Starting phenix.real_space_refine on Fri Aug 22 21:08:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9itz_60884/08_2025/9itz_60884.cif Found real_map, /net/cci-nas-00/data/ceres_data/9itz_60884/08_2025/9itz_60884.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9itz_60884/08_2025/9itz_60884.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9itz_60884/08_2025/9itz_60884.map" model { file = "/net/cci-nas-00/data/ceres_data/9itz_60884/08_2025/9itz_60884.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9itz_60884/08_2025/9itz_60884.cif" } resolution = 4.28 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 10 5.16 5 C 5129 2.51 5 N 1416 2.21 5 O 1484 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8039 Number of models: 1 Model: "" Number of chains: 16 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: 141 Unresolved non-hydrogen angles: 181 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'PHE:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 3, 'ARG:plan': 5, 'TYR:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 75 Chain: "X" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 125 Classifications: {'peptide': 25} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 1, 'TRANS': 23} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASN:plan1': 3, 'PHE:plan': 2, 'ARG:plan': 3, 'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 47 Chain: "T" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1093 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 181} Link IDs: {'PTRANS': 10, 'TRANS': 211} Chain breaks: 1 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 700 Unresolved non-hydrogen angles: 918 Unresolved non-hydrogen dihedrals: 588 Unresolved non-hydrogen chiralities: 84 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 9, 'PHE:plan': 31, 'ASP:plan': 3, 'ASN:plan1': 12, 'ARG:plan': 5, 'GLN:plan1': 3, 'TYR:plan': 6, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 369 Chain: "H" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 480 Classifications: {'peptide': 71} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 68} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "I" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 505 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "J" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 505 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "K" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 505 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "L" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 505 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "M" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 505 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "N" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 505 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "O" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 505 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "P" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 505 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "Q" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 505 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} 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: 143 Unresolved non-hydrogen angles: 184 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ASN:plan1': 4, 'PHE:plan': 3, 'GLN:plan1': 1, 'ARG:plan': 5, 'TYR:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 74 Chain: "Y" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 205 Classifications: {'peptide': 41} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 1, 'TRANS': 39} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 189 Unresolved non-hydrogen dihedrals: 116 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'PHE:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 3, 'ARG:plan': 5, 'TYR:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 75 Chain: "Z" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1206 Classifications: {'peptide': 245} Incomplete info: {'truncation_to_alanine': 199} Link IDs: {'PTRANS': 14, 'TRANS': 230} Chain breaks: 1 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 773 Unresolved non-hydrogen angles: 1011 Unresolved non-hydrogen dihedrals: 654 Unresolved non-hydrogen chiralities: 89 Planarities with less than four sites: {'PHE:plan': 34, 'TYR:plan': 7, 'HIS:plan': 1, 'GLU:plan': 9, 'ASP:plan': 3, 'ASN:plan1': 12, 'ARG:plan': 6, 'GLN:plan1': 4, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 403 Time building chain proxies: 1.84, per 1000 atoms: 0.23 Number of scatterers: 8039 At special positions: 0 Unit cell: (79.98, 120.9, 79.98, 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 10 16.00 O 1484 8.00 N 1416 7.00 C 5129 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.48 Conformation dependent library (CDL) restraints added in 499.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2328 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 0 sheets defined 85.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'U' and resid 9 through 30 removed outlier: 3.872A pdb=" N ALA U 13 " --> pdb=" O THR U 9 " (cutoff:3.500A) Processing helix chain 'U' and resid 31 through 44 removed outlier: 4.129A pdb=" N ILE U 44 " --> pdb=" O ARG U 40 " (cutoff:3.500A) Processing helix chain 'X' and resid 18 through 41 Proline residue: X 32 - end of helix Processing helix chain 'T' and resid 49 through 71 removed outlier: 3.671A pdb=" N ARG T 71 " --> pdb=" O VAL T 67 " (cutoff:3.500A) Processing helix chain 'T' and resid 81 through 87 Processing helix chain 'T' and resid 87 through 100 Processing helix chain 'T' and resid 101 through 106 Processing helix chain 'T' and resid 106 through 114 removed outlier: 3.506A pdb=" N VAL T 110 " --> pdb=" O ALA T 106 " (cutoff:3.500A) Processing helix chain 'T' and resid 117 through 125 Processing helix chain 'T' and resid 190 through 207 removed outlier: 3.552A pdb=" N ILE T 205 " --> pdb=" O SER T 201 " (cutoff:3.500A) Processing helix chain 'T' and resid 214 through 219 removed outlier: 4.400A pdb=" N TYR T 217 " --> pdb=" O GLY T 214 " (cutoff:3.500A) Processing helix chain 'T' and resid 225 through 230 removed outlier: 4.445A pdb=" N PHE T 230 " --> pdb=" O ILE T 227 " (cutoff:3.500A) Processing helix chain 'T' and resid 231 through 252 Proline residue: T 243 - end of helix Processing helix chain 'T' and resid 253 through 267 Processing helix chain 'T' and resid 275 through 304 Processing helix chain 'H' and resid 3 through 38 removed outlier: 3.503A pdb=" N VAL H 7 " --> pdb=" O GLY H 3 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N GLY H 19 " --> pdb=" O LEU H 15 " (cutoff:3.500A) Proline residue: H 20 - end of helix removed outlier: 4.110A pdb=" N ILE H 26 " --> pdb=" O VAL H 22 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA H 31 " --> pdb=" O ILE H 27 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 72 removed outlier: 3.706A pdb=" N ILE H 51 " --> pdb=" O THR H 47 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLY H 52 " --> pdb=" O TYR H 48 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR H 56 " --> pdb=" O GLY H 52 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU H 59 " --> pdb=" O PHE H 55 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ALA H 67 " --> pdb=" O GLY H 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 36 removed outlier: 4.403A pdb=" N GLY I 19 " --> pdb=" O LEU I 15 " (cutoff:3.500A) Proline residue: I 20 - end of helix removed outlier: 4.212A pdb=" N