Starting phenix.real_space_refine on Mon May 12 14:08:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9itx_60882/05_2025/9itx_60882.cif Found real_map, /net/cci-nas-00/data/ceres_data/9itx_60882/05_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_60882/05_2025/9itx_60882.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9itx_60882/05_2025/9itx_60882.map" model { file = "/net/cci-nas-00/data/ceres_data/9itx_60882/05_2025/9itx_60882.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9itx_60882/05_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-5687/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: 6.46, per 1000 atoms: 0.71 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: 2.62 Conformation dependent library (CDL) restraints added in 1.2 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: 0.68 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: 2.69 Time building geometry restraints manager: 2.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3023 1.34 - 1.46: 1412 1.46 - 1.57: 4721 1.57 - 1.69: 0 1.69 - 1.80: 48 Bond restraints: 9204 Sorted by residual: bond pdb=" N ILE J 70 " pdb=" CA ILE J 70 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.21e-02 6.83e+03 8.91e+00 bond pdb=" N VAL T 303 " pdb=" CA VAL T 303 " ideal model delta sigma weight residual 1.461 1.495 -0.035 1.19e-02 7.06e+03 8.53e+00 bond pdb=" N ILE K 70 " pdb=" CA ILE K 70 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.23e-02 6.61e+03 8.46e+00 bond pdb=" N ILE N 70 " pdb=" CA ILE N 70 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.19e-02 7.06e+03 8.23e+00 bond pdb=" N ILE T 301 " pdb=" CA ILE T 301 " ideal model delta sigma weight residual 1.461 1.494 -0.034 1.19e-02 7.06e+03 8.10e+00 ... (remaining 9199 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 12110 1.30 - 2.60: 375 2.60 - 3.89: 73 3.89 - 5.19: 8 5.19 - 6.49: 4 Bond angle restraints: 12570 Sorted by residual: angle pdb=" C ASP Z 171 " pdb=" CA ASP Z 171 " pdb=" CB ASP Z 171 " ideal model delta sigma weight residual 116.54 110.05 6.49 1.15e+00 7.56e-01 3.18e+01 angle pdb=" N ILE N 41 " pdb=" CA ILE N 41 " pdb=" C ILE N 41 " ideal model delta sigma weight residual 111.91 108.03 3.88 8.90e-01 1.26e+00 1.90e+01 angle pdb=" CA ASP Z 171 " pdb=" C ASP Z 171 " pdb=" N THR Z 172 " ideal model delta sigma weight residual 119.52 116.87 2.65 7.90e-01 1.60e+00 1.13e+01 angle pdb=" N ILE O 70 " pdb=" CA ILE O 70 " pdb=" C ILE O 70 " ideal model delta sigma weight residual 110.72 107.54 3.18 1.01e+00 9.80e-01 9.91e+00 angle pdb=" C LYS T 178 " pdb=" N LYS T 179 " pdb=" CA LYS T 179 " ideal model delta sigma weight residual 121.54 127.16 -5.62 1.91e+00 2.74e-01 8.65e+00 ... (remaining 12565 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 4907 17.41 - 34.83: 309 34.83 - 52.24: 26 52.24 - 69.66: 8 69.66 - 87.07: 6 Dihedral angle restraints: 5256 sinusoidal: 1469 harmonic: 3787 Sorted by residual: dihedral pdb=" CA LEU Z 270 " pdb=" C LEU Z 270 " pdb=" N LEU Z 271 " pdb=" CA LEU Z 271 " ideal model delta harmonic sigma weight residual 180.00 162.96 17.04 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CB GLU Z 89 " pdb=" CG GLU Z 89 " pdb=" CD GLU Z 89 " pdb=" OE1 GLU Z 89 " ideal model delta sinusoidal sigma weight residual 0.00 -83.29 83.29 1 3.00e+01 1.11e-03 9.42e+00 dihedral pdb=" CB GLU Q 42 " pdb=" CG GLU Q 42 " pdb=" CD GLU Q 42 " pdb=" OE1 GLU Q 42 " ideal model delta sinusoidal sigma weight residual 0.00 83.12 -83.12 1 3.00e+01 1.11e-03 9.39e+00 ... (remaining 5253 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1218 0.047 - 0.094: 329 0.094 - 0.141: 38 0.141 - 0.189: 3 0.189 - 0.236: 8 Chirality restraints: 1596 Sorted by residual: chirality pdb=" CA ILE O 70 " pdb=" N ILE O 70 " pdb=" C ILE O 70 " pdb=" CB ILE O 70 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CB ILE Q 41 " pdb=" CA ILE Q 41 " pdb=" CG1 ILE Q 41 " pdb=" CG2 ILE Q 41 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CA ILE T 301 " pdb=" N ILE T 301 " pdb=" C ILE T 301 " pdb=" CB ILE T 301 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 1593 not shown) Planarity restraints: 1626 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY N 19 " 0.036 5.00e-02 4.00e+02 5.49e-02 4.83e+00 pdb=" N PRO N 20 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO N 20 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO N 20 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY L 19 " 0.036 5.00e-02 4.00e+02 5.45e-02 4.75e+00 pdb=" N PRO L 20 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO L 20 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO L 20 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY O 19 " -0.035 5.00e-02 4.00e+02 5.32e-02 4.53e+00 pdb=" N PRO O 20 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO O 20 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO O 20 " -0.030 5.00e-02 4.00e+02 ... (remaining 1623 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 1867 2.78 - 3.31: 10103 3.31 - 3.84: 16051 3.84 - 4.37: 16396 4.37 - 4.90: 29318 Nonbonded interactions: 73735 Sorted by model distance: nonbonded pdb=" O ARG I 44 " pdb=" OG1 THR I 47 " model vdw 2.245 3.040 nonbonded pdb=" N MET K 1 " pdb=" O MET L 1 " model vdw 2.256 3.120 nonbonded pdb=" OH TYR I 48 " pdb=" OE2 GLU J 42 " model vdw 2.263 3.040 nonbonded pdb=" OH TYR H 48 " pdb=" OE2 GLU I 42 " model vdw 2.268 3.040 nonbonded pdb=" O ASN Z 223 " pdb=" OG SER Z 229 " model vdw 2.301 3.040 ... (remaining 73730 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = (chain 'P' and resid 1 through 72) selection = chain 'Q' } ncs_group { reference = (chain 'T' and (resid 47 through 134 or resid 136 or resid 171 through 304)) selection = (chain 'Z' and ((resid 47 through 78 and (name N or name CA or name C or name O \ or name CB )) or resid 79 or (resid 80 through 119 and (name N or name CA or nam \ e C or name O or name CB )) or resid 120 or (resid 121 through 123 and (name N o \ r name CA or name C or name O or name CB )) or resid 124 or (resid 125 through 1 \ 27 and (name N or name CA or name C or name O or name CB )) or resid 128 or (res \ id 129 and (name N or name CA or name C or name O or name CB )) or resid 130 or \ (resid 131 through 132 and (name N or name CA or name C or name O or name CB )) \ or resid 133 or (resid 134 and (name N or name CA or name C or name O or name CB \ )) or (resid 170 through 176 and (name N or name CA or name C or name O or name \ CB )) or resid 177 or (resid 178 through 208 and (name N or name CA or name C o \ r name O or name CB )) or resid 209 or (resid 210 through 213 and (name N or nam \ e CA or name C or name O or name CB )) or resid 214 or (resid 215 and (name N or \ name CA or name C or name O or name CB )) or resid 216 or (resid 217 through 22 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 226 or (resi \ d 227 through 231 and (name N or name CA or name C or name O or name CB )) or re \ sid 232 or (resid 233 through 251 and (name N or name CA or name C or name O or \ name CB )) or resid 252 or (resid 253 through 256 and (name N or name CA or name \ C or name O or name CB )) or resid 257 or (resid 258 through 277 and (name N or \ name CA or name C or name O or name CB )) or resid 278 or (resid 279 through 28 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 284 or (resi \ d 285 through 304 and (name N or name CA or name C or name O or name CB )))) } ncs_group { reference = (chain 'U' and resid 8 through 40) selection = (chain 'V' and resid 8 through 40) selection = (chain 'X' and resid 8 through 40) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.720 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.140 Find NCS groups from input model: 0.510 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: 0.010 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.650 ------------------------------------------------------------------------------- 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 : 1.052 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: 0.1741 time to fit residues: 105.1946 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 = 32)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.051967 restraints weight = 55274.