (tp30) REVERT: H 64 LEU cc_start: 0.9800 (mm) cc_final: 0.9513 (mt) REVERT: H 68 PHE cc_start: 0.9414 (m-10) cc_final: 0.9199 (m-80) REVERT: I 24 ILE cc_start: 0.9166 (pt) cc_final: 0.8948 (pt) REVERT: I 35 ILE cc_start: 0.9335 (mm) cc_final: 0.9103 (tp) REVERT: I 49 MET cc_start: 0.9471 (ptt) cc_final: 0.9119 (ppp) REVERT: I 55 PHE cc_start: 0.9369 (m-80) cc_final: 0.9071 (m-10) REVERT: I 68 PHE cc_start: 0.9441 (m-80) cc_final: 0.8989 (m-80) REVERT: J 15 LEU cc_start: 0.9598 (mp) cc_final: 0.9205 (tp) REVERT: J 48 TYR cc_start: 0.9381 (m-80) cc_final: 0.8749 (m-80) REVERT: J 49 MET cc_start: 0.9664 (tmm) cc_final: 0.9265 (tmm) REVERT: K 15 LEU cc_start: 0.9812 (mt) cc_final: 0.9535 (tp) REVERT: K 18 ILE cc_start: 0.9397 (pt) cc_final: 0.8880 (tp) REVERT: K 44 ARG cc_start: 0.9419 (tpp80) cc_final: 0.8622 (tpp80) REVERT: K 48 TYR cc_start: 0.9520 (m-10) cc_final: 0.9165 (m-80) REVERT: K 55 PHE cc_start: 0.9562 (m-80) cc_final: 0.9299 (m-80) REVERT: K 65 VAL cc_start: 0.9713 (p) cc_final: 0.9424 (p) REVERT: K 68 PHE cc_start: 0.9448 (m-10) cc_final: 0.9126 (m-80) REVERT: L 1 MET cc_start: 0.9045 (mtp) cc_final: 0.8714 (mtt) REVERT: L 50 PHE cc_start: 0.9650 (m-80) cc_final: 0.9321 (m-10) REVERT: L 51 ILE cc_start: 0.9832 (mt) cc_final: 0.9499 (mt) REVERT: L 53 ILE cc_start: 0.9798 (tt) cc_final: 0.9336 (tp) REVERT: L 55 PHE cc_start: 0.9442 (m-80) cc_final: 0.9054 (m-80) REVERT: L 57 GLU cc_start: 0.9482 (mm-30) cc_final: 0.9008 (mt-10) REVERT: M 68 PHE cc_start: 0.9447 (t80) cc_final: 0.9208 (t80) REVERT: N 55 PHE cc_start: 0.9643 (m-80) cc_final: 0.9217 (m-80) REVERT: O 15 LEU cc_start: 0.9737 (mp) cc_final: 0.9374 (tp) REVERT: O 29 SER cc_start: 0.9502 (t) cc_final: 0.9273 (p) REVERT: O 32 VAL cc_start: 0.9666 (p) cc_final: 0.9319 (m) REVERT: O 33 GLN cc_start: 0.9447 (mt0) cc_final: 0.9132 (mm-40) REVERT: O 37 ARG cc_start: 0.9088 (mtt180) cc_final: 0.8568 (mtm180) REVERT: O 57 GLU cc_start: 0.9379 (mm-30) cc_final: 0.8917 (pt0) REVERT: O 62 PHE cc_start: 0.9186 (m-80) cc_final: 0.8848 (m-80) REVERT: O 64 LEU cc_start: 0.9775 (tt) cc_final: 0.9475 (mt) REVERT: P 33 GLN cc_start: 0.9607 (mt0) cc_final: 0.9281 (mm110) REVERT: P 49 MET cc_start: 0.9495 (ttp) cc_final: 0.8488 (tpp) REVERT: P 55 PHE cc_start: 0.9267 (m-80) cc_final: 0.8392 (m-80) REVERT: P 68 PHE cc_start: 0.9225 (m-80) cc_final: 0.8785 (m-80) REVERT: Q 15 LEU cc_start: 0.9134 (mm) cc_final: 0.8659 (tp) REVERT: Q 18 ILE cc_start: 0.9451 (pt) cc_final: 0.9122 (mm) REVERT: Q 27 ILE cc_start: 0.9361 (mt) cc_final: 0.9127 (mt) REVERT: Q 33 GLN cc_start: 0.9144 (mm110) cc_final: 0.8839 (mm110) REVERT: Q 49 MET cc_start: 0.9277 (ppp) cc_final: 0.9038 (ppp) REVERT: Q 50 PHE cc_start: 0.9666 (m-80) cc_final: 0.9262 (m-80) REVERT: Q 55 PHE cc_start: 0.9550 (m-80) cc_final: 0.9147 (m-80) REVERT: Q 62 PHE cc_start: 0.9683 (m-80) cc_final: 0.9335 (m-80) REVERT: Z 80 LEU cc_start: 0.9185 (mm) cc_final: 0.8736 (tt) REVERT: Z 84 MET cc_start: 0.9186 (mmp) cc_final: 0.8884 (mmm) REVERT: Z 95 PHE cc_start: 0.9546 (m-10) cc_final: 0.9086 (m-80) REVERT: Z 114 PHE cc_start: 0.9400 (t80) cc_final: 0.9149 (t80) REVERT: Z 123 PHE cc_start: 0.9544 (t80) cc_final: 0.9216 (t80) REVERT: Z 207 TYR cc_start: 0.8081 (t80) cc_final: 0.7665 (t80) REVERT: Z 228 MET cc_start: 0.9230 (ptt) cc_final: 0.8862 (ptt) REVERT: Z 239 GLU cc_start: 0.9112 (mp0) cc_final: 0.8889 (mp0) REVERT: Z 248 PHE cc_start: 0.9610 (m-10) cc_final: 0.9192 (m-80) REVERT: Z 249 ARG cc_start: 0.9051 (mtt180) cc_final: 0.8655 (ttm110) REVERT: Z 258 GLU cc_start: 0.8976 (pp20) cc_final: 0.8693 (pp20) REVERT: Z 280 GLU cc_start: 0.9445 (mm-30) cc_final: 0.9198 (mm-30) REVERT: Z 282 PHE cc_start: 0.9571 (t80) cc_final: 0.9187 (t80) REVERT: Z 287 GLN cc_start: 0.9520 (mm110) cc_final: 0.9174 (mm110) REVERT: Z 289 LEU cc_start: 0.9797 (mm) cc_final: 0.9588 (mm) outliers start: 0 outliers final: 0 residues processed: 341 average time/residue: 0.1541 time to fit residues: 78.0687 Evaluate side-chains 298 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 67 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 95 optimal weight: 0.0010 chunk 41 optimal weight: 0.9990 chunk 117 optimal weight: 50.0000 chunk 96 optimal weight: 5.9990 chunk 119 optimal weight: 10.0000 chunk 71 optimal weight: 0.5980 chunk 29 optimal weight: 10.0000 overall best weight: 1.1190 ------------------------------------------------------------------------------- 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** ** 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 = 0.3553 r_free = 0.3553 target = 0.069223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.054957 restraints weight = 54639.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.055998 restraints weight = 42908.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.056829 restraints weight = 35639.180| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.5015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 9204 Z= 0.167 Angle : 0.628 7.261 12570 Z= 0.338 Chirality : 0.045 0.218 1596 Planarity : 0.005 0.073 1626 Dihedral : 3.902 20.604 1394 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 17.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.23), residues: 1332 helix: 1.64 (0.15), residues: 1112 sheet: None (None), residues: 0 loop : -1.79 (0.41), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Z 208 HIS 0.002 0.001 HIS Z 170 PHE 0.031 0.002 PHE N 62 TYR 0.023 0.002 TYR I 48 ARG 0.011 0.001 ARG I 37 Details of bonding type rmsd hydrogen bonds : bond 0.04152 ( 899) hydrogen bonds : angle 3.98698 ( 2676) covalent geometry : bond 0.00395 ( 9204) covalent geometry : angle 0.62809 (12570) *********************** 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 337 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 337 time to evaluate : 0.911 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 38 ASN cc_start: 0.9333 (t0) cc_final: 0.9089 (t0) REVERT: H 49 MET cc_start: 0.9679 (ttp) cc_final: 0.9419 (tmm) REVERT: H 50 PHE cc_start: 0.9569 (m-80) cc_final: 0.9175 (m-80) REVERT: H 57 GLU cc_start: 0.9824 (tp30) cc_final: 0.9463 (tp30) REVERT: H 64 LEU cc_start: 0.9797 (mm) cc_final: 0.9539 (mt) REVERT: H 68 PHE cc_start: 0.9427 (m-10) cc_final: 0.9203 (m-80) REVERT: I 35 ILE cc_start: 0.9365 (mm) cc_final: 0.9075 (tp) REVERT: I 49 MET cc_start: 0.9491 (ptt) cc_final: 0.9086 (ppp) REVERT: I 55 PHE cc_start: 0.9393 (m-80) cc_final: 0.9083 (m-10) REVERT: I 68 PHE cc_start: 0.9465 (m-80) cc_final: 0.8983 (m-80) REVERT: J 15 LEU cc_start: 0.9593 (mp) cc_final: 0.9192 (tp) REVERT: J 48 TYR cc_start: 0.9353 (m-80) cc_final: 0.8716 (m-80) REVERT: J 49 MET cc_start: 0.9612 (tmm) cc_final: 0.9270 (tmm) REVERT: J 64 LEU cc_start: 0.9639 (mt) cc_final: 0.9333 (pp) REVERT: K 15 LEU cc_start: 0.9821 (mt) cc_final: 0.9556 (tp) REVERT: K 18 ILE cc_start: 0.9423 (pt) cc_final: 0.8938 (tp) REVERT: K 44 ARG cc_start: 0.9449 (tpp80) cc_final: 0.8613 (tpp80) REVERT: K 48 TYR cc_start: 0.9569 (m-10) cc_final: 0.9131 (m-80) REVERT: K 55 PHE cc_start: 0.9571 (m-80) cc_final: 0.9321 (m-80) REVERT: K 65 VAL cc_start: 0.9715 (p) cc_final: 0.9443 (p) REVERT: K 68 PHE cc_start: 0.9467 (m-10) cc_final: 0.9136 (m-80) REVERT: L 1 MET cc_start: 0.9035 (mtp) cc_final: 0.8651 (mtt) REVERT: L 50 PHE cc_start: 0.9671 (m-80) cc_final: 0.9298 (m-10) REVERT: L 51 ILE cc_start: 0.9838 (mt) cc_final: 0.9515 (mt) REVERT: L 53 ILE cc_start: 0.9814 (tt) cc_final: 0.9401 (tp) REVERT: L 55 PHE cc_start: 0.9529 (m-80) cc_final: 0.9091 (m-80) REVERT: L 57 GLU cc_start: 0.9491 (mm-30) cc_final: 0.8987 (mt-10) REVERT: M 48 TYR cc_start: 0.8999 (m-80) cc_final: 0.8421 (m-80) REVERT: M 68 PHE cc_start: 0.9486 (t80) cc_final: 0.9261 (t80) REVERT: N 11 LEU cc_start: 0.9831 (mm) cc_final: 0.9620 (mm) REVERT: N 55 PHE cc_start: 0.9638 (m-80) cc_final: 0.9206 (m-80) REVERT: O 11 LEU cc_start: 0.9565 (mt) cc_final: 0.9342 (mt) REVERT: O 15 LEU cc_start: 0.9731 (mp) cc_final: 0.9352 (tp) REVERT: O 29 SER cc_start: 0.9512 (t) cc_final: 0.9276 (p) REVERT: O 32 VAL cc_start: 0.9665 (p) cc_final: 0.9324 (m) REVERT: O 33 GLN cc_start: 0.9472 (mt0) cc_final: 0.9151 (mm-40) REVERT: O 37 ARG cc_start: 0.9071 (mtt180) cc_final: 0.8554 (mtm180) REVERT: O 57 GLU cc_start: 0.9362 (mm-30) cc_final: 0.8956 (pt0) REVERT: O 62 PHE cc_start: 0.9223 (m-80) cc_final: 0.8868 (m-80) REVERT: O 64 LEU cc_start: 0.9724 (tt) cc_final: 0.9399 (mt) REVERT: P 33 GLN cc_start: 0.9608 (mt0) cc_final: 0.9292 (mm110) REVERT: P 49 MET cc_start: 0.9518 (ttp) cc_final: 0.8537 (tpp) REVERT: P 55 PHE cc_start: 0.9285 (m-80) cc_final: 0.8373 (m-80) REVERT: P 68 PHE cc_start: 0.9336 (m-80) cc_final: 0.8888 (m-80) REVERT: Q 18 ILE cc_start: 0.9402 (pt) cc_final: 0.8997 (mm) REVERT: Q 27 ILE cc_start: 0.9283 (mt) cc_final: 0.9040 (mt) REVERT: Q 33 GLN cc_start: 0.9123 (mm110) cc_final: 0.8824 (mm110) REVERT: Q 49 MET cc_start: 0.9233 (ppp) cc_final: 