GLY I 25 " --> pdb=" O GLY I 21 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE I 26 " --> pdb=" O VAL I 22 " (cutoff:3.500A) Processing helix chain 'I' and resid 38 through 40 No H-bonds generated for 'chain 'I' and resid 38 through 40' Processing helix chain 'I' and resid 41 through 72 Processing helix chain 'J' and resid 3 through 38 Proline residue: J 20 - end of helix removed outlier: 4.390A pdb=" N GLY J 23 " --> pdb=" O GLY J 19 " (cutoff:3.500A) Processing helix chain 'J' and resid 41 through 72 removed outlier: 3.625A pdb=" N PHE J 50 " --> pdb=" O VAL J 46 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ILE J 51 " --> pdb=" O THR J 47 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLY J 52 " --> pdb=" O TYR J 48 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR J 56 " --> pdb=" O GLY J 52 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA J 67 " --> pdb=" O GLY J 63 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 17 Processing helix chain 'K' and resid 18 through 38 Processing helix chain 'K' and resid 42 through 72 removed outlier: 3.930A pdb=" N TYR K 48 " --> pdb=" O ARG K 44 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU K 59 " --> pdb=" O PHE K 55 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 38 removed outlier: 4.110A pdb=" N VAL L 7 " --> pdb=" O GLY L 3 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N GLY L 19 " --> pdb=" O LEU L 15 " (cutoff:3.500A) Proline residue: L 20 - end of helix Processing helix chain 'L' and resid 41 through 72 removed outlier: 4.090A pdb=" N THR L 47 " --> pdb=" O ASN L 43 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR L 56 " --> pdb=" O GLY L 52 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU L 57 " --> pdb=" O ILE L 53 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA L 58 " --> pdb=" O ALA L 54 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY L 71 " --> pdb=" O ALA L 67 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 38 removed outlier: 3.903A pdb=" N GLY M 19 " --> pdb=" O LEU M 15 " (cutoff:3.500A) Proline residue: M 20 - end of helix removed outlier: 4.023A pdb=" N GLY M 25 " --> pdb=" O GLY M 21 " (cutoff:3.500A) Processing helix chain 'M' and resid 41 through 72 removed outlier: 4.254A pdb=" N ILE M 66 " --> pdb=" O PHE M 62 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ALA M 67 " --> pdb=" O GLY M 63 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE M 68 " --> pdb=" O LEU M 64 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY M 71 " --> pdb=" O ALA M 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 15 Processing helix chain 'N' and resid 17 through 38 removed outlier: 3.755A pdb=" N VAL N 28 " --> pdb=" O ILE N 24 " (cutoff:3.500A) Processing helix chain 'N' and resid 41 through 70 removed outlier: 3.613A pdb=" N VAL N 46 " --> pdb=" O GLU N 42 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLY N 52 " --> pdb=" O TYR N 48 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ALA N 58 " --> pdb=" O ALA N 54 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE N 66 " --> pdb=" O PHE N 62 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 17 Processing helix chain 'O' and resid 19 through 38 Processing helix chain 'O' and resid 43 through 71 removed outlier: 4.361A pdb=" N LEU O 59 " --> pdb=" O PHE O 55 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ALA O 60 " --> pdb=" O THR O 56 " (cutoff:3.500A) Processing helix chain 'P' and resid 3 through 15 Processing helix chain 'P' and resid 17 through 38 removed outlier: 3.860A pdb=" N GLY P 25 " --> pdb=" O GLY P 21 " (cutoff:3.500A) Processing helix chain 'P' and resid 41 through 72 removed outlier: 3.821A pdb=" N PHE P 50 " --> pdb=" O VAL P 46 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE P 51 " --> pdb=" O THR P 47 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE P 62 " --> pdb=" O ALA P 58 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE P 66 " --> pdb=" O PHE P 62 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA P 67 " --> pdb=" O GLY P 63 " (cutoff:3.500A) Processing helix chain 'Q' and resid 3 through 38 removed outlier: 4.612A pdb=" N GLY Q 19 " --> pdb=" O LEU Q 15 " (cutoff:3.500A) Proline residue: Q 20 - end of helix removed outlier: 3.534A pdb=" N ASN Q 38 " --> pdb=" O ALA Q 34 " (cutoff:3.500A) Processing helix chain 'Q' and resid 41 through 71 removed outlier: 3.771A pdb=" N LEU Q 59 " --> pdb=" O PHE Q 55 " (cutoff:3.500A) Processing helix chain 'V' and resid 8 through 28 Processing helix chain 'V' and resid 30 through 44 Processing helix chain 'Y' and resid 9 through 48 removed outlier: 3.721A pdb=" N LEU Y 28 " --> pdb=" O ILE Y 24 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N ARG Y 31 " --> pdb=" O ALA Y 27 " (cutoff:3.500A) Proline residue: Y 32 - end of helix Processing helix chain 'Z' and resid 49 through 71 Processing helix chain 'Z' and resid 80 through 99 removed outlier: 3.535A pdb=" N MET Z 84 " --> pdb=" O LEU Z 80 " (cutoff:3.500A) Processing helix chain 'Z' and resid 105 through 114 removed outlier: 4.569A pdb=" N LEU Z 109 " --> pdb=" O THR Z 105 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE Z 113 " --> pdb=" O LEU Z 109 " (cutoff:3.500A) Processing helix chain 'Z' and resid 116 through 122 Processing helix chain 'Z' and resid 190 through 219 removed outlier: 3.548A pdb=" N THR Z 194 " --> pdb=" O ASP Z 190 " (cutoff:3.500A) Proline residue: Z 215 - end of helix Processing helix chain 'Z' and resid 234 through 264 Proline residue: Z 243 - end of helix removed outlier: 3.660A pdb=" N LEU Z 250 " --> pdb=" O LEU Z 246 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ILE Z 254 " --> pdb=" O LEU Z 250 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N PHE Z 255 " --> pdb=" O PHE Z 251 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N GLY Z 257 " --> pdb=" O ASN Z 253 " (cutoff:3.500A) Processing helix chain 'Z' and resid 272 through 304 removed outlier: 3.520A pdb=" N PHE Z 276 " --> pdb=" O LEU Z 272 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR Z 296 " --> pdb=" O ALA Z 292 " (cutoff:3.500A) 827 hydrogen bonds defined for protein. 2469 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.25 Time building geometry restraints manager: 0.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1677 1.33 - 1.45: 1610 1.45 - 1.57: 4794 1.57 - 1.69: 0 1.69 - 1.80: 20 Bond restraints: 8101 Sorted by residual: bond pdb=" N ILE Q 41 " pdb=" CA ILE Q 41 " ideal model delta sigma weight residual 1.455 1.494 -0.039 1.04e-02 9.25e+03 1.42e+01 bond pdb=" N VAL Z 38 " pdb=" CA VAL Z 38 " ideal model delta sigma weight residual 1.458 1.494 -0.037 1.18e-02 7.18e+03 9.68e+00 bond pdb=" N VAL O 22 " pdb=" CA VAL O 22 " ideal model delta sigma weight residual 1.459 1.497 -0.037 1.21e-02 6.83e+03 9.43e+00 bond pdb=" N ILE Z 48 " pdb=" CA ILE Z 48 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.17e-02 7.31e+03 9.01e+00 bond pdb=" N ILE O 18 " pdb=" CA ILE O 18 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.69e+00 ... (remaining 8096 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 10246 1.52 - 3.03: 735 3.03 - 4.55: 91 4.55 - 6.06: 21 6.06 - 7.58: 9 Bond angle restraints: 11102 Sorted by residual: angle pdb=" N ILE M 41 " pdb=" CA ILE M 41 " pdb=" C ILE M 41 " ideal model delta sigma weight residual 111.91 105.39 6.52 8.90e-01 1.26e+00 5.36e+01 angle pdb=" N ILE Q 41 " pdb=" CA ILE Q 41 " pdb=" C ILE Q 41 " ideal model delta sigma weight residual 112.43 106.02 6.41 9.20e-01 1.18e+00 4.86e+01 angle