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.053114 restraints weight = 42293.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.053951 restraints weight = 34166.668| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 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 : 0.926 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: 0.9363 (mt) cc_final: 0.8969 (mt) REVERT: H 48 TYR cc_start: 0.9159 (m-80) cc_final: 0.8953 (m-10) REVERT: H 49 MET cc_start: 0.9713 (ttp) cc_final: 0.9353 (tmm) REVERT: H 50 PHE cc_start: 0.9639 (m-80) cc_final: 0.9164 (m-80) REVERT: H 57 GLU cc_start: 0.9742 (tp30) cc_final: 0.9446 (tp30) REVERT: I 28 VAL cc_start: 0.9591 (t) cc_final: 0.9344 (m) REVERT: I 42 GLU cc_start: 0.9411 (tt0) cc_final: 0.9011 (tp30) REVERT: I 49 MET cc_start: 0.9428 (ttp) cc_final: 0.8980 (tmm) REVERT: I 55 PHE cc_start: 0.9493 (m-80) cc_final: 0.9135 (m-80) REVERT: J 1 MET cc_start: 0.8347 (mmt) cc_final: 0.7294 (mmt) REVERT: J 48 TYR cc_start: 0.9444 (m-80) cc_final: 0.8795 (m-80) REVERT: J 49 MET cc_start: 0.9579 (ttp) cc_final: 0.9363 (tmm) REVERT: J 53 ILE cc_start: 0.9655 (mt) cc_final: 0.9425 (mt) REVERT: K 15 LEU cc_start: 0.9795 (mt) cc_final: 0.9525 (tp) REVERT: K 18 ILE cc_start: 0.9503 (pt) cc_final: 0.9164 (tp) REVERT: K 33 GLN cc_start: 0.9488 (mt0) cc_final: 0.8966 (mm110) REVERT: K 44 ARG cc_start: 0.9452 (tpp80) cc_final: 0.9115 (tpp80) REVERT: K 48 TYR cc_start: 0.9609 (m-80) cc_final: 0.9157 (m-80) REVERT: K 55 PHE cc_start: 0.9615 (m-80) cc_final: 0.9306 (m-80) REVERT: K 68 PHE cc_start: 0.9600 (m-10) cc_final: 0.9303 (m-80) REVERT: L 1 MET cc_start: 0.8949 (mtp) cc_final: 0.8166 (mtt) REVERT: L 43 ASN cc_start: 0.9432 (m-40) cc_final: 0.9176 (p0) REVERT: L 49 MET cc_start: 0.9802 (ttp) cc_final: 0.9422 (tmm) REVERT: L 50 PHE cc_start: 0.9616 (m-80) cc_final: 0.9142 (m-80) REVERT: L 51 ILE cc_start: 0.9863 (mt) cc_final: 0.9620 (mt) REVERT: L 53 ILE cc_start: 0.9806 (tt) cc_final: 0.9429 (tp) REVERT: L 55 PHE cc_start: 0.9565 (m-80) cc_final: 0.9199 (m-80) REVERT: L 57 GLU cc_start: 0.9534 (tp30) cc_final: 0.9188 (pt0) REVERT: M 11 LEU cc_start: 0.9826 (mt) cc_final: 0.9576 (tt) REVERT: M 27 ILE cc_start: 0.9779 (mt) cc_final: 0.9392 (mt) REVERT: M 33 GLN cc_start: 0.9474 (pm20) cc_final: 0.9064 (pm20) REVERT: M 49 MET cc_start: 0.9552 (ttp) cc_final: 0.8862 (tpt) REVERT: M 50 PHE cc_start: 0.9386 (m-80) cc_final: 0.9123 (m-80) REVERT: M 59 LEU cc_start: 0.9466 (tp) cc_final: 0.9248 (mt) REVERT: N 11 LEU cc_start: 0.9806 (mm) cc_final: 0.9507 (mm) REVERT: N 32 VAL cc_start: 0.9783 (p) cc_final: 0.9383 (p) REVERT: N 40 GLU cc_start: 0.9365 (pt0) cc_final: 0.9154 (pp20) REVERT: N 64 LEU cc_start: 0.9678 (tp) cc_final: 0.9464 (mt) REVERT: O 29 SER cc_start: 0.9543 (t) cc_final: 0.9219 (p) REVERT: O 32 VAL cc_start: 0.9626 (p) cc_final: 0.9234 (m) REVERT: O 33 GLN cc_start: 0.9455 (mt0) cc_final: 0.9009 (mm110) REVERT: O 37 ARG cc_start: 0.8995 (mtt180) cc_final: 0.8485 (mtt180) REVERT: O 53 ILE cc_start: 0.9457 (tt) cc_final: 0.9247 (tp) REVERT: O 57 GLU cc_start: 0.9439 (mm-30) cc_final: 0.8855 (pt0) REVERT: O 62 PHE cc_start: 0.8743 (m-10) cc_final: 0.8519 (m-80) REVERT: O 64 LEU cc_start: 0.9737 (tt) cc_final: 0.9378 (mt) REVERT: P 33 GLN cc_start: 0.9543 (mt0) cc_final: 0.8933 (mt0) REVERT: P 49 MET cc_start: 0.9569 (ttp) cc_final: 0.9060 (tmm) REVERT: P 68 PHE cc_start: 0.9285 (m-80) cc_final: 0.8937 (m-80) REVERT: Q 18 ILE cc_start: 0.9503 (pt) cc_final: 0.9125 (mm) REVERT: Q 27 ILE cc_start: 0.9547 (mt) cc_final: 0.9329 (mt) REVERT: Q 33 GLN cc_start: 0.9124 (mm-40) cc_final: 0.8914 (mm110) REVERT: Q 37 ARG cc_start: 0.9232 (mtt180) cc_final: 0.8821 (mtt90) REVERT: Q 50 PHE cc_start: 0.9664 (m-80) cc_final: 0.9267 (m-80) REVERT: Q 55 PHE cc_start: 0.9477 (m-80) cc_final: 0.9245 (m-80) REVERT: Q 62 PHE cc_start: 0.9580 (m-10) cc_final: 0.9292 (m-80) REVERT: Z 84 MET cc_start: 0.9303 (mmt) cc_final: 0.9100 (mmm) REVERT: Z 95 PHE cc_start: 0.9597 (m-10) cc_final: 0.9146 (m-80) REVERT: Z 123 PHE cc_start: 0.9574 (t80) cc_final: 0.9247 (t80) REVERT: Z 207 TYR cc_start: 0.8197 (t80) cc_final: 0.7800 (t80) REVERT: Z 228 MET cc_start: 0.9254 (ptt) cc_final: 0.9037 (ptt) REVERT: Z 248 PHE cc_start: 0.9594 (m-10) cc_final: 0.9130 (m-80) REVERT: Z 249 ARG cc_start: 0.9754 (ttm-80) cc_final: 0.9189 (ttm-80) REVERT: Z 260 LEU cc_start: 0.9829 (tt) cc_final: 0.9603 (pp) REVERT: Z 264 MET cc_start: 0.9155 (ttm) cc_final: 0.8820 (tpt) REVERT: Z 280 GLU cc_start: 0.9457 (mm-30) cc_final: 0.9002 (mm-30) REVERT: Z 282 PHE cc_start: 0.9641 (t80) cc_final: 0.9253 (t80) outliers start: 4 outliers final: 0 residues processed: 356 average time/residue: 0.1658 time to fit residues: 84.9801 Evaluate side-chains 294 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 294 time to evaluate : 0.918 ------------------------------------------------------------------------------- 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: 0.9980 chunk 114 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 89 optimal weight: 0.0170 chunk 22 optimal weight: 9.9990 chunk 27 optimal weight: 0.8980 chunk 30 optimal weight: 0.3980 chunk 61 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 70 optimal weight: 20.0000 overall best weight: 0.6618 ------------------------------------------------------------------------------- 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 = 0.3525 r_free = 0.3525 target = 0.067165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.052606 restraints weight = 52571.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.053750 restraints weight = 40473.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.054545 restraints weight = 33149.535| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9204 Z= 0.151 Angle : 0.581 7.728 12570 Z= 0.311 Chirality : 0.044 0.252 1596 Planarity : 0.005 0.062 1626 Dihedral : 3.765 18.625 1394 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % 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: 1.93 (0.23), residues: 1332 helix: 1.89 (0.15), residues: 1101 sheet: None (None), residues: 0 loop : -1.79 (0.42), residues: 231 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 M 62 TYR 0.015 0.001 TYR I 48 ARG 0.008 0.000 ARG P 44 Details of bonding type rmsd hydrogen bonds : bond 0.04262 ( 899) hydrogen bonds : angle 3.87001 ( 2676) covalent geometry : bond 0.00342 ( 9204) covalent geometry : angle 0.58142 (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 : 0.890 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: 0.9362 (mt) cc_final: 0.8970 (mt) REVERT: H 38 ASN cc_start: 0.9437 (t0) cc_final: 0.9192 (t0) REVERT: H 49 MET cc_start: 0.9656 (ttp) cc_final: 0.9352 (tmm) REVERT: H 50 PHE cc_start: 0.9605 (m-80) cc_final: 0.9118 (m-80) REVERT: H 57 GLU cc_start: 0.9742 (tp30) cc_final: 0.9464 (tp30) REVERT: I 26 ILE cc_start: 0.9510 (tt) cc_final: 0.9257 (pt) REVERT: I 27 ILE cc_start: 0.9584 (OUTLIER) cc_final: 0.9384 (mt) REVERT: I 28 VAL cc_start: 0.9518 (t) cc_final: 