Starting phenix.real_space_refine on Wed Mar 4 15:25:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hx0_35070/03_2026/8hx0_35070.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hx0_35070/03_2026/8hx0_35070.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hx0_35070/03_2026/8hx0_35070.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hx0_35070/03_2026/8hx0_35070.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hx0_35070/03_2026/8hx0_35070.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hx0_35070/03_2026/8hx0_35070.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.125 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 12 5.16 5 C 9222 2.51 5 N 2715 2.21 5 O 2970 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14919 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1250 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 155} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 1247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1247 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 1247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1247 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 1229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1229 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 155} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "E" Number of atoms: 1250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1250 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 155} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 1247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1247 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "I" Number of atoms: 1247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1247 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "K" Number of atoms: 1229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1229 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 155} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "F" Number of atoms: 1250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1250 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 155} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 1247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1247 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "J" Number of atoms: 1247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1247 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 154} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "L" Number of atoms: 1229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1229 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 155} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Time building chain proxies: 3.59, per 1000 atoms: 0.24 Number of scatterers: 14919 At special positions: 0 Unit cell: (105.08, 105.82, 99.9, 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 12 16.00 O 2970 8.00 N 2715 7.00 C 9222 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: 1.21 Conformation dependent library (CDL) restraints added in 556.8 milliseconds 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3618 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 4 sheets defined 77.2% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 16 through 43 Processing helix chain 'A' and resid 48 through 77 Processing helix chain 'A' and resid 84 through 92 Processing helix chain 'A' and resid 104 through 133 removed outlier: 4.226A pdb=" N ASP A 127 " --> pdb=" O ARG A 123 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N ALA A 128 " --> pdb=" O ARG A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 156 removed outlier: 3.761A pdb=" N LEU A 139 " --> pdb=" O SER A 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 44 removed outlier: 3.578A pdb=" N ASP B 29 " --> pdb=" O LYS B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 77 removed outlier: 3.855A pdb=" N LEU B 52 " --> pdb=" O ASN B 48 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP B 57 " --> pdb=" O HIS B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 92 Processing helix chain 'B' and resid 103 through 131 removed outlier: 4.519A pdb=" N ASP B 127 " --> pdb=" O ARG B 123 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N ALA B 128 " --> pdb=" O ARG B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 156 removed outlier: 3.578A pdb=" N LEU B 139 " --> pdb=" O SER B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 159 No H-bonds generated for 'chain 'B' and resid 157 through 159' Processing helix chain 'C' and resid 16 through 43 removed outlier: 3.599A pdb=" N ASP C 29 " --> pdb=" O LYS C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 77 Processing helix chain 'C' and resid 84 through 92 Processing helix chain 'C' and resid 104 through 