pdb=" N VAL Z 231 " pdb=" CA VAL Z 231 " pdb=" C VAL Z 231 " ideal model delta sigma weight residual 113.00 105.42 7.58 1.30e+00 5.92e-01 3.40e+01 angle pdb=" N ILE N 41 " pdb=" CA ILE N 41 " pdb=" C ILE N 41 " ideal model delta sigma weight residual 111.91 106.86 5.05 8.90e-01 1.26e+00 3.21e+01 angle pdb=" C GLU H 42 " pdb=" CA GLU H 42 " pdb=" CB GLU H 42 " ideal model delta sigma weight residual 116.54 110.66 5.88 1.15e+00 7.56e-01 2.61e+01 ... (remaining 11097 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 4403 17.60 - 35.20: 190 35.20 - 52.79: 24 52.79 - 70.39: 2 70.39 - 87.99: 3 Dihedral angle restraints: 4622 sinusoidal: 982 harmonic: 3640 Sorted by residual: dihedral pdb=" CA MET H 49 " pdb=" C MET H 49 " pdb=" N PHE H 50 " pdb=" CA PHE H 50 " ideal model delta harmonic sigma weight residual -180.00 -161.61 -18.39 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA LEU L 15 " pdb=" C LEU L 15 " pdb=" N GLY L 16 " pdb=" CA GLY L 16 " ideal model delta harmonic sigma weight residual 180.00 161.63 18.37 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA LEU H 64 " pdb=" C LEU H 64 " pdb=" N VAL H 65 " pdb=" CA VAL H 65 " ideal model delta harmonic sigma weight residual 180.00 -163.61 -16.39 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 4619 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1017 0.052 - 0.104: 319 0.104 - 0.156: 72 0.156 - 0.209: 41 0.209 - 0.261: 2 Chirality restraints: 1451 Sorted by residual: chirality pdb=" CB ILE P 18 " pdb=" CA ILE P 18 " pdb=" CG1 ILE P 18 " pdb=" CG2 ILE P 18 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CB ILE H 18 " pdb=" CA ILE H 18 " pdb=" CG1 ILE H 18 " pdb=" CG2 ILE H 18 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA ILE Q 41 " pdb=" N ILE Q 41 " pdb=" C ILE Q 41 " pdb=" CB ILE Q 41 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 1448 not shown) Planarity restraints: 1478 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN Q 38 " -0.037 5.00e-02 4.00e+02 5.62e-02 5.06e+00 pdb=" N PRO Q 39 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO Q 39 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO Q 39 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE N 53 " -0.010 2.00e-02 2.50e+03 1.97e-02 3.87e+00 pdb=" C ILE N 53 " 0.034 2.00e-02 2.50e+03 pdb=" O ILE N 53 " -0.013 2.00e-02 2.50e+03 pdb=" N ALA N 54 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY Q 19 " 0.030 5.00e-02 4.00e+02 4.50e-02 3.24e+00 pdb=" N PRO Q 20 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO Q 20 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO Q 20 " 0.025 5.00e-02 4.00e+02 ... (remaining 1475 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 829 2.74 - 3.28: 9778 3.28 - 3.82: 14154 3.82 - 4.36: 15235 4.36 - 4.90: 24544 Nonbonded interactions: 64540 Sorted by model distance: nonbonded pdb=" O LEU N 6 " pdb=" OG1 THR N 9 " model vdw 2.204 3.040 nonbonded pdb=" O ILE I 53 " pdb=" OG1 THR I 56 " model vdw 2.204 3.040 nonbonded pdb=" O ARG P 44 " pdb=" OG1 THR P 47 " model vdw 2.240 3.040 nonbonded pdb=" O ARG J 44 " pdb=" OG1 THR J 47 " model vdw 2.294 3.040 nonbonded pdb=" O LEU X 29 " pdb=" N VAL X 33 " model vdw 2.311 3.120 ... (remaining 64535 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'H' selection = (chain 'I' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB )) or resid 16 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 or (resid 42 through 44 and (n \ ame N or name CA or name C or name O or name CB )) or resid 45 through 46 or (re \ sid 47 and (name N or name CA or name C or name O or name CB )) or resid 48 thro \ ugh 63 or (resid 64 and (name N or name CA or name C or name O or name CB )) or \ resid 65 through 72)) selection = (chain 'J' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB )) or resid 16 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 or (resid 42 through 44 and (n \ ame N or name CA or name C or name O or name CB )) or resid 45 through 46 or (re \ sid 47 and (name N or name CA or name C or name O or name CB )) or resid 48 thro \ ugh 63 or (resid 64 and (name N or name CA or name C or name O or name CB )) or \ resid 65 through 72)) selection = (chain 'K' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB )) or resid 16 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 or (resid 42 through 44 and (n \ ame N or name CA or name C or name O or name CB )) or resid 45 through 46 or (re \ sid 47 and (name N or name CA or name C or name O or name CB )) or resid 48 thro \ ugh 63 or (resid 64 and (name N or name CA or name C or name O or name CB )) or \ resid 65 through 72)) selection = (chain 'L' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB )) or resid 16 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 or (resid 42 through 44 and (n \ ame N or name CA or name C or name O or name CB )) or resid 45 through 46 or (re \ sid 47 and (name N or name CA or name C or name O or name CB )) or resid 48 thro \ ugh 63 or (resid 64 and (name N or name CA or name C or name O or name CB )) or \ resid 65 through 72)) selection = (chain 'M' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB )) or resid 16 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 or (resid 42 through 44 and (n \ ame N or name CA or name C or name O or name CB )) or resid 45 through 46 or (re \ sid 47 and (name N or name CA or name C or name O or name CB )) or resid 48 thro \ ugh 63 or (resid 64 and (name N or name CA or name C or name O or name CB )) or \ resid 65 through 72)) selection = (chain 'N' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB )) or resid 16 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 or (resid 42 through 44 and (n \ ame N or name CA or name C or name O or name CB )) or resid 45 through 46 or (re \ sid 47 and (name N or name CA or name C or name O or name CB )) or resid 48 thro \ ugh 63 or (resid 64 and (name N or name CA or name C or name O or name CB )) or \ resid 65 through 72)) selection = (chain 'O' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB )) or resid 16 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 or (resid 42 through 44 and (n \ ame N or name CA or name C or name O or name CB )) or resid 45 through 46 or (re \ sid 47 and (name N or name CA or name C or name O or name CB )) or resid 48 thro \ ugh 63 or (resid 64 and (name N or name CA or name C or name O or name CB )) or \ resid 65 through 72)) selection = (chain 'P' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB )) or resid 16 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 or (resid 42 through 44 and (n \ ame N or name CA or name C or name O or name CB )) or resid 45 through 46 or (re \ sid 47 and (name N or name CA or name C or name O or name CB )) or resid 48 thro \ ugh 63 or (resid 64 and (name N or name CA or name C or name O or name CB )) or \ resid 65 through 72)) selection = (chain 'Q' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB )) or resid 16 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 or (resid 42 through 44 and (n \ ame N or name CA or name C or name O or name CB )) or resid 45 through 46 or (re \ sid 47 and (name N or name CA or name C or name O or name CB )) or resid 48 thro \ ugh 63 or (resid 64 and (name N or name CA or name C or name O or name CB )) or \ resid 65 through 72)) } ncs_group { reference = chain 'T' selection = (chain 'Z' and (resid 31 through 135 or resid 188 through 304)) } ncs_group { reference = (chain 'U' and resid 9 through 45) selection = (chain 'V' and resid 9 through 45) selection = (chain 