0.9312 (m) REVERT: I 49 MET cc_start: 0.9422 (ttp) cc_final: 0.8930 (tmm) REVERT: I 55 PHE cc_start: 0.9502 (m-80) cc_final: 0.9152 (m-80) REVERT: J 48 TYR cc_start: 0.9407 (m-80) cc_final: 0.8735 (m-80) REVERT: J 53 ILE cc_start: 0.9679 (mt) cc_final: 0.9436 (mt) REVERT: K 1 MET cc_start: 0.4828 (mmt) cc_final: 0.4488 (tpp) REVERT: K 15 LEU cc_start: 0.9771 (mt) cc_final: 0.9505 (tp) REVERT: K 18 ILE cc_start: 0.9477 (pt) cc_final: 0.9155 (tp) REVERT: K 27 ILE cc_start: 0.9564 (mt) cc_final: 0.9266 (mt) REVERT: K 33 GLN cc_start: 0.9486 (mt0) cc_final: 0.8957 (mm110) REVERT: K 44 ARG cc_start: 0.9451 (tpp80) cc_final: 0.8894 (mmm-85) REVERT: K 48 TYR cc_start: 0.9617 (m-80) cc_final: 0.8946 (m-80) REVERT: K 49 MET cc_start: 0.9627 (ttp) cc_final: 0.9390 (ppp) REVERT: K 55 PHE cc_start: 0.9626 (m-80) cc_final: 0.9295 (m-80) REVERT: K 68 PHE cc_start: 0.9570 (m-10) cc_final: 0.9256 (m-80) REVERT: L 1 MET cc_start: 0.8860 (mtp) cc_final: 0.8237 (mtt) REVERT: L 33 GLN cc_start: 0.9334 (pt0) cc_final: 0.8962 (pt0) REVERT: L 43 ASN cc_start: 0.9162 (m-40) cc_final: 0.8956 (p0) REVERT: L 50 PHE cc_start: 0.9624 (m-80) cc_final: 0.9306 (m-10) REVERT: L 51 ILE cc_start: 0.9845 (mt) cc_final: 0.9537 (mt) REVERT: L 53 ILE cc_start: 0.9789 (tt) cc_final: 0.9443 (tp) REVERT: L 55 PHE cc_start: 0.9514 (m-80) cc_final: 0.9053 (m-80) REVERT: L 57 GLU cc_start: 0.9532 (tp30) cc_final: 0.9159 (pt0) REVERT: M 11 LEU cc_start: 0.9829 (mt) cc_final: 0.9564 (tt) REVERT: M 27 ILE cc_start: 0.9725 (mt) cc_final: 0.9483 (mt) REVERT: M 50 PHE cc_start: 0.9353 (m-80) cc_final: 0.8653 (m-80) REVERT: M 62 PHE cc_start: 0.8983 (m-80) cc_final: 0.8772 (m-80) REVERT: N 1 MET cc_start: 0.6417 (tpt) cc_final: 0.5648 (tpt) REVERT: N 11 LEU cc_start: 0.9810 (mm) cc_final: 0.9496 (mm) REVERT: N 55 PHE cc_start: 0.9624 (m-80) cc_final: 0.9118 (m-80) REVERT: O 29 SER cc_start: 0.9514 (t) cc_final: 0.9201 (p) REVERT: O 32 VAL cc_start: 0.9589 (p) cc_final: 0.9297 (m) REVERT: O 33 GLN cc_start: 0.9429 (mt0) cc_final: 0.8997 (mm-40) REVERT: O 50 PHE cc_start: 0.9433 (m-80) cc_final: 0.9213 (m-80) REVERT: O 57 GLU cc_start: 0.9357 (mm-30) cc_final: 0.8793 (pt0) REVERT: O 64 LEU cc_start: 0.9658 (tt) cc_final: 0.9390 (mt) REVERT: P 1 MET cc_start: 0.6769 (mtm) cc_final: 0.6002 (mtt) REVERT: P 49 MET cc_start: 0.9427 (ttp) cc_final: 0.9010 (tmm) REVERT: P 68 PHE cc_start: 0.9220 (m-80) cc_final: 0.8866 (m-80) REVERT: Q 18 ILE cc_start: 0.9490 (pt) cc_final: 0.9086 (mm) REVERT: Q 33 GLN cc_start: 0.8939 (mm-40) cc_final: 0.8582 (mm110) REVERT: Q 37 ARG cc_start: 0.9180 (mtt180) cc_final: 0.7931 (ttm110) REVERT: Q 49 MET cc_start: 0.9493 (ppp) cc_final: 0.9216 (ppp) REVERT: Q 50 PHE cc_start: 0.9604 (m-80) cc_final: 0.9196 (m-80) REVERT: Q 55 PHE cc_start: 0.9461 (m-80) cc_final: 0.9193 (m-80) REVERT: Z 95 PHE cc_start: 0.9548 (m-10) cc_final: 0.9239 (m-80) REVERT: Z 123 PHE cc_start: 0.9521 (t80) cc_final: 0.9121 (t80) REVERT: Z 132 ILE cc_start: 0.9202 (mt) cc_final: 0.8925 (mm) REVERT: Z 207 TYR cc_start: 0.8166 (t80) cc_final: 0.7759 (t80) REVERT: Z 228 MET cc_start: 0.9187 (ptt) cc_final: 0.8979 (ptt) REVERT: Z 248 PHE cc_start: 0.9464 (m-10) cc_final: 0.9092 (m-80) REVERT: Z 264 MET cc_start: 0.9179 (ttm) cc_final: 0.8844 (tpt) REVERT: Z 272 LEU cc_start: 0.9492 (tt) cc_final: 0.9288 (tt) REVERT: Z 280 GLU cc_start: 0.9416 (mm-30) cc_final: 0.9197 (mm-30) REVERT: Z 282 PHE cc_start: 0.9575 (t80) cc_final: 0.9168 (t80) REVERT: Z 289 LEU cc_start: 0.9759 (mt) cc_final: 0.9536 (mt) outliers start: 4 outliers final: 1 residues processed: 363 average time/residue: 0.1673 time to fit residues: 88.0101 Evaluate side-chains 298 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 296 time to evaluate : 0.926 ------------------------------------------------------------------------------- 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: 3.9990 chunk 81 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 107 optimal weight: 40.0000 chunk 100 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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** 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 = 0.3510 r_free = 0.3510 target = 0.066661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.052427 restraints weight = 53282.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.053516 restraints weight = 41669.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.054225 restraints weight = 34081.240| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.3780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9204 Z= 0.178 Angle : 0.588 7.376 12570 Z= 0.319 Chirality : 0.044 0.249 1596 Planarity : 0.005 0.069 1626 Dihedral : 3.783 20.333 1394 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.56 % Allowed : 3.38 % Favored : 96.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.23), residues: 1332 helix: 1.78 (0.15), residues: 1102 sheet: None (None), residues: 0 loop : -1.81 (0.41), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Z 208 HIS 0.004 0.002 HIS Z 31 PHE 0.033 0.002 PHE Q 62 TYR 0.018 0.002 TYR I 48 ARG 0.006 0.001 ARG P 37 Details of bonding type rmsd hydrogen bonds : bond 0.04123 ( 899) hydrogen bonds : angle 3.97609 ( 2676) covalent geometry : bond 0.00395 ( 9204) covalent geometry : angle 0.58784 (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 347 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 343 time to evaluate : 1.054 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: 0.9466 (t0) cc_final: 0.9080 (t0) REVERT: H 49 MET cc_start: 0.9667 (ttp) cc_final: 0.9368 (tmm) REVERT: H 50 PHE cc_start: 0.9588 (m-80) cc_final: 0.9147 (m-80) REVERT: H 57 GLU cc_start: 0.9753 (tp30) cc_final: 0.9421 (tp30) REVERT: H 62 PHE cc_start: 0.9670 (m-80) cc_final: 0.9468 (m-80) REVERT: H 64 LEU cc_start: 0.9802 (mm) cc_final: 0.9577 (mm) REVERT: H 68 PHE cc_start: 0.9393 (m-10) cc_final: 0.9170 (m-80) REVERT: I 49 MET cc_start: 0.9462 (ttp) cc_final: 0.8945 (tmm) REVERT: I 55 PHE cc_start: 0.9500 (m-80) cc_final: 0.9228 (m-80) REVERT: J 48 TYR cc_start: 0.9368 (m-80) cc_final: 0.8770 (m-80) REVERT: J 49 MET cc_start: 0.9487 (tmm) cc_final: 0.9243 (tmm) REVERT: K 1 MET cc_start: 0.4976 (mmt) cc_final: 0.4676 (tpp) REVERT: K 18 ILE cc_start: 0.9499 (pt) cc_final: 0.9193 (tp) REVERT: K 22 VAL cc_start: 0.9254 (p) cc_final: 0.9048 (p) REVERT: K 44 ARG cc_start: 0.9457 (tpp80) cc_final: 0.9171 (tpp80) REVERT: K 48 TYR cc_start: 0.9559 (m-80) cc_final: 0.9338 (m-80) REVERT: K 55 PHE cc_start: 0.9606 (m-80) cc_final: 0.9195 (m-80) REVERT: K 59 LEU cc_start: 0.9597 (mt) cc_final: 0.9387 (mt) REVERT: K 68 PHE cc_start: 0.9488 (m-10) cc_final: 0.9188 (m-80) REVERT: L 24 ILE cc_start: 0.9832 (mt) cc_final: 0.9620 (mt) REVERT: L 33 GLN cc_start: 0.9354 (pt0) cc_final: 0.8988 (pt0) REVERT: L 43 ASN cc_start: 0.9383 (m-40) cc_final: 0.9034 (p0) REVERT: L 50 PHE cc_start: 0.9616 (m-80) cc_final: 0.9314 (m-10) REVERT: L 51 ILE cc_start: 0.9852 (mt) cc_final: 0.9564 (mt) REVERT: L 53 ILE cc_start: 0.9795 (tt) cc_final: 0.9523 (tp) REVERT: L 55 PHE cc_start: 0.9552 (m-80) cc_final: 0.9016 (m-80) REVERT: M 11 LEU cc_start: 0.9830 (mt) cc_final: 0.9591 (tt) REVERT: M 27 ILE cc_start: 0.9752 (mt) cc_final: 0.9289 (mt) REVERT: M 49 MET cc_start: 0.9030 (tmm) cc_final: 0.8588 (tpt) REVERT: N 1 MET cc_start: 0.6079 (tpt) cc_final: 0.5722 (tpt) REVERT: N 11 LEU cc_start: 0.9818 (mm) cc_final: 0.9511 (mm) REVERT: N 55 PHE cc_start: 0.9643 (m-80) cc_final: 0.9095 (m-80) REVERT: O 29 SER cc_start: 0.9524 (t) cc_final: 0.9181 (p) REVERT: O 32 VAL cc_start: 0.9617 (p) cc_final: 0.9190 (m) REVERT: O 33 GLN