133 removed outlier: 4.585A pdb=" N ASP C 127 " --> pdb=" O ARG C 123 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ALA C 128 " --> pdb=" O ARG C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 156 removed outlier: 3.673A pdb=" N LEU C 139 " --> pdb=" O SER C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 159 No H-bonds generated for 'chain 'C' and resid 157 through 159' Processing helix chain 'D' and resid 16 through 44 removed outlier: 3.760A pdb=" N VAL D 26 " --> pdb=" O ASN D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 77 removed outlier: 4.025A pdb=" N LEU D 52 " --> pdb=" O ASN D 48 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASP D 57 " --> pdb=" O HIS D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 92 Processing helix chain 'D' and resid 103 through 133 removed outlier: 4.302A pdb=" N ASP D 127 " --> pdb=" O ARG D 123 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N ALA D 128 " --> pdb=" O ARG D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 156 removed outlier: 3.677A pdb=" N LEU D 139 " --> pdb=" O SER D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 159 No H-bonds generated for 'chain 'D' and resid 157 through 159' Processing helix chain 'E' and resid 16 through 44 Processing helix chain 'E' and resid 48 through 77 Processing helix chain 'E' and resid 84 through 92 Processing helix chain 'E' and resid 103 through 133 removed outlier: 4.200A pdb=" N ASP E 127 " --> pdb=" O ARG E 123 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N ALA E 128 " --> pdb=" O ARG E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 156 removed outlier: 3.782A pdb=" N LEU E 139 " --> pdb=" O SER E 135 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 44 removed outlier: 3.551A pdb=" N ASP G 29 " --> pdb=" O LYS G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 77 removed outlier: 3.936A pdb=" N LEU G 52 " --> pdb=" O ASN G 48 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP G 57 " --> pdb=" O HIS G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 92 Processing helix chain 'G' and resid 103 through 131 removed outlier: 4.483A pdb=" N ASP G 127 " --> pdb=" O ARG G 123 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N ALA G 128 " --> pdb=" O ARG G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 156 removed outlier: 3.586A pdb=" N LEU G 139 " --> pdb=" O SER G 135 " (cutoff:3.500A) Processing helix chain 'G' and resid 157 through 159 No H-bonds generated for 'chain 'G' and resid 157 through 159' Processing helix chain 'I' and resid 16 through 43 removed outlier: 3.608A pdb=" N ASP I 29 " --> pdb=" O LYS I 25 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 77 Processing helix chain 'I' and resid 84 through 92 Processing helix chain 'I' and resid 104 through 133 removed outlier: 4.591A pdb=" N ASP I 127 " --> pdb=" O ARG I 123 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ALA I 128 " --> pdb=" O ARG I 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 133 through 156 removed outlier: 3.661A pdb=" N LEU I 139 " --> pdb=" O SER I 135 " (cutoff:3.500A) Processing helix chain 'K' and resid 16 through 44 removed outlier: 3.688A pdb=" N VAL K 26 " --> pdb=" O ASN K 22 " (cutoff:3.500A) Processing helix chain 'K' and resid 48 through 77 removed outlier: 4.025A pdb=" N LEU K 52 " --> pdb=" O ASN K 48 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP K 57 " --> pdb=" O HIS K 53 " (cutoff:3.500A) Processing helix chain 'K' and resid 84 through 92 Processing helix chain 'K' and resid 103 through 133 removed outlier: 4.175A pdb=" N ASP K 127 " --> pdb=" O ARG K 123 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ALA K 128 " --> pdb=" O ARG K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 133 through 156 removed outlier: 3.649A pdb=" N LEU K 139 " --> pdb=" O SER K 135 " (cutoff:3.500A) Processing helix chain 'K' and resid 157 through 159 No H-bonds generated for 'chain 'K' and resid 157 through 159' Processing helix chain 'F' and resid 16 through 44 Processing helix chain 'F' and resid 48 through 77 Processing helix chain 'F' and resid 84 through 92 Processing helix chain 'F' and resid 103 through 133 removed outlier: 4.181A pdb=" N ASP F 127 " --> pdb=" O ARG F 123 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N ALA F 128 " --> pdb=" O ARG F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 156 removed outlier: 3.814A pdb=" N LEU F 139 " --> pdb=" O SER F 135 " (cutoff:3.500A) Processing helix chain 'H' and resid 16 through 44 removed outlier: 3.582A pdb=" N ASP H 29 " --> pdb=" O LYS H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 77 removed outlier: 3.835A pdb=" N LEU H 52 " --> pdb=" O ASN H 48 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP H 57 " --> pdb=" O HIS H 53 " (cutoff:3.500A) Processing helix chain 'H' and resid 84 through 92 Processing helix chain 'H' and resid 103 through 131 removed outlier: 4.565A pdb=" N ASP H 127 " --> pdb=" O ARG H 123 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ALA H 128 " --> pdb=" O ARG H 124 " (cutoff:3.500A) Processing helix chain 'H' and resid 133 through 156 removed outlier: 3.575A pdb=" N LEU H 139 " --> pdb=" O SER H 135 " (cutoff:3.500A) Processing helix chain 'H' and resid 157 through 159 No H-bonds generated for 'chain 'H' and resid 157 through 159' Processing helix chain 'J' and resid 16 through 43 removed outlier: 3.604A pdb=" N ASP J 29 " --> pdb=" O LYS J 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 48 through 77 Processing helix chain 'J' and resid 84 through 92 Processing helix chain 'J' and resid 104 through 133 removed outlier: 4.588A pdb=" N ASP J 127 " --> pdb=" O ARG J 123 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N ALA J 128 " --> pdb=" O ARG J 124 " (cutoff:3.500A) Processing helix chain 'J' and resid 133 through 156 removed outlier: 3.681A pdb=" N LEU J 139 " --> pdb=" O SER J 135 " (cutoff:3.500A) Processing helix chain 'J' and resid 157 through 159 No H-bonds generated for 'chain 'J' and resid 157 through 159' Processing helix chain 'L' and resid 16 through 44 removed outlier: 3.680A pdb=" N VAL L 26 " --> pdb=" O ASN L 22 " (cutoff:3.500A) Processing helix chain 'L' and resid 48 through 77 removed outlier: 4.037A pdb=" N LEU L 52 " --> pdb=" O ASN L 48 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP L 57 " --> pdb=" O HIS L 53 " (cutoff:3.500A) Processing helix chain 'L' and resid 84 through 92 Processing helix chain 'L' and resid 103 through 133 removed outlier: 4.196A pdb=" N ASP L 127 " --> pdb=" O ARG L 123 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ALA L 128 " --> pdb=" O ARG L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 133 through 156 removed outlier: 3.624A pdb=" N LEU L 139 " --> pdb=" O SER L 135 " (cutoff:3.500A) Processing helix chain 'L' and resid 157 through 159 No H-bonds generated for 'chain 'L' and resid 157 through 159' Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 45 Processing sheet with id=AA2, first strand: chain 'C' and resid 44 through 45 Processing sheet with id=AA3, first strand: chain 'I' and resid 44 through 45 Processing sheet with id=AA4, first strand: chain 'J' and resid 44 through 45 1169 hydrogen bonds defined for protein. 3507 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.23 Time building geometry restraints manager: 1.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5348 1.34 - 1.45: 1292 1.45 - 1.57: 8483 1.57 - 1.69: 0 1.69 - 1.80: 24 Bond restraints: 15147 Sorted by residual: bond pdb=" C VAL E 125 " pdb=" O VAL E 125 " ideal model delta sigma weight residual 1.237 1.252 -0.014 1.29e-02 6.01e+03 1.26e+00 bond pdb=" C VAL F 125 " pdb=" O VAL F 125 " ideal model delta sigma weight residual 1.237 1.251 -0.014 1.29e-02 6.01e+03 1.14e+00 bond pdb=" C VAL A 125 " pdb=" O VAL A 125 " ideal model delta sigma weight residual 1.236 1.251 -0.014 1.35e-02 5.49e+03 1.13e+00 bond pdb=" SD MET H 74 " pdb=" CE MET H 74 " ideal model delta sigma weight residual 1.791 1.766 0.025 2.50e-02 1.60e+03 9.90e-01 bond pdb=" CB VAL D 125 " pdb=" CG2 VAL D 125 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.48e-01 ... (remaining 15142 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 20155 1.61 - 3.23: 393 3.23 - 4.84: 43 4.84 - 6.46: 0 6.46 - 8.07: 1 Bond angle restraints: 20592 Sorted by residual: angle pdb=" N HIS G 126 " pdb=" CA HIS G 126 " pdb=" C HIS G 126 " ideal model delta sigma weight residual 111.07 115.72 -4.65 1.07e+00 8.73e-01 1.89e+01 angle pdb=" N HIS B 126 " pdb=" CA HIS B 126 " pdb=" C HIS B 126 " ideal model delta sigma weight residual 111.07 115.19 -4.12 1.07e+00 8.73e-01 1.48e+01 angle pdb=" N HIS H 126 " pdb=" CA HIS H 126 " pdb=" C HIS H 126 " ideal model delta sigma weight residual 111.07 114.32 -3.25 1.07e+00 8.73e-01 9.21e+00 angle pdb=" N HIS I 126 " pdb=" CA HIS I 126 " pdb=" C HIS I 126 " ideal model delta sigma weight residual 111.28 114.44 -3.16 1.09e+00 8.42e-01 8.39e+00 angle pdb=" N HIS C 126 " pdb=" CA HIS C 126 " pdb=" C HIS C 126 " ideal model delta sigma weight residual 111.28 114.32 -3.04 1.09e+00 8.42e-01 7.76e+00 ... (remaining 20587 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.33: 8473 17.33 - 34.66: 503 34.66 - 51.99: 102 51.99 - 69.32: 39 69.32 - 86.65: 27 Dihedral angle restraints: 9144 sinusoidal: 3612 harmonic: 5532 Sorted by residual: dihedral pdb=" CA PRO E 98 " pdb=" C PRO E 98 " pdb=" N ALA E 99 " pdb=" CA ALA E 99 " ideal model delta harmonic sigma weight residual -180.00 -161.89 -18.11 