'Y' and resid 9 through 45) } 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: 6.760 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.040 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 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 : 0.006 0.045 8101 Z= 0.422 Angle : 0.834 7.576 11102 Z= 0.608 Chirality : 0.058 0.261 1451 Planarity : 0.004 0.056 1478 Dihedral : 10.759 87.988 2294 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.37 % Favored : 94.55 % Rotamer: Outliers : 0.21 % Allowed : 1.24 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.23), residues: 1284 helix: 0.85 (0.16), residues: 1033 sheet: None (None), residues: 0 loop : -2.92 (0.35), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG N 44 TYR 0.006 0.001 TYR M 48 PHE 0.014 0.001 PHE Q 62 TRP 0.000 0.000 TRP T 122 Details of bonding type rmsd covalent geometry : bond 0.00578 ( 8101) covalent geometry : angle 0.83440 (11102) hydrogen bonds : bond 0.16026 ( 827) hydrogen bonds : angle 6.12756 ( 2469) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 337 time to evaluate : 0.285 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: H 29 SER cc_start: 0.9570 (t) cc_final: 0.9140 (p) REVERT: H 50 PHE cc_start: 0.9038 (m-80) cc_final: 0.8739 (t80) REVERT: I 33 GLN cc_start: 0.9240 (mm-40) cc_final: 0.8863 (mm-40) REVERT: I 49 MET cc_start: 0.9764 (ptm) cc_final: 0.9504 (ptt) REVERT: I 50 PHE cc_start: 0.9212 (m-10) cc_final: 0.8894 (m-10) REVERT: I 55 PHE cc_start: 0.9652 (m-80) cc_final: 0.9371 (m-80) REVERT: I 68 PHE cc_start: 0.9561 (m-10) cc_final: 0.8961 (m-80) REVERT: J 11 LEU cc_start: 0.9771 (tt) cc_final: 0.9465 (tt) REVERT: J 27 ILE cc_start: 0.9614 (mm) cc_final: 0.9281 (mm) REVERT: J 48 TYR cc_start: 0.9202 (m-80) cc_final: 0.8644 (m-80) REVERT: J 49 MET cc_start: 0.9896 (ppp) cc_final: 0.9690 (ppp) REVERT: J 50 PHE cc_start: 0.9681 (m-80) cc_final: 0.9183 (m-80) REVERT: J 51 ILE cc_start: 0.9439 (pt) cc_final: 0.9031 (pt) REVERT: J 55 PHE cc_start: 0.9516 (m-10) cc_final: 0.9041 (m-80) REVERT: J 57 GLU cc_start: 0.9434 (mt-10) cc_final: 0.8779 (tm-30) REVERT: J 61 ILE cc_start: 0.9124 (mm) cc_final: 0.8923 (mm) REVERT: J 64 LEU cc_start: 0.9732 (tt) cc_final: 0.9385 (pp) REVERT: J 68 PHE cc_start: 0.9531 (m-80) cc_final: 0.9298 (m-80) REVERT: K 44 ARG cc_start: 0.9388 (mmm-85) cc_final: 0.8954 (mmm160) REVERT: K 45 VAL cc_start: 0.9376 (p) cc_final: 0.8928 (p) REVERT: K 48 TYR cc_start: 0.9073 (m-80) cc_final: 0.8461 (m-80) REVERT: K 51 ILE cc_start: 0.9395 (pt) cc_final: 0.8960 (pt) REVERT: K 55 PHE cc_start: 0.9427 (m-10) cc_final: 0.9126 (m-80) REVERT: L 18 ILE cc_start: 0.9521 (tt) cc_final: 0.9134 (pt) REVERT: L 45 VAL cc_start: 0.9475 (p) cc_final: 0.8993 (p) REVERT: L 48 TYR cc_start: 0.9327 (m-80) cc_final: 0.9043 (m-80) REVERT: L 50 PHE cc_start: 0.9132 (m-10) cc_final: 0.8648 (t80) REVERT: M 48 TYR cc_start: 0.9226 (m-80) cc_final: 0.9016 (m-80) REVERT: N 26 ILE cc_start: 0.9720 (mm) cc_final: 0.9302 (tt) REVERT: N 33 GLN cc_start: 0.9257 (mm-40) cc_final: 0.9000 (mm110) REVERT: N 40 GLU cc_start: 0.9602 (mm-30) cc_final: 0.9296 (mp0) REVERT: N 48 TYR cc_start: 0.9257 (m-10) cc_final: 0.8775 (m-80) REVERT: N 51 ILE cc_start: 0.9777 (tp) cc_final: 0.9510 (tp) REVERT: N 55 PHE cc_start: 0.9442 (m-80) cc_final: 0.8918 (m-80) REVERT: N 62 PHE cc_start: 0.9616 (m-10) cc_final: 0.9276 (m-80) REVERT: N 68 PHE cc_start: 0.9702 (m-10) cc_final: 0.9315 (m-80) REVERT: O 15 LEU cc_start: 0.9307 (mm) cc_final: 0.9047 (mm) REVERT: O 18 ILE cc_start: 0.7399 (OUTLIER) cc_final: 0.7192 (tp) REVERT: O 26 ILE cc_start: 0.9626 (mm) cc_final: 0.9391 (mm) REVERT: O 27 ILE cc_start: 0.9683 (mt) cc_final: 0.9300 (mt) REVERT: O 29 SER cc_start: 0.9556 (t) cc_final: 0.9175 (p) REVERT: O 62 PHE cc_start: 0.9250 (m-80) cc_final: 0.8973 (m-80) REVERT: P 15 LEU cc_start: 0.9580 (mm) cc_final: 0.8803 (tp) REVERT: P 26 ILE cc_start: 0.9785 (mm) cc_final: 0.9456 (tp) REVERT: P 27 ILE cc_start: 0.8994 (mt) cc_final: 0.8640 (mt) REVERT: P 50 PHE cc_start: 0.8956 (m-80) cc_final: 0.7833 (t80) REVERT: P 51 ILE cc_start: 0.9112 (pt) cc_final: 0.8765 (pt) REVERT: P 59 LEU cc_start: 0.9338 (tp) cc_final: 0.9128 (tp) REVERT: P 62 PHE cc_start: 0.9458 (m-10) cc_final: 0.9215 (m-80) REVERT: Q 11 LEU cc_start: 0.9657 (mt) cc_final: 0.9445 (mt) REVERT: Q 51 ILE cc_start: 0.9474 (mt) cc_final: 0.9113 (mt) REVERT: Q 53 ILE cc_start: 0.9232 (pt) cc_final: 0.9001 (pt) REVERT: Q 55 PHE cc_start: 0.9176 (m-10) cc_final: 0.8844 (m-80) REVERT: Q 56 THR cc_start: 0.9196 (p) cc_final: 0.8869 (t) REVERT: Q 59 LEU cc_start: 0.9609 (mm) cc_final: 0.9333 (mm) REVERT: Q 62 PHE cc_start: 0.8980 (m-80) cc_final: 0.8693 (m-80) outliers start: 1 outliers final: 0 residues processed: 337 average time/residue: 0.0518 time to fit residues: 26.8398 Evaluate side-chains 301 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 300 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 33 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.065967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.048505 restraints weight = 44475.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.049598 restraints weight = 33370.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.050377 restraints weight = 26899.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.051321 restraints weight = 23131.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.051967 restraints weight = 19969.714| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 8101 Z= 0.222 Angle : 0.628 10.093 11102 Z= 0.363 Chirality : 0.044 0.225 1451 Planarity : 0.004 0.042 1478 Dihedral : 4.287 26.433 1331 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.14 % Favored : 94.78 % Rotamer: Outliers : 0.41 % Allowed : 7.66 % Favored : 91.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.23), residues: 1284 helix: 1.13 (0.16), residues: 1069 sheet: None (None), residues: 0 loop : -3.11 (0.39), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG O 44 TYR 0.023 0.002 TYR O 48 PHE 0.048 0.002 PHE K 62 TRP 0.000 0.000 TRP T 122 Details of bonding type rmsd covalent geometry : bond 0.00438 ( 8101) covalent geometry : angle 0.62819 (11102) hydrogen bonds : bond 0.05206 ( 827) hydrogen bonds : angle 4.81088 ( 2469) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 323 time to evaluate : 0.186 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 68 PHE cc_start: 0.9323 (m-80) cc_final: 0.8646 (m-80) REVERT: I 55 PHE cc_start: 0.9793 (m-80) cc_final: 0.9391 (m-80) REVERT: I 57 GLU cc_start: 0.9263 (OUTLIER) cc_final: 0.8827 (pp20) REVERT: I 64 LEU cc_start: 0.9822 (mm) cc_final: 0.9558 (mt) REVERT: I 68 PHE cc_start: 0.9488 (m-10) cc_final: 0.8953 (m-80) REVERT: J 27 ILE cc_start: 0.9511 (mm) cc_final: 0.9297 (mm) REVERT: J 41 ILE cc_start: 0.8855 (tp) cc_final: 0.8598 (tp) REVERT: J 48 TYR cc_start: 0.9360 (m-80) cc_final: 0.8803 (m-80) REVERT: J 50 PHE cc_start: 0.9689 (m-80) cc_final: 0.9328 (m-80) REVERT: J 51 ILE cc_start: 0.9461 (pt) cc_final: 0.9214 (pt) REVERT: J 53 ILE cc_start: 0.9808 (mt) cc_final: 0.9510 (mt) REVERT: J 55 PHE cc_start: 0.9362 (m-10) cc_final: 0.8902 (m-80) REVERT: J 57 GLU cc_start: 0.9445 (mt-10) cc_final: 0.8828 (tm-30) REVERT: J 64 LEU cc_start: 0.9859 (tt) cc_final: 0.9495 (pp) REVERT: J 68 PHE cc_start: 0.9601 (m-80) cc_final: 0.9327 (m-80) REVERT: K 15 LEU cc_start: 0.9268 (mm) cc_final: 0.9019 (mp) REVERT: K 24 ILE cc_start: 0.9544 (mm) cc_final: 0.9267 (mm) REVERT: K 27 ILE cc_start: 0.9366 (mt) cc_final: 0.9023 (mt) REVERT: K 32 VAL cc_start: 0.9659 (p) cc_final: 0.9430 (p) REVERT: K 44 ARG cc_start: 0.9358 (mmm-85) cc_final: 0.9157 (tpt170) REVERT: K 51 ILE cc_start: 0.9369 (pt) cc_final: 0.9152 (pt) REVERT: K 55 PHE cc_start: 0.9354 (m-10) cc_final: 0.9132 (m-80) REVERT: K 62 PHE cc_start: 0.9391 (m-80) cc_final: 0.9061 (m-80) REVERT: L 18 ILE cc_start: 0.9419 (tt) cc_final: 0.9110 (pt) REVERT: L 26 ILE cc_start: 0.9079 (tp) cc_final: 0.8762 (tt) REVERT: L 32 VAL cc_start: 0.9471 (p) cc_final: 0.9033 (p) REVERT: L 45 VAL cc_start: 0.9350 (p) cc_final: 0.8879 (p) REVERT: L 48 TYR cc_start: 0.9245 (m-80) cc_final: 0.8857 (m-80) REVERT: L 55 PHE cc_start: 0.9385 (m-80) cc_final: 0.8985 (m-80) REVERT: M 40 GLU cc_start: 0.9142 (mm-30) cc_final: 0.8935 (mm-30) REVERT: M 46 VAL cc_start: 0.9629 (m) cc_final: 0.9344 (p) REVERT: M 49 MET cc_start: 0.9626 (ttp) cc_final: 0.9405 (tmm) REVERT: M 50 PHE cc_start: 0.9421 (m-80) cc_final: 0.9086 (m-80) REVERT: M 53 ILE cc_start: 0.9716 (mm) cc_final: 0.9493 (mm) REVERT: N 33 GLN cc_start: 0.9334 (mm-40) cc_final: 0.9012 (mm110) REVERT: N 48 TYR cc_start: 0.9282 (m-10) cc_final: 0.8955 (m-80) REVERT: N 53 ILE cc_start: 0.9670 (mm) cc_final: 0.9449 (mm) REVERT: N 55 PHE cc_start: 0.9472 (m-80) cc_final: 0.9073 (m-80) REVERT: N 57 GLU cc_start: 0.9261 (pp20) cc_final: 0.9032 (pp20) REVERT: N 59 LEU cc_start: 0.9782 (mt) cc_final: 0.9541 (mt) REVERT: N 62 PHE cc_start: 0.9464 (m-10) cc_final: 0.9063 (m-80) REVERT: N 64 LEU cc_start: 0.9778 (mt) cc_final: 0.9548 (mt) REVERT: N 68 PHE cc_start: 0.9730 (m-10) cc_final: 0.9219 (m-80) REVERT: N 69 LEU cc_start: 0.9123 (tp) cc_final: 0.8901 (pp) REVERT: O 15 LEU cc_start: 0.9631 (mm) cc_final: 0.9297 (tp) REVERT: O 46 VAL cc_start: 0.9252 (t) cc_final: 0.8362 (t) REVERT: O 50 PHE cc_start: 0.9560 (m-80) cc_final: 0.9064 (m-80) REVERT: O 62 PHE cc_start: 0.9291 (m-80) cc_final: 0.8943 (m-80) REVERT: P 15 LEU cc_start: 0.9537 (mm) cc_final: 0.9168 (tp) REVERT: P 26 ILE cc_start: 0.9681 (mm) cc_final: 0.9420 (tp) REVERT: P 49 MET cc_start: 0.9169 (ptp) cc_final: 0.8764 (ptp) REVERT: P 50 PHE cc_start: 0.9172 (m-80) cc_final: 0.8969 (m-80) REVERT: P 53 ILE cc_start: 0.9605 (pt) cc_final: 0.9226 (tp) REVERT: P 62 PHE cc_start: 0.9556 (m-10) cc_final: 0.9334 (m-80) REVERT: Q 53 ILE cc_start: 0.9386 (pt) cc_final: 0.9132 (pt) REVERT: Q 59 LEU cc_start: 0.9654 (mm) cc_final: 0.9399 (mm) REVERT: Q 62 PHE cc_start: 0.9050 (m-80) cc_final: 0.8775 (m-80) outliers start: 2 outliers final: 0 residues processed: 324 average time/residue: 0.0509 time to fit residues: 25.2924 Evaluate side-chains 290 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 289 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 28 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 chunk 106 optimal weight: 0.2980 chunk 50 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 70 optimal weight: 0.5980 chunk 95 optimal weight: 3.9990 chunk 113 optimal weight: 0.0050 chunk 112 optimal weight: 10.0000 chunk 104 optimal weight: 8.9990 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.068593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.049962 restraints weight = 41139.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.051306 restraints weight = 30718.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.052130 restraints weight = 24342.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.053006 restraints weight = 20872.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.053422 restraints weight = 18619.419| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 8101 Z= 0.162 Angle : 0.614 8.425 11102 Z= 0.336 Chirality : 0.045 0.197 1451 Planarity : 0.004 0.040 1478 Dihedral : 4.174 20.764 1331 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.30 % Favored : 94.63 % Rotamer: Outliers : 0.41 % Allowed : 3.11 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.23), residues: 1284 helix: 1.19 (0.16), residues: 1068 sheet: None (None), residues: 0 loop : -3.13 (0.38), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG I 44 TYR 0.015 0.002 TYR O 48 PHE 0.042 0.001 PHE I 62 TRP 0.000 0.000 TRP T 122 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 8101) covalent geometry : angle 0.61373 (11102) hydrogen bonds : bond 0.04711 ( 827) hydrogen bonds : angle 4.51419 ( 2469) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 319 time to evaluate : 0.292 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 55 PHE cc_start: 0.9175 (m-80) cc_final: 0.8809 (m-80) REVERT: H 68 PHE cc_start: 0.9292 (m-80) cc_final: 0.8618 (m-80) REVERT: I 55 PHE cc_start: 0.9772 (m-80) cc_final: 0.9381 (m-80) REVERT: I 57 GLU cc_start: 0.9220 (OUTLIER) cc_final: 0.8789 (pp20) REVERT: I 64 LEU cc_start: 0.9839 (mm) cc_final: 0.9611 (mm) REVERT: I 68 PHE cc_start: 0.9446 (m-10) cc_final: 0.8959 (m-80) REVERT: J 27 ILE cc_start: 0.9503 (mm) cc_final: 0.9226 (mm) REVERT: J 41 ILE cc_start: 0.8644 (tp) cc_final: 0.8411 (tp) REVERT: J 50 PHE cc_start: 0.9674 (m-80) cc_final: 0.9363 (m-80) REVERT: J 51 ILE cc_start: 0.9457 (pt) cc_final: 0.9196 (pt) REVERT: J 53 ILE cc_start: 0.9774 (mt) cc_final: 0.9484 (mt) REVERT: J 55 PHE cc_start: 0.9246 (m-10) cc_final: 0.8982 (m-80) REVERT: J 57 GLU cc_start: 0.9427 (mt-10) cc_final: 0.8903 (tm-30) REVERT: J 64 LEU cc_start: 0.9833 (tt) cc_final: 0.9517 (pp) REVERT: J 68 PHE cc_start: 0.9494 (m-80) cc_final: 0.9211 (m-80) REVERT: K 15 LEU cc_start: 0.9178 (mm) cc_final: 0.8962 (mp) REVERT: K 24 ILE cc_start: 0.9460 (mm) cc_final: 0.9201 (mm) REVERT: K 27 ILE cc_start: 0.9320 (mt) cc_final: 0.9069 (mt) REVERT: K 44 ARG cc_start: 0.9307 (mmm-85) cc_final: 0.9018 (tpt170) REVERT: K 50 PHE cc_start: 0.9652 (m-10) cc_final: 0.9269 (m-80) REVERT: K 55 PHE cc_start: 0.9317 (m-10) cc_final: 0.9040 (m-80) REVERT: L 18 ILE cc_start: 0.9322 (tt) cc_final: 0.9001 (pt) REVERT: L 26 ILE cc_start: 0.8964 (tp) cc_final: 0.8760 (tt) REVERT: L 45 VAL cc_start: 0.9285 (p) cc_final: 0.8856 (p) REVERT: L 48 TYR cc_start: 0.9226 (m-80) cc_final: 0.8868 (m-80) REVERT: L 55 PHE cc_start: 0.9340 (m-80) cc_final: 0.9078 (m-80) REVERT: M 40 GLU cc_start: 0.9250 (mm-30) cc_final: 0.8973 (mm-30) REVERT: M 46 VAL cc_start: 0.9619 (m) cc_final: 0.9313 (p) REVERT: M 50 PHE cc_start: 0.9348 (m-80) cc_final: 0.8993 (m-80) REVERT: M 62 PHE cc_start: 0.9458 (m-80) cc_final: 0.9147 (m-80) REVERT: N 11 LEU cc_start: 0.9396 (mm) cc_final: 0.9158 (mm) REVERT: N 33 GLN cc_start: 0.9271 (mm-40) cc_final: 0.8943 (mm110) REVERT: N 40 GLU cc_start: 0.9533 (mm-30) cc_final: 0.9199 (mp0) REVERT: N 48 TYR cc_start: 0.9274 (m-10) cc_final: 0.8870 (m-80) REVERT: N 55 PHE cc_start: 0.9474 (m-80) cc_final: 0.9157 (m-80) REVERT: N 62 PHE cc_start: 0.9463 (m-10) cc_final: 0.9223 (m-80) REVERT: N 64 LEU cc_start: 0.9827 (mt) cc_final: 0.9557 (mt) REVERT: N 68 PHE cc_start: 0.9756 (m-10) cc_final: 0.9265 (m-80) REVERT: N 69 LEU cc_start: 0.9130 (tp) cc_final: 0.8888 (pp) REVERT: O 45 VAL cc_start: 0.9114 (p) cc_final: 0.8874 (m) REVERT: O 50 PHE cc_start: 0.9609 (m-80) cc_final: 0.9318 (m-10) REVERT: O 62 PHE cc_start: 0.9294 (m-80) cc_final: 0.8950 (m-80) REVERT: P 53 ILE cc_start: 0.9580 (pt) cc_final: 0.9172 (tp) REVERT: P 62 PHE cc_start: 0.9543 (m-10) cc_final: 0.9314 (m-80) REVERT: Q 53 ILE cc_start: 0.9307 (pt) cc_final: 0.8980 (pt) REVERT: Q 59 LEU cc_start: 0.9648 (mm) cc_final: 0.9422 (mm) REVERT: Q 62 PHE cc_start: 0.9041 (m-80) cc_final: 0.8826 (m-80) outliers start: 2 outliers final: 0 residues processed: 320 average time/residue: 0.0501 time to fit residues: 24.7004 Evaluate side-chains 286 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 285 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 36 optimal weight: 0.9980 chunk 116 optimal weight: 0.0870 chunk 14 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 118 optimal weight: 20.0000 chunk 63 optimal weight: 9.9990 chunk 90 optimal weight: 8.9990 chunk 98 optimal weight: 10.0000 chunk 83 optimal weight: 0.9990 chunk 122 optimal weight: 10.0000 overall best weight: 0.