cc_start: 0.9517 (mt0) cc_final: 0.9098 (mm-40) REVERT: O 57 GLU cc_start: 0.9355 (mm-30) cc_final: 0.8808 (pt0) REVERT: O 64 LEU cc_start: 0.9761 (tt) cc_final: 0.9470 (mt) REVERT: P 49 MET cc_start: 0.9524 (ttp) cc_final: 0.9065 (tmm) REVERT: P 68 PHE cc_start: 0.9237 (m-80) cc_final: 0.8853 (m-80) REVERT: Q 18 ILE cc_start: 0.9408 (pt) cc_final: 0.9034 (mm) REVERT: Q 33 GLN cc_start: 0.9136 (mm110) cc_final: 0.8882 (mm110) REVERT: Q 49 MET cc_start: 0.9438 (ppp) cc_final: 0.9178 (ppp) REVERT: Q 50 PHE cc_start: 0.9642 (m-80) cc_final: 0.9228 (m-80) REVERT: Q 55 PHE cc_start: 0.9500 (m-80) cc_final: 0.9228 (m-80) REVERT: Q 57 GLU cc_start: 0.9428 (mt-10) cc_final: 0.9003 (mt-10) REVERT: Q 62 PHE cc_start: 0.9624 (m-80) cc_final: 0.9303 (m-80) REVERT: Z 80 LEU cc_start: 0.9220 (mm) cc_final: 0.8920 (pt) REVERT: Z 84 MET cc_start: 0.9192 (mmp) cc_final: 0.8959 (mmm) REVERT: Z 95 PHE cc_start: 0.9582 (m-10) cc_final: 0.9274 (m-80) REVERT: Z 123 PHE cc_start: 0.9549 (t80) cc_final: 0.9166 (t80) REVERT: Z 132 ILE cc_start: 0.9207 (mt) cc_final: 0.8924 (mm) REVERT: Z 207 TYR cc_start: 0.8151 (t80) cc_final: 0.7747 (t80) REVERT: Z 228 MET cc_start: 0.9176 (ptt) cc_final: 0.8936 (ptt) REVERT: Z 248 PHE cc_start: 0.9527 (m-10) cc_final: 0.9137 (m-80) REVERT: Z 249 ARG cc_start: 0.9472 (mtp180) cc_final: 0.9146 (ttm170) REVERT: Z 264 MET cc_start: 0.9214 (ttm) cc_final: 0.8879 (tpt) REVERT: Z 280 GLU cc_start: 0.9455 (mm-30) cc_final: 0.9190 (mm-30) REVERT: Z 282 PHE cc_start: 0.9575 (t80) cc_final: 0.9186 (t80) REVERT: Z 289 LEU cc_start: 0.9769 (mt) cc_final: 0.9536 (mt) outliers start: 4 outliers final: 0 residues processed: 343 average time/residue: 0.1588 time to fit residues: 80.1763 Evaluate side-chains 283 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 283 time to evaluate : 1.076 ------------------------------------------------------------------------------- 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: 0.8980 chunk 59 optimal weight: 0.3980 chunk 44 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 120 optimal weight: 0.0030 overall best weight: 0.6192 ------------------------------------------------------------------------------- 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 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.067591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.052922 restraints weight = 53567.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.054003 restraints weight = 41584.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.054822 restraints weight = 34105.113| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9204 Z= 0.146 Angle : 0.585 8.256 12570 Z= 0.311 Chirality : 0.044 0.177 1596 Planarity : 0.005 0.070 1626 Dihedral : 3.767 21.441 1394 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.56 % Allowed : 2.68 % Favored : 96.76 % 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: 1.82 (0.23), residues: 1332 helix: 1.81 (0.15), residues: 1103 sheet: None (None), residues: 0 loop : -1.82 (0.41), residues: 229 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 0.026 0.001 PHE K 62 TYR 0.019 0.002 TYR H 48 ARG 0.003 0.000 ARG Q 44 Details of bonding type rmsd hydrogen bonds : bond 0.04057 ( 899) hydrogen bonds : angle 3.85373 ( 2676) covalent geometry : bond 0.00333 ( 9204) covalent geometry : angle 0.58498 (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 351 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 347 time to evaluate : 0.945 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: 0.9131 (t0) cc_final: 0.8769 (t0) REVERT: H 49 MET cc_start: 0.9663 (ttp) cc_final: 0.9377 (tmm) REVERT: H 50 PHE cc_start: 0.9606 (m-80) cc_final: 0.9152 (m-80) REVERT: H 57 GLU cc_start: 0.9771 (tp30) cc_final: 0.9415 (tp30) REVERT: H 64 LEU cc_start: 0.9806 (mm) cc_final: 0.9527 (mt) REVERT: H 68 PHE cc_start: 0.9419 (m-10) cc_final: 0.9200 (m-80) REVERT: I 55 PHE cc_start: 0.9529 (m-80) cc_final: 0.9240 (m-80) REVERT: I 68 PHE cc_start: 0.9353 (m-80) cc_final: 0.8995 (m-80) REVERT: J 48 TYR cc_start: 0.9376 (m-80) cc_final: 0.8691 (m-80) REVERT: J 49 MET cc_start: 0.9554 (tmm) cc_final: 0.9196 (tmm) REVERT: K 1 MET cc_start: 0.5033 (mmt) cc_final: 0.4738 (tpp) REVERT: K 15 LEU cc_start: 0.9752 (mt) cc_final: 0.9274 (tp) REVERT: K 18 ILE cc_start: 0.9451 (pt) cc_final: 0.9137 (tp) REVERT: K 22 VAL cc_start: 0.9209 (p) cc_final: 0.8987 (p) REVERT: K 27 ILE cc_start: 0.9581 (mt) cc_final: 0.9259 (mt) REVERT: K 44 ARG cc_start: 0.9439 (tpp80) cc_final: 0.9124 (tpp80) REVERT: K 48 TYR cc_start: 0.9597 (m-80) cc_final: 0.9337 (m-80) REVERT: K 49 MET cc_start: 0.9632 (ttp) cc_final: 0.9369 (ppp) REVERT: K 55 PHE cc_start: 0.9551 (m-80) cc_final: 0.9305 (m-80) REVERT: K 68 PHE cc_start: 0.9480 (m-10) cc_final: 0.9179 (m-80) REVERT: L 1 MET cc_start: 0.8988 (mtp) cc_final: 0.8519 (mtt) REVERT: L 50 PHE cc_start: 0.9635 (m-80) cc_final: 0.9296 (m-10) REVERT: L 51 ILE cc_start: 0.9847 (mt) cc_final: 0.9530 (mt) REVERT: L 53 ILE cc_start: 0.9828 (tt) cc_final: 0.9472 (tp) REVERT: L 55 PHE cc_start: 0.9454 (m-80) cc_final: 0.8983 (m-80) REVERT: L 57 GLU cc_start: 0.9485 (mm-30) cc_final: 0.8959 (mt-10) REVERT: M 27 ILE cc_start: 0.9704 (mt) cc_final: 0.9316 (mt) REVERT: M 50 PHE cc_start: 0.9550 (m-80) cc_final: 0.9220 (m-10) REVERT: N 1 MET cc_start: 0.6306 (tpt) cc_final: 0.5583 (tpt) REVERT: N 11 LEU cc_start: 0.9800 (mm) cc_final: 0.9535 (mm) REVERT: N 55 PHE cc_start: 0.9649 (m-80) cc_final: 0.9136 (m-80) REVERT: O 1 MET cc_start: 0.6887 (mmt) cc_final: 0.6399 (mmt) REVERT: O 29 SER cc_start: 0.9508 (t) cc_final: 0.9192 (p) REVERT: O 32 VAL cc_start: 0.9608 (p) cc_final: 0.9151 (m) REVERT: O 33 GLN cc_start: 0.9503 (mt0) cc_final: 0.9074 (mm110) REVERT: O 57 GLU cc_start: 0.9296 (mm-30) cc_final: 0.8792 (pt0) REVERT: O 62 PHE cc_start: 0.9233 (m-80) cc_final: 0.8929 (m-80) REVERT: O 64 LEU cc_start: 0.9729 (tt) cc_final: 0.9363 (mt) REVERT: O 66 ILE cc_start: 0.9571 (tp) cc_final: 0.9359 (tp) REVERT: P 49 MET cc_start: 0.9385 (ttp) cc_final: 0.8305 (tpp) REVERT: P 68 PHE cc_start: 0.9231 (m-80) cc_final: 0.8854 (m-80) REVERT: Q 18 ILE cc_start: 0.9399 (pt) cc_final: 0.9008 (mm) REVERT: Q 27 ILE cc_start: 0.9478 (mt) cc_final: 0.9268 (mt) REVERT: Q 33 GLN cc_start: 0.9153 (mm110) cc_final: 0.8864 (mm-40) REVERT: Q 49 MET cc_start: 0.9419 (ppp) cc_final: 0.9190 (ppp) REVERT: Q 50 PHE cc_start: 0.9634 (m-80) cc_final: 0.9210 (m-80) REVERT: Q 55 PHE cc_start: 0.9493 (m-80) cc_final: 0.9258 (m-80) REVERT: Q 62 PHE cc_start: 0.9632 (m-80) cc_final: 0.9325 (m-80) REVERT: Z 80 LEU cc_start: 0.9244 (mm) cc_final: 0.8957 (pt) REVERT: Z 84 MET cc_start: 0.9240 (mmp) cc_final: 0.9019 (mmm) REVERT: Z 95 PHE cc_start: 0.9560 (m-10) cc_final: 0.9140 (m-80) REVERT: Z 123 PHE cc_start: 0.9532 (t80) cc_final: 0.9143 (t80) REVERT: Z 132 ILE cc_start: 0.9227 (mt) cc_final: 0.8891 (mm) REVERT: Z 207 TYR cc_start: 0.8168 (t80) cc_final: 0.7759 (t80) REVERT: Z 228 MET cc_start: 0.9239 (ptt) cc_final: 0.9010 (ptt) REVERT: Z 248 PHE cc_start: 0.9468 (m-10) cc_final: 0.9108 (m-80) REVERT: Z 249 ARG cc_start: 0.9481 (mtp180) cc_final: 0.9100 (ttm-80) REVERT: Z 264 MET cc_start: 0.9243 (ttm) cc_final: 0.8875 (tpt) REVERT: Z 280 GLU cc_start: 0.9439 (mm-30) cc_final: 0.9190 (mm-30) REVERT: Z 282 PHE cc_start: 0.9518 (t80) cc_final: 0.9101 (t80) REVERT: Z 289 LEU cc_start: 0.9752 (mt) cc_final: 0.9537 (mt) outliers start: 4 outliers final: 0 residues processed: 347 average time/residue: 0.1736 time to fit residues: 89.6488 Evaluate side-chains 290 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 290 time to evaluate : 1.009 ------------------------------------------------------------------------------- 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: 2.9990 chunk 110 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 124 optimal weight: 9.9990 chunk 75 optimal weight: 1.9990 chunk 53 optimal weight: 0.2980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.068027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.053404 restraints weight = 52703.