0.9021 (ppp) REVERT: Q 50 PHE cc_start: 0.9692 (m-80) cc_final: 0.9308 (m-80) REVERT: Q 55 PHE cc_start: 0.9587 (m-80) cc_final: 0.9175 (m-80) REVERT: Q 62 PHE cc_start: 0.9697 (m-80) cc_final: 0.9365 (m-80) REVERT: Z 80 LEU cc_start: 0.9266 (mm) cc_final: 0.8761 (tt) REVERT: Z 84 MET cc_start: 0.9223 (mmp) cc_final: 0.8883 (mmm) REVERT: Z 95 PHE cc_start: 0.9565 (m-10) cc_final: 0.9106 (m-80) REVERT: Z 114 PHE cc_start: 0.9386 (t80) cc_final: 0.9118 (t80) REVERT: Z 123 PHE cc_start: 0.9600 (t80) cc_final: 0.9307 (t80) REVERT: Z 207 TYR cc_start: 0.8128 (t80) cc_final: 0.7701 (t80) REVERT: Z 228 MET cc_start: 0.9267 (ptt) cc_final: 0.8914 (ptt) REVERT: Z 248 PHE cc_start: 0.9632 (m-10) cc_final: 0.9208 (m-80) REVERT: Z 249 ARG cc_start: 0.9030 (mtt180) cc_final: 0.8759 (ttm110) REVERT: Z 258 GLU cc_start: 0.9030 (pp20) cc_final: 0.8742 (pp20) REVERT: Z 280 GLU cc_start: 0.9459 (mm-30) cc_final: 0.9199 (mm-30) REVERT: Z 282 PHE cc_start: 0.9575 (t80) cc_final: 0.9173 (t80) REVERT: Z 287 GLN cc_start: 0.9520 (mm110) cc_final: 0.9212 (mm110) REVERT: Z 289 LEU cc_start: 0.9793 (mm) cc_final: 0.9578 (mm) outliers start: 0 outliers final: 0 residues processed: 337 average time/residue: 0.1579 time to fit residues: 79.4752 Evaluate side-chains 287 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 287 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 60 optimal weight: 0.9980 chunk 117 optimal weight: 50.0000 chunk 94 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 118 optimal weight: 40.0000 chunk 35 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 17 optimal weight: 7.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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** ** 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 = 0.3529 r_free = 0.3529 target = 0.067805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.053435 restraints weight = 51968.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.054433 restraints weight = 40545.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.055341 restraints weight = 33528.094| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.5139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 9204 Z= 0.160 Angle : 0.636 8.410 12570 Z= 0.336 Chirality : 0.045 0.226 1596 Planarity : 0.005 0.073 1626 Dihedral : 3.894 21.775 1394 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.23), residues: 1332 helix: 1.63 (0.15), residues: 1113 sheet: None (None), residues: 0 loop : -1.75 (0.41), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Z 208 HIS 0.002 0.001 HIS Z 170 PHE 0.037 0.001 PHE L 62 TYR 0.012 0.001 TYR Z 217 ARG 0.009 0.001 ARG I 37 Details of bonding type rmsd hydrogen bonds : bond 0.04130 ( 899) hydrogen bonds : angle 3.94920 ( 2676) covalent geometry : bond 0.00383 ( 9204) covalent geometry : angle 0.63582 (12570) ********************** 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 336 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 