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.072732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.057612 restraints weight = 56692.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.058874 restraints weight = 43620.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.059776 restraints weight = 35287.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.060489 restraints weight = 29929.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.061145 restraints weight = 26163.438| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 8101 Z= 0.155 Angle : 0.603 8.753 11102 Z= 0.332 Chirality : 0.044 0.226 1451 Planarity : 0.004 0.051 1478 Dihedral : 4.076 21.277 1331 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.22 % Favored : 94.70 % Rotamer: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.24), residues: 1284 helix: 1.27 (0.16), residues: 1068 sheet: None (None), residues: 0 loop : -3.14 (0.38), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG K 44 TYR 0.012 0.001 TYR H 48 PHE 0.046 0.001 PHE K 62 TRP 0.000 0.000 TRP T 122 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 8101) covalent geometry : angle 0.60316 (11102) hydrogen bonds : bond 0.04404 ( 827) hydrogen bonds : angle 4.36351 ( 2469) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 317 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 33 GLN cc_start: 0.9371 (pm20) cc_final: 0.8930 (pm20) REVERT: H 55 PHE cc_start: 0.9163 (m-80) cc_final: 0.8747 (m-80) REVERT: H 68 PHE cc_start: 0.9269 (m-80) cc_final: 0.9000 (t80) REVERT: I 55 PHE cc_start: 0.9706 (m-80) cc_final: 0.9361 (m-80) REVERT: J 41 ILE cc_start: 0.8829 (tp) cc_final: 0.8589 (tp) REVERT: J 47 THR cc_start: 0.9520 (p) cc_final: 0.9264 (p) REVERT: J 50 PHE cc_start: 0.9727 (m-80) cc_final: 0.9152 (m-80) REVERT: J 51 ILE cc_start: 0.9483 (pt) cc_final: 0.9032 (pt) REVERT: J 53 ILE cc_start: 0.9849 (mt) cc_final: 0.9630 (mt) REVERT: J 55 PHE cc_start: 0.9439 (m-10) cc_final: 0.9044 (m-80) REVERT: J 56 THR cc_start: 0.9662 (p) cc_final: 0.9246 (p) REVERT: J 57 GLU cc_start: 0.9389 (mt-10) cc_final: 0.8899 (tm-30) REVERT: J 59 LEU cc_start: 0.9605 (mm) cc_final: 0.9403 (pp) REVERT: J 61 ILE cc_start: 0.9115 (mm) cc_final: 0.8901 (mm) REVERT: J 64 LEU cc_start: 0.9800 (tt) cc_final: 0.9446 (pp) REVERT: J 65 VAL cc_start: 0.9670 (m) cc_final: 0.9447 (m) REVERT: K 24 ILE cc_start: 0.9445 (mm) cc_final: 0.9180 (mm) REVERT: K 44 ARG cc_start: 0.9240 (mmm-85) cc_final: 0.9026 (tpt170) REVERT: K 50 PHE cc_start: 0.9604 (m-10) cc_final: 0.9099 (m-80) REVERT: K 51 ILE cc_start: 0.9369 (pt) cc_final: 0.8997 (pt) REVERT: K 55 PHE cc_start: 0.9369 (m-10) cc_final: 0.9063 (m-80) REVERT: K 62 PHE cc_start: 0.9367 (m-80) cc_final: 0.8944 (m-80) REVERT: L 26 ILE cc_start: 0.9429 (tp) cc_final: 0.9156 (tt) REVERT: L 32 VAL cc_start: 0.9621 (p) cc_final: 0.9349 (p) REVERT: L 45 VAL cc_start: 0.9320 (p) cc_final: 0.8940 (p) REVERT: L 48 TYR cc_start: 0.9101 (m-80) cc_final: 0.8799 (m-80) REVERT: L 55 PHE cc_start: 0.9365 (m-80) cc_final: 0.9070 (m-80) REVERT: M 40 GLU cc_start: 0.9092 (mm-30) cc_final: 0.8840 (mm-30) REVERT: M 46 VAL cc_start: 0.9541 (m) cc_final: 0.9185 (p) REVERT: M 50 PHE cc_start: 0.9432 (m-80) cc_final: 0.8941 (m-80) REVERT: M 62 PHE cc_start: 0.9286 (m-80) cc_final: 0.9074 (m-80) REVERT: N 11 LEU cc_start: 0.9494 (mm) cc_final: 0.9232 (mm) REVERT: N 33 GLN cc_start: 0.9351 (mm-40) cc_final: 0.9040 (mm110) REVERT: N 40 GLU cc_start: 0.9447 (mm-30) cc_final: 0.9128 (mp0) REVERT: N 48 TYR cc_start: 0.9313 (m-10) cc_final: 0.8890 (m-80) REVERT: N 55 PHE cc_start: 0.9489 (m-80) cc_final: 0.9064 (m-80) REVERT: N 59 LEU cc_start: 0.9674 (mt) cc_final: 0.9414 (mt) REVERT: N 62 PHE cc_start: 0.9267 (m-10) cc_final: 0.8967 (m-80) REVERT: N 64 LEU cc_start: 0.9776 (mt) cc_final: 0.9546 (mt) REVERT: N 68 PHE cc_start: 0.9603 (m-10) cc_final: 0.9216 (m-80) REVERT: N 69 LEU cc_start: 0.9106 (tp) cc_final: 0.8895 (pp) REVERT: O 15 LEU cc_start: 0.9622 (mm) cc_final: 0.9417 (mm) REVERT: O 46 VAL cc_start: 0.9165 (t) cc_final: 0.8289 (t) REVERT: O 50 PHE cc_start: 0.9498 (m-80) cc_final: 0.8892 (m-80) REVERT: O 62 PHE cc_start: 0.9194 (m-80) cc_final: 0.8896 (m-80) REVERT: O 64 LEU cc_start: 0.9708 (mt) cc_final: 0.9488 (mt) REVERT: O 68 PHE cc_start: 0.9266 (m-80) cc_final: 0.8739 (m-80) REVERT: P 15 LEU cc_start: 0.9504 (mm) cc_final: 0.8797 (tp) REVERT: P 50 PHE cc_start: 0.9041 (m-10) cc_final: 0.8839 (m-10) REVERT: P 53 ILE cc_start: 0.9487 (pt) cc_final: 0.9088 (tp) REVERT: P 62 PHE cc_start: 0.9536 (m-10) cc_final: 0.9310 (m-80) REVERT: Q 53 ILE cc_start: 0.9207 (pt) cc_final: 0.8889 (pt) REVERT: Q 59 LEU cc_start: 0.9546 (mm) cc_final: 0.9177 (mm) REVERT: Q 62 PHE cc_start: 0.8939 (m-80) cc_final: 0.8735 (m-80) outliers start: 0 outliers final: 0 residues processed: 317 average time/residue: 0.0547 time to fit residues: 26.8264 Evaluate side-chains 285 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 285 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 3.9990 chunk 8 optimal weight: 20.0000 chunk 60 optimal weight: 0.9990 chunk 105 optimal weight: 30.0000 chunk 40 optimal weight: 0.6980 chunk 99 optimal weight: 9.9990 chunk 59 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 4 optimal weight: 7.9990 chunk 124 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.071280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.056660 restraints weight = 57965.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.057824 restraints weight = 44781.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.058746 restraints weight = 36418.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.059413 restraints weight = 30639.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.060004 restraints weight = 26800.454| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6663 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 8101 Z= 0.167 Angle : 0.606 7.094 11102 Z= 0.341 Chirality : 0.044 0.245 1451 Planarity : 0.004 0.047 1478 Dihedral : 4.045 21.391 1331 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.22 % Favored : 94.70 % Rotamer: Outliers : 0.41 % Allowed : 2.90 % Favored : 96.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.24), residues: 1284 helix: 1.31 (0.16), residues: 1068 sheet: None (None), residues: 0 loop : -3.14 (0.38), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 37 TYR 0.010 0.001 TYR H 48 PHE 0.049 0.002 PHE I 62 TRP 0.000 0.000 TRP T 122 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 8101) covalent geometry : angle 0.60609 (11102) hydrogen bonds : bond 0.04289 ( 827) hydrogen bonds : angle 4.32839 ( 2469) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 309 time to evaluate : 0.