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.054468 restraints weight = 41142.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.055249 restraints weight = 34008.233| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.4344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9204 Z= 0.149 Angle : 0.595 7.809 12570 Z= 0.315 Chirality : 0.044 0.235 1596 Planarity : 0.005 0.071 1626 Dihedral : 3.793 21.141 1394 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % 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: 1.81 (0.23), residues: 1332 helix: 1.81 (0.15), residues: 1103 sheet: None (None), residues: 0 loop : -1.85 (0.41), 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 0.031 0.001 PHE K 62 TYR 0.019 0.002 TYR H 48 ARG 0.016 0.001 ARG I 37 Details of bonding type rmsd hydrogen bonds : bond 0.04015 ( 899) hydrogen bonds : angle 3.85030 ( 2676) covalent geometry : bond 0.00348 ( 9204) covalent geometry : angle 0.59547 (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 342 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 342 time to evaluate : 1.741 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: H 38 ASN cc_start: 0.9151 (t0) cc_final: 0.8929 (t0) REVERT: H 49 MET cc_start: 0.9636 (ttp) cc_final: 0.9362 (tmm) REVERT: H 50 PHE cc_start: 0.9595 (m-80) cc_final: 0.9138 (m-80) REVERT: H 57 GLU cc_start: 0.9759 (tp30) cc_final: 0.9482 (tp30) REVERT: H 64 LEU cc_start: 0.9799 (mm) cc_final: 0.9508 (mt) REVERT: H 68 PHE cc_start: 0.9386 (m-10) cc_final: 0.9174 (m-80) REVERT: I 27 ILE cc_start: 0.9565 (mp) cc_final: 0.9364 (mp) REVERT: I 35 ILE cc_start: 0.9243 (mm) cc_final: 0.9002 (tp) REVERT: I 49 MET cc_start: 0.9433 (ttp) cc_final: 0.8997 (tmm) REVERT: I 55 PHE cc_start: 0.9508 (m-80) cc_final: 0.9220 (m-80) REVERT: J 15 LEU cc_start: 0.9611 (mp) cc_final: 0.9310 (tp) REVERT: J 48 TYR cc_start: 0.9346 (m-80) cc_final: 0.8758 (m-80) REVERT: J 49 MET cc_start: 0.9472 (tmm) cc_final: 0.9181 (tmm) REVERT: K 1 MET cc_start: 0.5058 (mmt) cc_final: 0.4760 (tpp) REVERT: K 15 LEU cc_start: 0.9759 (mt) cc_final: 0.9532 (tp) REVERT: K 18 ILE cc_start: 0.9446 (pt) cc_final: 0.8999 (tp) REVERT: K 22 VAL cc_start: 0.9143 (p) cc_final: 0.8912 (p) REVERT: K 44 ARG cc_start: 0.9427 (tpp80) cc_final: 0.8914 (tpp80) REVERT: K 48 TYR cc_start: 0.9552 (m-80) cc_final: 0.8995 (m-80) REVERT: K 55 PHE cc_start: 0.9531 (m-80) cc_final: 0.9286 (m-80) REVERT: K 68 PHE cc_start: 0.9424 (m-10) cc_final: 0.9157 (m-80) REVERT: L 1 MET cc_start: 0.8875 (mtp) cc_final: 0.8375 (mtt) REVERT: L 43 ASN cc_start: 0.9325 (p0) cc_final: 0.9018 (m-40) REVERT: L 50 PHE cc_start: 0.9595 (m-80) cc_final: 0.9278 (m-10) REVERT: L 51 ILE cc_start: 0.9834 (mt) cc_final: 0.9516 (mt) REVERT: L 53 ILE cc_start: 0.9805 (tt) cc_final: 0.9427 (tp) REVERT: L 55 PHE cc_start: 0.9428 (m-80) cc_final: 0.8947 (m-80) REVERT: L 57 GLU cc_start: 0.9461 (mm-30) cc_final: 0.8887 (mt-10) REVERT: M 50 PHE cc_start: 0.9513 (m-80) cc_final: 0.9206 (m-80) REVERT: M 68 PHE cc_start: 0.9442 (t80) cc_final: 0.9184 (t80) REVERT: N 1 MET cc_start: 0.6245 (tpt) cc_final: 0.5495 (mmm) REVERT: N 55 PHE cc_start: 0.9651 (m-80) cc_final: 0.9136 (m-80) REVERT: O 1 MET cc_start: 0.6756 (mmt) cc_final: 0.6255 (mmt) REVERT: O 29 SER cc_start: 0.9501 (t) cc_final: 0.9226 (p) REVERT: O 32 VAL cc_start: 0.9607 (p) cc_final: 0.9191 (m) REVERT: O 33 GLN cc_start: 0.9517 (mt0) cc_final: 0.9085 (mm-40) REVERT: O 57 GLU cc_start: 0.9406 (mm-30) cc_final: 0.8892 (pt0) REVERT: O 62 PHE cc_start: 0.9160 (m-80) cc_final: 0.8801 (m-80) REVERT: O 64 LEU cc_start: 0.9767 (tt) cc_final: 0.9490 (mt) REVERT: P 49 MET cc_start: 0.9450 (ttp) cc_final: 0.9029 (tmm) REVERT: P 68 PHE cc_start: 0.9183 (m-80) cc_final: 0.8829 (m-80) REVERT: Q 18 ILE cc_start: 0.9433 (pt) cc_final: 0.9128 (mm) REVERT: Q 33 GLN cc_start: 0.9178 (mm110) cc_final: 0.8919 (mm110) REVERT: Q 49 MET cc_start: 0.9435 (ppp) cc_final: 0.9184 (ppp) REVERT: Q 50 PHE cc_start: 0.9633 (m-80) cc_final: 0.9183 (m-80) REVERT: Q 62 PHE cc_start: 0.9679 (m-80) cc_final: 0.9333 (m-80) REVERT: Z 80 LEU cc_start: 0.9200 (mm) cc_final: 0.8944 (pt) REVERT: Z 95 PHE cc_start: 0.9493 (m-10) cc_final: 0.9033 (m-80) REVERT: Z 123 PHE cc_start: 0.9506 (t80) cc_final: 0.9159 (t80) REVERT: Z 207 TYR cc_start: 0.7997 (t80) cc_final: 0.7622 (t80) REVERT: Z 228 MET cc_start: 0.9198 (ptt) cc_final: 0.8963 (ptt) REVERT: Z 248 PHE cc_start: 0.9476 (m-10) cc_final: 0.9100 (m-80) REVERT: Z 249 ARG cc_start: 0.9477 (mtp180) cc_final: 0.9111 (ttm-80) REVERT: Z 264 MET cc_start: 0.9202 (ttm) cc_final: 0.8879 (tpt) REVERT: Z 280 GLU cc_start: 0.9416 (mm-30) cc_final: 0.9157 (mm-30) REVERT: Z 282 PHE cc_start: 0.9496 (t80) cc_final: 0.9078 (t80) REVERT: Z 289 LEU cc_start: 0.9759 (mt) cc_final: 0.9530 (mt) outliers start: 0 outliers final: 0 residues processed: 342 average time/residue: 0.1624 time to fit residues: 83.2247 Evaluate side-chains 288 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 288 time to evaluate : 0.898 ------------------------------------------------------------------------------- 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: 2.9990 chunk 127 optimal weight: 8.9990 chunk 1 optimal weight: 0.9980 chunk 71 optimal weight: 0.0870 chunk 16 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 118 optimal weight: 30.0000 chunk 66 optimal weight: 0.7980 chunk 110 optimal weight: 7.9990 chunk 115 optimal weight: 7.9990 chunk 7 optimal weight: 0.6980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.068386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.053301 restraints weight = 52081.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.054311 restraints weight = 41380.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.055106 restraints weight = 34578.540| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.4584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 9204 Z= 0.155 Angle : 0.624 7.542 12570 Z= 0.331 Chirality : 0.045 0.228 1596 Planarity : 0.005 0.070 1626 Dihedral : 3.826 21.760 1394 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 16.28 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: 1.72 (0.23), residues: 1332 helix: 1.74 (0.15), residues: 1106 sheet: None (None), residues: 0 loop : -1.92 (0.41), residues: 226 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 0.036 0.001 PHE H 62 TYR 0.016 0.001 TYR H 48 ARG 0.010 0.000 ARG I 37 Details of bonding type rmsd hydrogen bonds : bond 0.04089 ( 899) hydrogen bonds : angle 3.87857 ( 2676) covalent geometry : bond 0.00363 ( 9204) covalent geometry : angle 0.62443 (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 342 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 342 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 27 ILE cc_start: 0.9478 (mm) cc_final: 0.9073 (mm) REVERT: H 38 ASN cc_start: 0.9245 (t0) cc_final: 0.9014 (t0) REVERT: H 49 MET cc_start: 0.9651 (ttp) cc_final: 0.9352 (tmm) REVERT: H 50 PHE cc_start: 0.9604 (m-80) cc_final: 0.9205 (m-80) REVERT: H 57 GLU cc_start: 0.9808 (tp30) cc_final: 0.9439 (tp30) REVERT: H 64 LEU cc_start: 0.9801 (mm) cc_final: 0.9508 (mt) REVERT: H 68 PHE cc_start: 0.9392 (m-10) cc_final: 0.9167 (m-80) REVERT: I 35 ILE cc_start: 0.9267 (mm) cc_final: 0.9043 (tp) REVERT: I 51 ILE cc_start: 0.9690 (mt) cc_final: 0.9392 (mt) REVERT: I 55 PHE cc_start: 0.9531 (m-80) cc_final: 0.9188 (m-80) REVERT: I 68 PHE cc_start: 0.9358 (m-80) cc_final: 0.8961 (m-80) REVERT: J 15 LEU cc_start: 0.9601 (mp) cc_final: 0.9254 (tp) REVERT: J 48 TYR cc_start: 0.9363 (m-80) cc_final: 0.8748 (m-80) REVERT: J 49 MET cc_start: 0.9574 (tmm) cc_final: 0.9208 (tmm) REVERT: K 1 MET cc_start: 0.4807 (mmt) cc_final: 0.4507 (tpp) REVERT: K 15 LEU cc_start: 0.9744 (mt) cc_final: 0.9514 (tp) REVERT: K 18 ILE cc_start: 0.9398 (pt) cc_final: 0.8946 (tp) REVERT: K 22 VAL cc_start: 0.9171 (p) cc_final: 0.8968 (p) REVERT: K 27 ILE cc_start: 0.9689 (mt) cc_final: 0.9452 (mt) REVERT: K 44 ARG cc_start: 0.9461 (tpp80) cc_final: 0.8911 (tpp80) REVERT: K 48 TYR cc_start: 0.9554 (m-80) cc_final: 0.8977 (m-80) REVERT: K 55 PHE cc_start: 0.9569 (m-80) cc_final: 0.9340 (m-80) REVERT: K 56 THR cc_start: 0.9654 (t) cc_final: 0.9392 (p) REVERT: K 68 PHE cc_start: 0.9439 (m-10) cc_final: 0.9156 (m-80) REVERT: L 1 MET cc_start: 0.9038 (mtp) cc_final: 0.8718 (mtt) REVERT: L 43 ASN cc_start: 0.9323 (p0) cc_final: 0.9077 (m-40) REVERT: L 50 PHE cc_start: 0.9611 (m-80) cc_final: 0.9284 (m-10) REVERT: L 51 ILE cc_start: 0.9827 (mt) cc_final: 0.9500 (mt) REVERT: L 53 ILE cc_start: 0.9813 (tt) cc_final: 0.9427 (tp) REVERT: L 55 PHE cc_start: 0.9420 (m-80) cc_final: 0.8897 (m-80) REVERT: L 57 GLU cc_start: 0.9471 (mm-30) cc_final: 0.8902 (mt-10) REVERT: M 50 PHE cc_start: 0.9472 (m-80) cc_final: 0.9263 (m-80) REVERT: M 59 LEU cc_start: 0.9402 (mt) cc_final: 0.9201 (mt) REVERT: M 68 PHE cc_start: 0.9448 (t80) cc_final: 0.9205 (t80) REVERT: N 1 MET cc_start: 0.6121 (tpt) cc_final: 0.5867 (mmt) REVERT: N 15 LEU cc_start: 0.9626 (mt) cc_final: 0.9415 (mm) REVERT: N 33 GLN cc_start: 0.9282 (mp10) cc_final: 0.9052 (mp10) REVERT: N 55 PHE cc_start: 0.9634 (m-80) cc_final: 0.9214 (m-80) REVERT: O 15 LEU cc_start: 0.9751 (mp) cc_final: 0.9301 (tp) REVERT: O 29 SER cc_start: 0.9494 (t) cc_final: 0.9253 (p) REVERT: O 32 VAL cc_start: 0.9588 (p) cc_final: 0.9229 (m) REVERT: O 33 GLN cc_start: 0.9493 (mt0) cc_final: 0.9099 (mm-40) REVERT: O 55 PHE cc_start: 0.8859 (m-10) cc_final: 0.8655 (m-10) REVERT: O 57 GLU cc_start: 0.9317 (mm-30) cc_final: 0.8809 (pt0) REVERT: O 62 PHE cc_start: 0.9223 (m-80) cc_final: 0.8835 (m-80) REVERT: O 64 LEU cc_start: 0.9731 (tt) cc_final: 0.9396 (mt) REVERT: P 37 ARG cc_start: 0.9200 (ptm160) cc_final: 0.8678 (ptm-80) REVERT: P 49 MET cc_start: 0.9402 (ttp) cc_final: 0.9004 (tmm) REVERT: P 55 PHE cc_start: 0.8926 (m-10) cc_final: 0.8714 (m-80) REVERT: P 68 PHE cc_start: 0.9221 (m-80) cc_final: 0.8803 (m-80) REVERT: Q 18 ILE cc_start: 0.9408 (pt) cc_final: 0.9075 (mm) REVERT: Q 27 ILE cc_start: 0.9435 (mt) cc_final: 0.9149 (mt) REVERT: Q 33 GLN cc_start: 0.9106 (mm110) cc_final: 0.8763 (mm-40) REVERT: Q 50 PHE cc_start: 0.9672 (m-80) cc_final: 0.9304 (m-80) REVERT: Q 55 PHE cc_start: 0.9620 (m-10) cc_final: 0.9317 (m-80) REVERT: Q 57 GLU cc_start: 0.9213 (mt-10) cc_final: 0.8801 (mp0) REVERT: Q 62 PHE cc_start: 0.9684 (m-80) cc_final: 0.9325 (m-80) REVERT: Z 80 LEU cc_start: 0.9202 (mm) cc_final: 0.8947 (pt) REVERT: Z 95 PHE cc_start: 0.9511 (m-10) cc_final: 0.9119 (m-80) REVERT: Z 123 PHE cc_start: 0.9508 (t80) cc_final: 0.9161 (t80) REVERT: Z 207 TYR cc_start: 0.8050 (t80) cc_final: 0.7639 (t80) REVERT: Z 248 PHE cc_start: 0.9537 (m-10) cc_final: 0.9101 (m-80) REVERT: Z 264 MET cc_start: 0.9241 (ttm) cc_final: 0.8908 (tpt) REVERT: Z 280 GLU cc_start: 0.9424 (mm-30) cc_final: 0.9161 (mm-30) REVERT: Z 282 PHE cc_start: 0.9532 (t80) cc_final: 0.9095 (t80) REVERT: Z 287 GLN cc_start: 0.9496 (mm110) cc_final: 0.9120 (mm110) outliers start: 0 outliers final: 0 residues processed: 342 average time/residue: 0.1526 time to fit residues: 77.6847 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 : 0.922 ------------------------------------------------------------------------------- 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: 4.9990 chunk 18 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 128 optimal weight: 7.9990 chunk 35 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 73 optimal weight: 9.9990 chunk 87 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.068212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.053315 restraints weight = 52301.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.054384 restraints weight = 41343.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.055092 restraints weight = 34317.216| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.4773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 9204 Z= 0.167 Angle : 0.624 7.512 12570 Z= 0.336 Chirality : 0.045 0.209 1596 Planarity : 0.005 0.072 1626 Dihedral : 3.862 21.767 1394 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % 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: 1.65 (0.23), residues: 1332 helix: 1.68 (0.15), residues: 1106 sheet: None (None), residues: 0 loop : -1.81 (0.41), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP Z 208 HIS 0.002 0.001 HIS Z 31 PHE 0.026 0.001 PHE K 62 TYR 0.021 0.002 TYR Z 217 ARG 0.007 0.001 ARG I 37 Details of bonding type rmsd hydrogen bonds : bond 0.04072 ( 899) hydrogen bonds : angle 3.98441 ( 2676) covalent geometry : bond 0.00398 ( 9204) covalent geometry : angle 0.62410 (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 338 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 338 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 15 LEU cc_start: 0.9606 (mp) cc_final: 0.9177 (tp) REVERT: H 38 ASN cc_start: 0.9288 (t0) cc_final: 0.9007 (t0) REVERT: H 49 MET cc_start: 0.9612 (ttp) cc_final: 0.9301 (tmm) REVERT: H 50 PHE cc_start: 0.9579 (m-80) cc_final: 0.9163 (m-80) REVERT: H 57 GLU cc_start: 0.9790 (tp30) cc_final: 0.9485 (tp30) REVERT: H 64 LEU cc_start: 0.9797 (mm) cc_final: 0.9494 (mt) REVERT: H 68 PHE cc_start: 0.9387 (m-10) cc_final: 0.9165 (m-80) REVERT: I 35 ILE cc_start: 0.9308 (mm) cc_final: 0.9089 (tp) REVERT: I 49 MET cc_start: 0.9298 (ttp) cc_final: 0.8834 (tmm) REVERT: I 55 PHE cc_start: 0.9331 (m-80) cc_final: 0.9044 (m-10) REVERT: I 68 PHE cc_start: 0.9370 (m-80) cc_final: 0.8908 (m-80) REVERT: J 48 TYR cc_start: 0.9354 (m-80) cc_final: 0.8744 (m-80) REVERT: J 49 MET cc_start: 0.9624 (tmm) cc_final: 0.9228 (tmm) REVERT: J 64 LEU cc_start: 0.9625 (mt) cc_final: 0.9332 (pp) REVERT: K 18 ILE cc_start: 0.9442 (pt) cc_final: 0.9054 (tp) REVERT: K 33 GLN cc_start: 0.9522 (mt0) cc_final: 0.9042 (mm110) REVERT: K 44 ARG cc_start: 0.9411 (tpp80) cc_final: 0.8704 (tpp80) REVERT: K 48 TYR cc_start: 0.9521 (m-80) cc_final: 0.8735 (m-80) REVERT: K 55 PHE cc_start: 0.9542 (m-80) cc_final: 0.9288 (m-80) REVERT: K 66 ILE cc_start: 0.9621 (mm) cc_final: 0.9408 (tp) REVERT: K 68 PHE cc_start: 0.9412 (m-10) cc_final: 0.9128 (m-80) REVERT: L 1 MET cc_start: 0.9071 (mtp) cc_final: 0.8727 (mtt) REVERT: L 43 ASN cc_start: 0.9339 (p0) cc_final: 0.9066 (m-40) REVERT: L 50 PHE cc_start: 0.9599 (m-80) cc_final: 0.9274 (m-10) REVERT: L 51 ILE cc_start: 0.9825 (mt) cc_final: 0.9501 (mt) REVERT: L 53 ILE cc_start: 0.9822 (tt) cc_final: 0.9421 (tp) REVERT: L 55 PHE cc_start: 0.9405 (m-80) cc_final: 0.8883 (m-80) REVERT: L 57 GLU cc_start: 0.9470 (mm-30) cc_final: 0.8874 (mt-10) REVERT: M 68 PHE cc_start: 0.9430 (t80) cc_final: 0.9190 (t80) REVERT: N 1 MET cc_start: 0.6429 (tpt) cc_final: 0.5817 (mmm) REVERT: N 55 PHE cc_start: 0.9635 (m-80) cc_final: 0.9195 (m-80) REVERT: O 1 MET cc_start: 0.6540 (mmt) cc_final: 