336 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 38 ASN cc_start: 0.9350 (t0) cc_final: 0.9047 (t0) REVERT: H 49 MET cc_start: 0.9644 (ttp) cc_final: 0.9402 (tmm) REVERT: H 50 PHE cc_start: 0.9562 (m-80) cc_final: 0.9184 (m-80) REVERT: H 57 GLU cc_start: 0.9800 (tp30) cc_final: 0.9526 (tp30) REVERT: H 68 PHE cc_start: 0.9414 (m-10) cc_final: 0.9157 (m-80) REVERT: I 24 ILE cc_start: 0.9088 (pt) cc_final: 0.8865 (pt) REVERT: I 35 ILE cc_start: 0.9337 (mm) cc_final: 0.9112 (tp) REVERT: I 49 MET cc_start: 0.9462 (ptt) cc_final: 0.9128 (ppp) REVERT: I 55 PHE cc_start: 0.9333 (m-80) cc_final: 0.9031 (m-10) REVERT: I 68 PHE cc_start: 0.9470 (m-80) cc_final: 0.8956 (m-80) REVERT: J 18 ILE cc_start: 0.9082 (mt) cc_final: 0.8820 (mt) REVERT: J 48 TYR cc_start: 0.9380 (m-80) cc_final: 0.8750 (m-80) REVERT: J 49 MET cc_start: 0.9654 (tmm) cc_final: 0.9273 (tmm) REVERT: J 64 LEU cc_start: 0.9630 (mt) cc_final: 0.9331 (pp) REVERT: K 15 LEU cc_start: 0.9812 (mt) cc_final: 0.9383 (tp) REVERT: K 18 ILE cc_start: 0.9431 (pt) cc_final: 0.9078 (tp) REVERT: K 44 ARG cc_start: 0.9435 (tpp80) cc_final: 0.8594 (tpp80) REVERT: K 48 TYR cc_start: 0.9532 (m-10) cc_final: 0.9050 (m-80) REVERT: K 55 PHE cc_start: 0.9536 (m-80) cc_final: 0.9313 (m-80) REVERT: K 65 VAL cc_start: 0.9729 (p) cc_final: 0.9357 (p) REVERT: K 66 ILE cc_start: 0.9653 (mm) cc_final: 0.9450 (tp) REVERT: K 68 PHE cc_start: 0.9482 (m-10) cc_final: 0.9170 (m-80) REVERT: L 1 MET cc_start: 0.8999 (mtp) cc_final: 0.8660 (mtt) REVERT: L 50 PHE cc_start: 0.9667 (m-80) cc_final: 0.9312 (m-10) REVERT: L 51 ILE cc_start: 0.9843 (mt) cc_final: 0.9527 (mt) REVERT: L 53 ILE cc_start: 0.9810 (tt) cc_final: 0.9411 (tp) REVERT: L 55 PHE cc_start: 0.9539 (m-80) cc_final: 0.9084 (m-80) REVERT: L 57 GLU cc_start: 0.9516 (mm-30) cc_final: 0.9052 (mt-10) REVERT: M 68 PHE cc_start: 0.9472 (t80) cc_final: 0.9250 (t80) REVERT: N 11 LEU cc_start: 0.9833 (mm) cc_final: 0.9622 (mm) REVERT: N 55 PHE cc_start: 0.9666 (m-80) cc_final: 0.9228 (m-80) REVERT: O 29 SER cc_start: 0.9524 (t) cc_final: 0.9281 (p) REVERT: O 32 VAL cc_start: 0.9683 (p) cc_final: 0.9333 (m) REVERT: O 33 GLN cc_start: 0.9473 (mt0) cc_final: 0.9162 (mm-40) REVERT: O 37 ARG cc_start: 0.9088 (mtt180) cc_final: 0.8579 (mtm180) REVERT: O 50 PHE cc_start: 0.9240 (m-80) cc_final: 0.9008 (m-80) REVERT: O 57 GLU cc_start: 0.9356 (mm-30) cc_final: 0.8953 (pt0) REVERT: O 62 PHE cc_start: 0.9229 (m-80) cc_final: 0.8845 (m-80) REVERT: O 64 LEU cc_start: 0.9774 (tt) cc_final: 0.9461 (mt) REVERT: P 33 GLN cc_start: 0.9604 (mt0) cc_final: 0.9304 (mm110) REVERT: P 49 MET cc_start: 0.9504 (ttp) cc_final: 0.8515 (tpp) REVERT: P 55 PHE cc_start: 0.9297 (m-80) cc_final: 0.8398 (m-80) REVERT: P 68 PHE cc_start: 0.9320 (m-80) cc_final: 0.8886 (m-80) REVERT: Q 18 ILE cc_start: 0.9456 (pt) cc_final: 0.9056 (mm) REVERT: Q 24 ILE cc_start: 0.9247 (pt) cc_final: 0.9047 (pt) REVERT: Q 27 ILE cc_start: 0.9347 (mt) cc_final: 