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 27 ILE cc_start: 0.9737 (mt) cc_final: 0.9526 (mt) REVERT: H 45 VAL cc_start: 0.9549 (p) cc_final: 0.9325 (p) REVERT: H 55 PHE cc_start: 0.9186 (m-80) cc_final: 0.8856 (m-80) REVERT: H 68 PHE cc_start: 0.9287 (m-80) cc_final: 0.9047 (t80) REVERT: I 55 PHE cc_start: 0.9745 (m-80) cc_final: 0.9393 (m-80) REVERT: I 62 PHE cc_start: 0.9357 (m-80) cc_final: 0.9157 (m-80) REVERT: I 64 LEU cc_start: 0.9820 (mm) cc_final: 0.9620 (mm) REVERT: J 27 ILE cc_start: 0.9597 (mm) cc_final: 0.9382 (mm) REVERT: J 47 THR cc_start: 0.9625 (p) cc_final: 0.9398 (p) REVERT: J 50 PHE cc_start: 0.9653 (m-80) cc_final: 0.9276 (m-80) REVERT: J 51 ILE cc_start: 0.9508 (pt) cc_final: 0.9245 (pt) REVERT: J 53 ILE cc_start: 0.9797 (mt) cc_final: 0.9518 (mt) REVERT: J 55 PHE cc_start: 0.9243 (m-10) cc_final: 0.8960 (m-80) REVERT: J 57 GLU cc_start: 0.9431 (mt-10) cc_final: 0.8868 (tm-30) REVERT: J 68 PHE cc_start: 0.9547 (m-80) cc_final: 0.9098 (m-80) REVERT: K 24 ILE cc_start: 0.9509 (mm) cc_final: 0.9245 (mm) REVERT: K 27 ILE cc_start: 0.9429 (mt) cc_final: 0.9220 (mt) REVERT: K 32 VAL cc_start: 0.9627 (p) cc_final: 0.9301 (p) REVERT: K 33 GLN cc_start: 0.9321 (mp-120) cc_final: 0.9090 (mm-40) REVERT: K 44 ARG cc_start: 0.9251 (mmm-85) cc_final: 0.8977 (tpt170) REVERT: K 50 PHE cc_start: 0.9645 (m-10) cc_final: 0.9265 (m-80) REVERT: K 62 PHE cc_start: 0.9428 (m-80) cc_final: 0.9042 (m-80) REVERT: L 18 ILE cc_start: 0.9316 (tt) cc_final: 0.8938 (pt) REVERT: L 26 ILE cc_start: 0.9034 (tp) cc_final: 0.8817 (tt) REVERT: L 27 ILE cc_start: 0.9747 (tt) cc_final: 0.9535 (tt) REVERT: L 48 TYR cc_start: 0.9276 (m-80) cc_final: 0.8980 (m-80) REVERT: L 55 PHE cc_start: 0.9372 (m-80) cc_final: 0.9145 (m-80) REVERT: M 40 GLU cc_start: 0.9342 (mm-30) cc_final: 0.9072 (mm-30) REVERT: M 46 VAL cc_start: 0.9531 (m) cc_final: 0.9312 (p) REVERT: M 50 PHE cc_start: 0.9173 (m-80) cc_final: 0.8903 (m-80) REVERT: N 33 GLN cc_start: 0.9211 (mm-40) cc_final: 0.8995 (mm110) REVERT: N 48 TYR cc_start: 0.9158 (m-10) cc_final: 0.8924 (m-80) REVERT: N 55 PHE cc_start: 0.9438 (m-80) cc_final: 0.9042 (m-80) REVERT: N 59 LEU cc_start: 0.9683 (mt) cc_final: 0.9477 (mt) REVERT: N 62 PHE cc_start: 0.9342 (m-10) cc_final: 0.9019 (m-80) REVERT: N 68 PHE cc_start: 0.9685 (m-10) cc_final: 0.9292 (m-80) REVERT: O 46 VAL cc_start: 0.9192 (t) cc_final: 0.8550 (t) REVERT: O 50 PHE cc_start: 0.9597 (m-80) cc_final: 0.9159 (m-80) REVERT: O 62 PHE cc_start: 0.9246 (m-80) cc_final: 0.8976 (m-80) REVERT: O 64 LEU cc_start: 0.9787 (mt) cc_final: 0.9556 (mt) REVERT: O 68 PHE cc_start: 0.9412 (m-80) cc_final: 0.8976 (m-80) REVERT: P 15 LEU cc_start: 0.9226 (mm) cc_final: 0.8602 (tp) REVERT: P 49 MET cc_start: 0.9325 (ptp) cc_final: 0.8913 (ptt) REVERT: P 62 PHE cc_start: 0.9512 (m-10) cc_final: 0.9292 (m-80) REVERT: Q 27 ILE cc_start: 0.9692 (mt) cc_final: 0.9474 (mt) REVERT: Q 53 ILE cc_start: 0.9272 (pt) cc_final: 0.8983 (pt) REVERT: Q 59 LEU cc_start: 0.9659 (mm) cc_final: 0.9433 (mm) REVERT: Q 62 PHE cc_start: 0.9036 (m-80) cc_final: 0.8810 (m-80) outliers start: 2 outliers final: 1 residues processed: 309 average time/residue: 0.0517 time to fit residues: 24.5626 Evaluate side-chains 277 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 276 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 86 optimal weight: 0.7980 chunk 7 optimal weight: 30.0000 chunk 0 optimal weight: 30.0000 chunk 122 optimal weight: 9.9990 chunk 110 optimal weight: 0.5980 chunk 113 optimal weight: 7.9990 chunk 75 optimal weight: 6.9990 chunk 93 optimal weight: 0.8980 chunk 70 optimal weight: 0.0970 chunk 119 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.067820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.051857 restraints weight = 44327.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.052585 restraints weight = 35335.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.053399 restraints weight = 30384.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.054085 restraints weight = 26547.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.054605 restraints weight = 23567.969| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 8101 Z= 0.146 Angle : 0.610 8.011 11102 Z= 0.332 Chirality : 0.045 0.222 1451 Planarity : 0.004 0.054 1478 Dihedral : 4.046 22.490 1331 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.37 % Favored : 94.55 % Rotamer: Outliers : 0.21 % Allowed : 2.48 % Favored : 97.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.24), residues: 1284 helix: 1.36 (0.16), residues: 1074 sheet: None (None), residues: 0 loop : -3.17 (0.38), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG O 37 TYR 0.022 0.002 TYR M 48 PHE 0.037 0.001 PHE I 62 TRP 0.000 0.000 TRP T 122 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 8101) covalent geometry : angle 0.60994 (11102) hydrogen bonds : bond 0.04165 ( 827) hydrogen bonds : angle 4.23286 ( 2469) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 319 time to evaluate : 0.265 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 33 GLN cc_start: 0.9369 (pm20) cc_final: 0.8897 (pm20) REVERT: H 68 PHE cc_start: 0.9299 (m-80) cc_final: 0.8983 (t80) REVERT: I 55 PHE cc_start: 0.9738 (m-80) cc_final: 0.9349 (m-80) REVERT: I 57 GLU cc_start: 0.9238 (OUTLIER) cc_final: 0.8863 (pp20) REVERT: I 64 LEU cc_start: 0.9840 (mm) cc_final: 0.9588 (mm) REVERT: J 27 ILE cc_start: 0.9600 (mm) cc_final: 0.9335 (mm) REVERT: J 47 THR cc_start: 0.9588 (p) cc_final: 0.9361 (p) REVERT: J 50 PHE cc_start: 0.9646 (m-80) cc_final: 0.9233 (m-80) REVERT: J 53 ILE cc_start: 0.9764 (mt) cc_final: 0.9452 (mt) REVERT: J 55 PHE cc_start: 0.9209 (m-10) cc_final: 0.8962 (m-80) REVERT: J 56 THR cc_start: 0.9654 (p) cc_final: 0.9151 (p) REVERT: J 57 GLU cc_start: 0.9427 (mt-10) cc_final: 0.9004 (tm-30) REVERT: J 59 LEU cc_start: 0.9694 (mm) cc_final: 0.9440 (pp) REVERT: J 64 LEU cc_start: 0.9863 (tt) cc_final: 0.9522 (pp) REVERT: J 68 PHE cc_start: 0.9561 (m-80) cc_final: 0.9271 (m-80) REVERT: K 15 LEU cc_start: 0.9134 (mm) cc_final: 0.8918 (mt) REVERT: K 24 ILE cc_start: 0.9476 (mm) cc_final: 0.9175 (mm) REVERT: K 27 ILE cc_start: 0.9375 (mt) cc_final: 0.9111 (mt) REVERT: K 44 ARG cc_start: 0.9230 (mmm-85) cc_final: 0.8962 (tpt170) REVERT: K 55 PHE cc_start: 0.9433 (m-10) cc_final: 0.9179 (m-80) REVERT: K 62 PHE cc_start: 0.9480 (m-80) cc_final: 0.9124 (m-80) REVERT: L 45 VAL cc_start: 0.9363 (p) cc_final: 0.9136 (p) REVERT: L 55 PHE cc_start: 0.9398 (m-80) cc_final: 0.9046 (m-80) REVERT: M 40 GLU cc_start: 0.9275 (mm-30) cc_final: 0.8985 (mm-30) REVERT: M 46 VAL cc_start: 0.9520 (m) cc_final: 0.9298 (p) REVERT: M 48 TYR cc_start: 0.9084 (m-80) cc_final: 0.8836 (m-80) REVERT: M 50 PHE cc_start: 0.9217 (m-80) cc_final: 0.8887 (m-80) REVERT: M 55 PHE cc_start: 0.9468 (m-10) cc_final: 0.9236 (m-80) REVERT: N 33 GLN cc_start: 0.9251 (mm-40) cc_final: 0.9012 (mm110) REVERT: N 40 GLU cc_start: 0.9525 (mm-30) cc_final: 0.9194 (mp0) REVERT: N 48 TYR cc_start: 0.9133 (m-10) cc_final: 0.8749 (m-80) REVERT: N 53 ILE cc_start: 0.9579 (mm) cc_final: 0.9368 (mm) REVERT: N 55 PHE cc_start: 0.9423 (m-80) cc_final: 0.9062 (m-80) REVERT: N 59 LEU cc_start: 0.9656 (mt) cc_final: 0.9406 (mt) REVERT: N 62 PHE cc_start: 0.9294 (m-10) cc_final: 0.8956 (m-80) REVERT: N 64 LEU cc_start: 0.9904 (mt) cc_final: 0.9631 (mt) REVERT: N 68 PHE cc_start: 0.9647 (m-10) cc_final: 0.9203 (m-80) REVERT: N 69 LEU cc_start: 0.8956 (tt) cc_final: 0.8732 (pp) REVERT: O 62 PHE cc_start: 0.9241 (m-80) cc_final: 0.8860 (m-80) REVERT: O 64 LEU cc_start: 0.9751 (mt) cc_final: 0.9493 (mt) REVERT: O 68 PHE cc_start: 0.9407 (m-80) cc_final: 0.8856 (m-80) REVERT: P 15 LEU cc_start: 0.9387 (mm) cc_final: 0.8703 (tp) REVERT: P 49 MET cc_start: 0.9193 (ptp) cc_final: 0.8952 (ptt) REVERT: P 62 PHE cc_start: 0.9522 (m-10) cc_final: 0.9279 (m-80) REVERT: Q 33 GLN cc_start: 0.9525 (tm-30) cc_final: 0.9320 (tm-30) REVERT: Q 53 ILE cc_start: 0.9246 (pt) cc_final: 0.9028 (pt) REVERT: Q 59 LEU cc_start: 0.9605 (mm) cc_final: 0.9324 (mm) REVERT: Q 62 PHE cc_start: 0.8976 (m-80) cc_final: 0.8699 (m-80) REVERT: Q 66 ILE cc_start: 0.9843 (mm) cc_final: 0.9583 (tp) outliers start: 1 outliers final: 0 residues processed: 320 average time/residue: 0.0515 time to fit residues: 25.4574 Evaluate side-chains 286 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 285 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 78 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 100 optimal weight: 20.0000 chunk 115 optimal weight: 30.0000 chunk 3 optimal weight: 20.0000 chunk 87 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 chunk 127 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.068065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.053948 restraints weight = 59668.