0.5994 (mmt) REVERT: O 11 LEU cc_start: 0.9563 (mt) cc_final: 0.9328 (mt) REVERT: O 15 LEU cc_start: 0.9742 (mp) cc_final: 0.9338 (tp) REVERT: O 29 SER cc_start: 0.9520 (t) cc_final: 0.9294 (p) REVERT: O 32 VAL cc_start: 0.9633 (p) cc_final: 0.9278 (m) REVERT: O 33 GLN cc_start: 0.9403 (mt0) cc_final: 0.9152 (mm-40) REVERT: O 57 GLU cc_start: 0.9380 (mm-30) cc_final: 0.8921 (pt0) REVERT: O 62 PHE cc_start: 0.9142 (m-80) cc_final: 0.8727 (m-80) REVERT: O 64 LEU cc_start: 0.9766 (tt) cc_final: 0.9485 (mt) REVERT: P 37 ARG cc_start: 0.9114 (ptm160) cc_final: 0.8744 (ptm160) REVERT: P 49 MET cc_start: 0.9316 (ttp) cc_final: 0.9046 (tmm) REVERT: P 68 PHE cc_start: 0.9199 (m-80) cc_final: 0.8809 (m-80) REVERT: Q 15 LEU cc_start: 0.9162 (mm) cc_final: 0.8703 (tp) REVERT: Q 18 ILE cc_start: 0.9481 (pt) cc_final: 0.9160 (mm) REVERT: Q 27 ILE cc_start: 0.9438 (mt) cc_final: 0.9228 (mt) REVERT: Q 33 GLN cc_start: 0.9185 (mm110) cc_final: 0.8780 (mm-40) REVERT: Q 49 MET cc_start: 0.9224 (ppp) cc_final: 0.9007 (ppp) REVERT: Q 50 PHE cc_start: 0.9658 (m-80) cc_final: 0.9276 (m-80) REVERT: Q 55 PHE cc_start: 0.9583 (m-10) cc_final: 0.9367 (m-80) REVERT: Q 62 PHE cc_start: 0.9719 (m-80) cc_final: 0.9395 (m-80) REVERT: Z 80 LEU cc_start: 0.9173 (mm) cc_final: 0.8940 (pt) REVERT: Z 84 MET cc_start: 0.9131 (mmp) cc_final: 0.8931 (mmm) REVERT: Z 95 PHE cc_start: 0.9524 (m-10) cc_final: 0.9078 (m-80) REVERT: Z 123 PHE cc_start: 0.9503 (t80) cc_final: 0.9188 (t80) REVERT: Z 207 TYR cc_start: 0.8000 (t80) cc_final: 0.7669 (t80) REVERT: Z 228 MET cc_start: 0.9179 (ptt) cc_final: 0.8977 (ptt) REVERT: Z 248 PHE cc_start: 0.9555 (m-10) cc_final: 0.9150 (m-80) REVERT: Z 249 ARG cc_start: 0.9611 (ttm110) cc_final: 0.9199 (mtt180) REVERT: Z 264 MET cc_start: 0.9174 (ttm) cc_final: 0.8869 (ttm) REVERT: Z 280 GLU cc_start: 0.9424 (mm-30) cc_final: 0.9165 (mm-30) REVERT: Z 282 PHE cc_start: 0.9527 (t80) cc_final: 0.9089 (t80) REVERT: Z 287 GLN cc_start: 0.9532 (mm110) cc_final: 0.9037 (mm110) outliers start: 0 outliers final: 0 residues processed: 338 average time/residue: 0.1577 time to fit residues: 78.5565 Evaluate side-chains 282 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 282 time to evaluate : 0.925 ------------------------------------------------------------------------------- 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: 3.9990 chunk 66 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 95 optimal weight: 7.9990 chunk 41 optimal weight: 0.1980 chunk 117 optimal weight: 50.0000 chunk 96 optimal weight: 6.9990 chunk 119 optimal weight: 0.8980 chunk 71 optimal weight: 0.0010 chunk 29 optimal weight: 0.7980 overall best weight: 0.5786 ------------------------------------------------------------------------------- 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** ** P 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 = 0.3530 r_free = 0.3530 target = 0.068599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.053622 restraints weight = 51016.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.054732 restraints weight = 40639.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.055498 restraints weight = 33940.093| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.4975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 9204 Z= 0.155 Angle : 0.649 9.174 12570 Z= 0.344 Chirality : 0.046 0.221 1596 Planarity : 0.005 0.073 1626 Dihedral : 3.877 21.082 1394 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.67 (0.15), residues: 1108 sheet: None (None), residues: 0 loop : -1.86 (0.40), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Z 208 HIS 0.001 0.001 HIS Z 170 PHE 0.046 0.002 PHE M 62 TYR 0.016 0.002 TYR Z 217 ARG 0.005 0.000 ARG I 37 Details of bonding type rmsd hydrogen bonds : bond 0.04108 ( 899) hydrogen bonds : angle 3.92914 ( 2676) covalent geometry : bond 0.00373 ( 9204) covalent geometry : angle 0.64949 (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 336 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 336 time to evaluate : 0.928 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: H 38 ASN cc_start: 0.9282 (t0) cc_final: 0.9049 (t0) REVERT: H 49 MET cc_start: 0.9613 (ttp) cc_final: 0.9327 (tmm) REVERT: H 50 PHE cc_start: 0.9555 (m-80) cc_final: 0.9179 (m-80) REVERT: H 57 GLU cc_start: 0.9807 (tp30) cc_final: 0.9486 (tp30) REVERT: H 64 LEU cc_start: 0.9795 (mm) cc_final: 0.9483 (mt) REVERT: H 68 PHE cc_start: 0.9417 (m-10) cc_final: 0.9204 (m-80) REVERT: I 35 ILE cc_start: 0.9295 (mm) cc_final: 0.9056 (tp) REVERT: I 55 PHE cc_start: 0.9324 (m-80) cc_final: 0.9051 (m-10) REVERT: I 68 PHE cc_start: 0.9403 (m-80) cc_final: 0.8935 (m-80) REVERT: J 15 LEU cc_start: 0.9606 (mp) cc_final: 0.9231 (tp) REVERT: J 48 TYR cc_start: 0.9378 (m-80) cc_final: 0.8762 (m-80) REVERT: J 49 MET cc_start: 0.9548 (tmm) cc_final: 0.9212 (tmm) REVERT: J 64 LEU cc_start: 0.9616 (mt) cc_final: 0.9320 (pp) REVERT: K 18 ILE cc_start: 0.9391 (pt) cc_final: 0.8905 (tp) REVERT: K 44 ARG cc_start: 0.9458 (tpp80) cc_final: 0.8711 (tpp80) REVERT: K 48 TYR cc_start: 0.9520 (m-80) cc_final: 0.8768 (m-80) REVERT: K 55 PHE cc_start: 0.9555 (m-80) cc_final: 0.9288 (m-80) REVERT: K 66 ILE cc_start: 0.9628 (mm) cc_final: 0.9412 (tp) REVERT: K 68 PHE cc_start: 0.9450 (m-10) cc_final: 0.9145 (m-80) REVERT: L 1 MET cc_start: 0.9016 (mtp) cc_final: 0.8656 (mtt) REVERT: L 43 ASN cc_start: 0.9337 (p0) cc_final: 0.9088 (m-40) REVERT: L 50 PHE cc_start: 0.9614 (m-80) cc_final: 0.9313 (m-10) REVERT: L 51 ILE cc_start: 0.9821 (mt) cc_final: 0.9500 (mt) REVERT: L 53 ILE cc_start: 0.9826 (tt) cc_final: 0.9408 (tp) REVERT: L 55 PHE cc_start: 0.9427 (m-80) cc_final: 0.9034 (m-80) REVERT: L 57 GLU cc_start: 0.9456 (mm-30) cc_final: 0.8978 (mt-10) REVERT: M 68 PHE cc_start: 0.9462 (t80) cc_final: 0.9234 (t80) REVERT: N 11 LEU cc_start: 0.9830 (mm) cc_final: 0.9616 (mm) REVERT: N 55 PHE cc_start: 0.9627 (m-80) cc_final: 0.9206 (m-80) REVERT: O 11 LEU cc_start: 0.9564 (mt) cc_final: 0.9332 (mt) REVERT: O 15 LEU cc_start: 0.9739 (mp) cc_final: 0.9351 (tp) REVERT: O 29 SER cc_start: 0.9481 (t) cc_final: 0.9250 (p) REVERT: O 32 VAL cc_start: 0.9619 (p) cc_final: 0.9226 (m) REVERT: O 33 GLN cc_start: 0.9370 (mt0) cc_final: 0.9106 (mm110) REVERT: O 57 GLU cc_start: 0.9322 (mm-30) cc_final: 0.8850 (pt0) REVERT: O 62 PHE cc_start: 0.9174 (m-80) cc_final: 0.8809 (m-80) REVERT: O 64 LEU cc_start: 0.9709 (tt) cc_final: 0.9387 (mt) REVERT: P 49 MET cc_start: 0.9318 (ttp) cc_final: 0.8986 (tmm) REVERT: P 68 PHE cc_start: 0.9203 (m-80) cc_final: 0.8819 (m-80) REVERT: Q 18 ILE cc_start: 0.9480 (pt) cc_final: 0.9087 (mm) REVERT: Q 27 ILE cc_start: 0.9424 (mt) cc_final: 0.9215 (mt) REVERT: Q 33 GLN cc_start: 0.9145 (mm110) cc_final: 0.8910 (mm-40) REVERT: Q 50 PHE cc_start: 0.9637 (m-80) cc_final: 0.9182 (m-80) REVERT: Q 55 PHE cc_start: 0.9576 (m-10) cc_final: 0.9359 (m-80) REVERT: Q 62 PHE cc_start: 0.9709 (m-80) cc_final: 0.9341 (m-80) REVERT: Z 80 LEU cc_start: 0.9170 (mm) cc_final: 0.8702 (tt) REVERT: Z 84 MET cc_start: 0.9163 (mmp) cc_final: 0.8874 (mmm) REVERT: Z 95 PHE cc_start: 0.9524 (m-10) cc_final: 0.9117 (m-80) REVERT: Z 114 PHE cc_start: 0.9352 (t80) cc_final: 0.9131 (t80) REVERT: Z 123 PHE cc_start: 0.9522 (t80) cc_final: 0.9206 (t80) REVERT: Z 207 TYR cc_start: 0.8014 (t80) cc_final: 0.7584 (t80) REVERT: Z 228 MET cc_start: 0.9186 (ptt) cc_final: 0.8960 (ptt) REVERT: Z 248 PHE cc_start: 0.9596 (m-10) cc_final: 0.9139 (m-80) REVERT: Z 249 ARG cc_start: 0.9645 (ttm110) cc_final: 0.9228 (mtp85) REVERT: Z 264 MET cc_start: 0.9196 (ttm) cc_final: 0.8920 (ttm) REVERT: Z 280 GLU cc_start: 0.9428 (mm-30) cc_final: 0.9159 (mm-30) REVERT: Z 282 PHE cc_start: 0.9532 (t80) cc_final: 0.9122 (t80) REVERT: Z 287 GLN cc_start: 0.9588 (mm110) cc_final: 0.9060 (mm110) outliers start: 0 outliers final: 0 residues processed: 336 average time/residue: 0.1514 time to fit residues: 75.6668 Evaluate side-chains 286 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 286 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: 0.4980 chunk 117 optimal weight: 50.0000 chunk 94 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 chunk 52 optimal weight: 0.0970 chunk 118 optimal weight: 40.0000 chunk 35 optimal weight: 0.4980 chunk 82 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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** ** P 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 = 0.3549 r_free = 0.3549 target = 0.069265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.054045 restraints weight = 52630.