0.9095 (mt) REVERT: Q 33 GLN cc_start: 0.9131 (mm110) cc_final: 0.8836 (mm110) REVERT: Q 49 MET cc_start: 0.9249 (ppp) cc_final: 0.9036 (ppp) REVERT: Q 50 PHE cc_start: 0.9681 (m-80) cc_final: 0.9304 (m-80) REVERT: Q 53 ILE cc_start: 0.8965 (pt) cc_final: 0.8593 (pt) REVERT: Q 55 PHE cc_start: 0.9592 (m-80) cc_final: 0.9148 (m-80) REVERT: Z 80 LEU cc_start: 0.9236 (mm) cc_final: 0.8746 (tt) REVERT: Z 84 MET cc_start: 0.9202 (mmp) cc_final: 0.8884 (mmm) REVERT: Z 95 PHE cc_start: 0.9562 (m-10) cc_final: 0.9171 (m-80) REVERT: Z 114 PHE cc_start: 0.9397 (t80) cc_final: 0.9152 (t80) REVERT: Z 123 PHE cc_start: 0.9573 (t80) cc_final: 0.9252 (t80) REVERT: Z 207 TYR cc_start: 0.8075 (t80) cc_final: 0.7649 (t80) REVERT: Z 228 MET cc_start: 0.9240 (ptt) cc_final: 0.8871 (ptt) REVERT: Z 248 PHE cc_start: 0.9672 (m-10) cc_final: 0.9231 (m-80) REVERT: Z 249 ARG cc_start: 0.9090 (mtt180) cc_final: 0.8577 (ttm110) REVERT: Z 258 GLU cc_start: 0.9048 (pp20) cc_final: 0.8762 (pp20) REVERT: Z 280 GLU cc_start: 0.9410 (mm-30) cc_final: 0.9147 (mm-30) REVERT: Z 282 PHE cc_start: 0.9597 (t80) cc_final: 0.9202 (t80) REVERT: Z 287 GLN cc_start: 0.9529 (mm110) cc_final: 0.9187 (mm110) REVERT: Z 289 LEU cc_start: 0.9792 (mm) cc_final: 0.9576 (mm) outliers start: 0 outliers final: 0 residues processed: 336 average time/residue: 0.1589 time to fit residues: 79.1152 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 : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 113 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 1 optimal weight: 0.0000 chunk 65 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 117 optimal weight: 50.0000 chunk 128 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 = 0.3511 r_free = 0.3511 target = 0.067056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.052722 restraints weight = 52147.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.053749 restraints weight = 41489.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.054340 restraints weight = 34571.243| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.5292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 9204 Z= 0.196 Angle : 0.664 14.833 12570 Z= 0.357 Chirality : 0.046 0.221 1596 Planarity : 0.005 0.073 1626 Dihedral : 3.938 22.076 1394 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 18.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.23), residues: 1332 helix: 1.60 (0.15), residues: 1113 sheet: None (None), residues: 0 loop : -1.68 (0.42), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Z 208 HIS 0.003 0.002 HIS Z 31 PHE 0.033 0.002 PHE N 62 TYR 0.022 0.002 TYR I 48 ARG 0.013 0.001 ARG I 37 Details of bonding type rmsd hydrogen bonds : bond 0.04241 ( 899) hydrogen bonds : angle 4.11796 ( 2676) covalent geometry : bond 0.00447 ( 9204) covalent geometry : angle 0.66388 (12570) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3451.28 seconds wall clock time: 61 minutes 19.25 seconds (3679.25 seconds total)