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.055062 restraints weight = 45747.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.055953 restraints weight = 37023.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.056590 restraints weight = 31106.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.057116 restraints weight = 27206.038| |-----------------------------------------------------------------------------| r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.3969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 8101 Z= 0.258 Angle : 0.687 7.797 11102 Z= 0.398 Chirality : 0.046 0.304 1451 Planarity : 0.004 0.051 1478 Dihedral : 4.182 23.272 1331 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 18.20 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.45 % Favored : 94.47 % Rotamer: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.24), residues: 1284 helix: 1.21 (0.16), residues: 1075 sheet: None (None), residues: 0 loop : -3.27 (0.37), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG J 37 TYR 0.026 0.002 TYR M 48 PHE 0.043 0.002 PHE M 62 TRP 0.000 0.000 TRP T 122 Details of bonding type rmsd covalent geometry : bond 0.00495 ( 8101) covalent geometry : angle 0.68700 (11102) hydrogen bonds : bond 0.04596 ( 827) hydrogen bonds : angle 4.65009 ( 2469) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 311 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 55 PHE cc_start: 0.9273 (m-80) cc_final: 0.8774 (m-80) REVERT: H 68 PHE cc_start: 0.9314 (m-80) cc_final: 0.8973 (t80) REVERT: I 50 PHE cc_start: 0.9317 (m-10) cc_final: 0.9026 (m-10) REVERT: I 55 PHE cc_start: 0.9729 (m-80) cc_final: 0.9404 (m-80) REVERT: I 64 LEU cc_start: 0.9754 (mm) cc_final: 0.9499 (mm) REVERT: J 40 GLU cc_start: 0.9076 (mp0) cc_final: 0.8868 (mp0) REVERT: J 41 ILE cc_start: 0.9061 (tp) cc_final: 0.8695 (tp) REVERT: J 50 PHE cc_start: 0.9724 (m-80) cc_final: 0.9268 (m-80) REVERT: J 51 ILE cc_start: 0.9466 (pt) cc_final: 0.9050 (pt) REVERT: J 55 PHE cc_start: 0.9454 (m-10) cc_final: 0.9030 (m-80) REVERT: J 57 GLU cc_start: 0.9476 (mt-10) cc_final: 0.8869 (tm-30) REVERT: J 59 LEU cc_start: 0.9654 (mm) cc_final: 0.9445 (mm) REVERT: J 61 ILE cc_start: 0.9161 (mm) cc_final: 0.8885 (mm) REVERT: J 64 LEU cc_start: 0.9811 (tt) cc_final: 0.9440 (pp) REVERT: J 68 PHE cc_start: 0.9501 (m-80) cc_final: 0.9275 (m-80) REVERT: K 15 LEU cc_start: 0.9389 (mm) cc_final: 0.9188 (mp) REVERT: K 24 ILE cc_start: 0.9424 (mm) cc_final: 0.9197 (mm) REVERT: K 33 GLN cc_start: 0.9455 (mp-120) cc_final: 0.9237 (mm-40) REVERT: K 44 ARG cc_start: 0.9251 (mmm-85) cc_final: 0.8954 (tpt170) REVERT: K 50 PHE cc_start: 0.9609 (m-10) cc_final: 0.9062 (m-10) REVERT: K 51 ILE cc_start: 0.9409 (pt) cc_final: 0.9020 (pt) REVERT: K 55 PHE cc_start: 0.9414 (m-10) cc_final: 0.9199 (m-80) REVERT: K 62 PHE cc_start: 0.9503 (m-80) cc_final: 0.9195 (m-80) REVERT: L 18 ILE cc_start: 0.9571 (tt) cc_final: 0.9280 (mt) REVERT: L 55 PHE cc_start: 0.9514 (m-80) cc_final: 0.9200 (m-80) REVERT: M 40 GLU cc_start: 0.9048 (mm-30) cc_final: 0.8824 (mm-30) REVERT: M 46 VAL cc_start: 0.9586 (m) cc_final: 0.9212 (p) REVERT: M 50 PHE cc_start: 0.9346 (m-80) cc_final: 0.8860 (m-80) REVERT: M 62 PHE cc_start: 0.9469 (m-80) cc_final: 0.9008 (m-80) REVERT: N 11 LEU cc_start: 0.9611 (mm) cc_final: 0.9404 (mm) REVERT: N 40 GLU cc_start: 0.9483 (mm-30) cc_final: 0.9219 (mp0) REVERT: N 48 TYR cc_start: 0.9366 (m-10) cc_final: 0.9035 (m-80) REVERT: N 53 ILE cc_start: 0.9654 (mm) cc_final: 0.9365 (mm) REVERT: N 55 PHE cc_start: 0.9527 (m-80) cc_final: 0.9018 (m-80) REVERT: N 59 LEU cc_start: 0.9667 (mt) cc_final: 0.9368 (mt) REVERT: N 62 PHE cc_start: 0.9327 (m-10) cc_final: 0.9011 (m-80) REVERT: N 68 PHE cc_start: 0.9610 (m-10) cc_final: 0.9209 (m-80) REVERT: O 27 ILE cc_start: 0.9543 (mt) cc_final: 0.9343 (mt) REVERT: O 50 PHE cc_start: 0.9529 (m-80) cc_final: 0.8895 (m-80) REVERT: O 62 PHE cc_start: 0.9228 (m-80) cc_final: 0.8885 (m-80) REVERT: O 68 PHE cc_start: 0.9480 (m-80) cc_final: 0.8955 (m-80) REVERT: P 49 MET cc_start: 0.9210 (ptp) cc_final: 0.8797 (ptp) REVERT: P 50 PHE cc_start: 0.9335 (m-80) cc_final: 0.9122 (m-10) REVERT: P 62 PHE cc_start: 0.9545 (m-10) cc_final: 0.9274 (m-80) REVERT: Q 33 GLN cc_start: 0.9375 (tm-30) cc_final: 0.9144 (tm-30) REVERT: Q 53 ILE cc_start: 0.9369 (pt) cc_final: 0.9123 (pt) REVERT: Q 59 LEU cc_start: 0.9604 (mm) cc_final: 0.9247 (mm) REVERT: Q 62 PHE cc_start: 0.9028 (m-80) cc_final: 0.8811 (m-80) outliers start: 0 outliers final: 0 residues processed: 311 average time/residue: 0.0535 time to fit residues: 25.4136 Evaluate side-chains 271 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.8107 > 50: distance: 34 - 56: 12.872 distance: 44 - 68: 9.261 distance: 51 - 56: 11.093 distance: 52 - 76: 10.229 distance: 56 - 57: 8.813 distance: 57 - 58: 17.641 distance: 57 - 60: 11.749 distance: 58 - 59: 23.640 distance: 58 - 64: 18.449 distance: 59 - 81: 17.583 distance: 60 - 61: 8.154 distance: 60 - 62: 6.979 distance: 61 - 63: 11.813 distance: 64 - 65: 50.811 distance: 65 - 66: 25.395 distance: 66 - 67: 16.142 distance: 66 - 68: 10.679 distance: 67 - 92: 14.078 distance: 68 - 69: 5.751 distance: 70 - 71: 3.704 distance: 70 - 76: 4.674 distance: 71 - 99: 7.656 distance: 72 - 73: 4.990 distance: 72 - 74: 12.102 distance: 73 - 75: 14.853 distance: 76 - 77: 11.501 distance: 77 - 78: 3.226 distance: 77 - 80: 14.849 distance: 78 - 79: 5.695 distance: 78 - 81: 5.313 distance: 81 - 82: 7.435 distance: 82 - 83: 3.157 distance: 82 - 85: 8.349 distance: 83 - 84: 6.078 distance: 83 - 92: 3.969 distance: 84 - 113: 16.356 distance: 85 - 86: 9.362 distance: 86 - 87: 10.155 distance: 86 - 88: 13.380 distance: 87 - 89: 6.774 distance: 88 - 90: 5.230 distance: 89 - 91: 10.962 distance: 90 - 91: 13.545 distance: 92 - 93: 6.353 distance: 93 - 94: 3.690 distance: 93 - 96: 8.586 distance: 94 - 99: 4.569 distance: 95 - 121: 15.229 distance: 96 - 97: 8.490 distance: 96 - 98: 10.314 distance: 99 - 100: 5.604 distance: 100 - 101: 9.028 distance: 100 - 103: 14.958 distance: 101 - 102: 6.990 distance: 101 - 108: 6.905 distance: 102 - 126: 3.346 distance: 103 - 104: 4.055 distance: 104 - 105: 9.052 distance: 105 - 106: 7.636 distance: 105 - 107: 15.717 distance: 108 - 109: 9.490 distance: 109 - 110: 7.530 distance: 109 - 112: 5.761 distance: 110 - 111: 5.471 distance: 110 - 113: 5.974 distance: 111 - 134: 16.618 distance: 113 - 114: 6.560 distance: 114 - 117: 8.557 distance: 116 - 145: 12.245 distance: 117 - 118: 4.867 distance: 118 - 119: 7.741 distance: 118 - 120: 3.582 distance: 121 - 122: 4.525 distance: 122 - 123: 4.974 distance: 122 - 125: 3.215 distance: 123 - 124: 3.198 distance: 123 - 126: 5.000 distance: 124 - 149: 9.406