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.055113 restraints weight = 42155.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.055896 restraints weight = 35219.342| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.5135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 9204 Z= 0.155 Angle : 0.669 15.026 12570 Z= 0.353 Chirality : 0.046 0.230 1596 Planarity : 0.005 0.072 1626 Dihedral : 3.849 22.096 1394 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.65 (0.15), residues: 1109 sheet: None (None), residues: 0 loop : -1.75 (0.41), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Z 208 HIS 0.001 0.001 HIS Z 170 PHE 0.029 0.001 PHE L 62 TYR 0.014 0.002 TYR H 48 ARG 0.005 0.000 ARG I 37 Details of bonding type rmsd hydrogen bonds : bond 0.04116 ( 899) hydrogen bonds : angle 3.95564 ( 2676) covalent geometry : bond 0.00369 ( 9204) covalent geometry : angle 0.66877 (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 340 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 340 time to evaluate : 1.069 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: H 38 ASN cc_start: 0.9283 (t0) cc_final: 0.9002 (t0) REVERT: H 49 MET cc_start: 0.9630 (ttp) cc_final: 0.9375 (tmm) REVERT: H 50 PHE cc_start: 0.9548 (m-80) cc_final: 0.9193 (m-80) REVERT: H 57 GLU cc_start: 0.9804 (tp30) cc_final: 0.9598 (tp30) REVERT: H 68 PHE cc_start: 0.9381 (m-10) cc_final: 0.9137 (m-80) REVERT: I 55 PHE cc_start: 0.9306 (m-80) cc_final: 0.9031 (m-10) REVERT: I 68 PHE cc_start: 0.9427 (m-80) cc_final: 0.8957 (m-80) REVERT: J 1 MET cc_start: 0.9157 (mmm) cc_final: 0.8877 (tpp) REVERT: J 15 LEU cc_start: 0.9586 (mp) cc_final: 0.9184 (tp) REVERT: J 48 TYR cc_start: 0.9394 (m-80) cc_final: 0.8784 (m-80) REVERT: J 49 MET cc_start: 0.9650 (tmm) cc_final: 0.9270 (tmm) REVERT: J 64 LEU cc_start: 0.9626 (mt) cc_final: 0.9292 (pp) REVERT: K 18 ILE cc_start: 0.9347 (pt) cc_final: 0.8819 (tp) REVERT: K 44 ARG cc_start: 0.9472 (tpp80) cc_final: 0.8679 (tpp80) REVERT: K 48 TYR cc_start: 0.9495 (m-80) cc_final: 0.8744 (m-80) REVERT: K 55 PHE cc_start: 0.9527 (m-80) cc_final: 0.9293 (m-80) REVERT: K 66 ILE cc_start: 0.9654 (mm) cc_final: 0.9444 (tp) REVERT: K 68 PHE cc_start: 0.9446 (m-10) cc_final: 0.9135 (m-80) REVERT: L 1 MET cc_start: 0.9035 (mtp) cc_final: 0.8620 (mtt) REVERT: L 43 ASN cc_start: 0.9315 (p0) cc_final: 0.9110 (m-40) REVERT: L 50 PHE cc_start: 0.9621 (m-80) cc_final: 0.9309 (m-10) REVERT: L 53 ILE cc_start: 0.9837 (tt) cc_final: 0.9389 (tp) REVERT: L 57 GLU cc_start: 0.9463 (mm-30) cc_final: 0.8966 (mt-10) REVERT: M 68 PHE cc_start: 0.9454 (t80) cc_final: 0.9227 (t80) REVERT: N 11 LEU cc_start: 0.9826 (mm) cc_final: 0.9610 (mm) REVERT: N 33 GLN cc_start: 0.9368 (mp10) cc_final: 0.9109 (mp10) REVERT: N 55 PHE cc_start: 0.9606 (m-80) cc_final: 0.9169 (m-80) REVERT: N 64 LEU cc_start: 0.9612 (mt) cc_final: 0.8884 (mt) REVERT: O 11 LEU cc_start: 0.9554 (mt) cc_final: 0.9315 (mt) REVERT: O 15 LEU cc_start: 0.9749 (mp) cc_final: 0.9398 (tp) REVERT: O 24 ILE cc_start: 0.9464 (pt) cc_final: 0.9225 (pt) REVERT: O 32 VAL cc_start: 0.9636 (p) cc_final: 0.9247 (m) REVERT: O 33 GLN cc_start: 0.9370 (mt0) cc_final: 0.9103 (mm110) REVERT: O 57 GLU cc_start: 0.9344 (mm-30) cc_final: 0.8905 (pt0) REVERT: O 62 PHE cc_start: 0.9141 (m-80) cc_final: 0.8773 (m-80) REVERT: O 64 LEU cc_start: 0.9733 (tt) cc_final: 0.9478 (mt) REVERT: P 49 MET cc_start: 0.9411 (ttp) cc_final: 0.9000 (tmm) REVERT: P 68 PHE cc_start: 0.9285 (m-80) cc_final: 0.8870 (m-80) REVERT: Q 18 ILE cc_start: 0.9410 (pt) cc_final: 0.8951 (mm) REVERT: Q 20 PRO cc_start: 0.9427 (Cg_exo) cc_final: 0.9215 (Cg_endo) REVERT: Q 27 ILE cc_start: 0.9354 (mt) cc_final: 0.9135 (mt) REVERT: Q 33 GLN cc_start: 0.9156 (mm110) cc_final: 0.8910 (mm-40) REVERT: Q 50 PHE cc_start: 0.9655 (m-80) cc_final: 0.9209 (m-80) REVERT: Q 55 PHE cc_start: 0.9593 (m-10) cc_final: 0.9368 (m-80) REVERT: Q 62 PHE cc_start: 0.9724 (m-80) cc_final: 0.9446 (m-80) REVERT: Z 80 LEU cc_start: 0.9230 (mm) cc_final: 0.8749 (tt) REVERT: Z 84 MET cc_start: 0.9224 (mmp) cc_final: 0.8951 (mmm) REVERT: Z 95 PHE cc_start: 0.9475 (m-10) cc_final: 0.9066 (m-80) REVERT: Z 114 PHE cc_start: 0.9337 (t80) cc_final: 0.9113 (t80) REVERT: Z 123 PHE cc_start: 0.9535 (t80) cc_final: 0.9215 (t80) REVERT: Z 207 TYR cc_start: 0.8030 (t80) cc_final: 0.7668 (t80) REVERT: Z 228 MET cc_start: 0.9207 (ptt) cc_final: 0.8985 (ptt) REVERT: Z 248 PHE cc_start: 0.9543 (m-10) cc_final: 0.9201 (m-80) REVERT: Z 264 MET cc_start: 0.9269 (ttm) cc_final: 0.8946 (tpt) REVERT: Z 280 GLU cc_start: 0.9408 (mm-30) cc_final: 0.9114 (mm-30) REVERT: Z 282 PHE cc_start: 0.9559 (t80) cc_final: 0.9122 (t80) REVERT: Z 287 GLN cc_start: 0.9590 (mm110) cc_final: 0.9200 (mm-40) outliers start: 0 outliers final: 0 residues processed: 340 average time/residue: 0.1626 time to fit residues: 81.7811 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 : 1.095 ------------------------------------------------------------------------------- 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: 6.9990 chunk 34 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 117 optimal weight: 50.0000 chunk 128 optimal weight: 5.9990 chunk 38 optimal weight: 0.3980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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** P 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 = 0.3538 r_free = 0.3538 target = 0.068749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.053758 restraints weight = 53546.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.054718 restraints weight = 42640.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.055552 restraints weight = 35771.976| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.5371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 9204 Z= 0.167 Angle : 0.659 8.844 12570 Z= 0.353 Chirality : 0.046 0.220 1596 Planarity : 0.005 0.072 1626 Dihedral : 3.864 21.153 1394 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 17.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % 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: 1.61 (0.15), residues: 1109 sheet: None (None), residues: 0 loop : -1.69 (0.41), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP Z 122 HIS 0.002 0.001 HIS Z 170 PHE 0.051 0.002 PHE H 62 TYR 0.014 0.002 TYR H 48 ARG 0.009 0.001 ARG Z 249 Details of bonding type rmsd hydrogen bonds : bond 0.04129 ( 899) hydrogen bonds : angle 3.93303 ( 2676) covalent geometry : bond 0.00401 ( 9204) covalent geometry : angle 0.65934 (12570) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3198.74 seconds wall clock time: 56 minutes 27.94 seconds (3387.94 seconds total)