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA PRO F 98 " pdb=" C PRO F 98 " pdb=" N ALA F 99 " pdb=" CA ALA F 99 " ideal model delta harmonic sigma weight residual 180.00 -162.60 -17.40 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA TRP F 42 " pdb=" C TRP F 42 " pdb=" N ASN F 43 " pdb=" CA ASN F 43 " ideal model delta harmonic sigma weight residual 180.00 -163.08 -16.92 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 9141 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1390 0.026 - 0.051: 625 0.051 - 0.077: 292 0.077 - 0.103: 79 0.103 - 0.129: 29 Chirality restraints: 2415 Sorted by residual: chirality pdb=" CA ASP F 145 " pdb=" N ASP F 145 " pdb=" C ASP F 145 " pdb=" CB ASP F 145 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.14e-01 chirality pdb=" CA ASP E 145 " pdb=" N ASP E 145 " pdb=" C ASP E 145 " pdb=" CB ASP E 145 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.12e-01 chirality pdb=" CB VAL G 45 " pdb=" CA VAL G 45 " pdb=" CG1 VAL G 45 " pdb=" CG2 VAL G 45 " both_signs ideal model delta sigma weight residual False -2.63 -2.51 -0.12 2.00e-01 2.50e+01 3.67e-01 ... (remaining 2412 not shown) Planarity restraints: 2754 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE J 97 " 0.023 5.00e-02 4.00e+02 3.44e-02 1.89e+00 pdb=" N PRO J 98 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO J 98 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO J 98 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE I 97 " 0.022 5.00e-02 4.00e+02 3.40e-02 1.85e+00 pdb=" N PRO I 98 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO I 98 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO I 98 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 97 " -0.022 5.00e-02 4.00e+02 3.39e-02 1.84e+00 pdb=" N PRO C 98 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO C 98 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 98 " -0.019 5.00e-02 4.00e+02 ... (remaining 2751 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2403 2.77 - 3.30: 15393 3.30 - 3.83: 25703 3.83 - 4.37: 29101 4.37 - 4.90: 52650 Nonbonded interactions: 125250 Sorted by model distance: nonbonded pdb=" OE1 GLN K 39 " pdb=" ND2 ASN K 43 " model vdw 2.234 3.120 nonbonded pdb=" O THR C 87 " pdb=" OG1 THR C 91 " model vdw 2.258 3.040 nonbonded pdb=" OE1 GLN D 39 " pdb=" ND2 ASN D 43 " model vdw 2.260 3.120 nonbonded pdb=" OE1 GLN L 39 " pdb=" ND2 ASN L 43 " model vdw 2.274 3.120 nonbonded pdb=" OE1 GLN I 39 " pdb=" ND2 ASN I 43 " model vdw 2.287 3.120 ... (remaining 125245 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 'A' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 5 or (resid 6 and (name N or name CA or name C or \ name O or name CB )) or (resid 7 through 8 and (name N or name CA or name C or \ name O )) or (resid 9 through 10 and (name N or name CA or name C or name O or n \ ame CB )) or resid 11 through 14 or (resid 15 and (name N or name CA or name C o \ r name O )) or resid 16 through 64 or (resid 65 and (name N or name CA or name C \ or name O or name CB )) or resid 66 through 159 or (resid 160 and (name N or na \ me CA or name C or name O or name CB )) or resid 161)) selection = (chain 'B' and (resid 2 through 5 or (resid 6 and (name N or name CA or name C o \ r name O or name CB )) or (resid 7 through 8 and (name N or name CA or name C or \ name O )) or (resid 9 through 10 and (name N or name CA or name C or name O or \ name CB )) or resid 11 through 14 or (resid 15 and (name N or name CA or name C \ or name O )) or resid 16 through 64 or (resid 65 and (name N or name CA or name \ C or name O or name CB )) or resid 66 through 159 or (resid 160 and (name N or n \ ame CA or name C or name O or name CB )) or resid 161)) selection = (chain 'C' and (resid 2 through 5 or (resid 6 and (name N or name CA or name C o \ r name O or name CB )) or (resid 7 through 8 and (name N or name CA or name C or \ name O )) or (resid 9 through 10 and (name N or name CA or name C or name O or \ name CB )) or resid 11 through 14 or (resid 15 and (name N or name CA or name C \ or name O )) or resid 16 through 64 or (resid 65 and (name N or name CA or name \ C or name O or name CB )) or resid 66 through 159 or (resid 160 and (name N or n \ ame CA or name C or name O or name CB )) or resid 161)) selection = (chain 'D' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 161)) selection = (chain 'E' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 5 or (resid 6 and (name N or name CA or name C or \ name O or name CB )) or (resid 7 through 8 and (name N or name CA or name C or \ name O )) or (resid 9 through 10 and (name N or name CA or name C or name O or n \ ame CB )) or resid 11 through 14 or (resid 15 and (name N or name CA or name C o \ r name O )) or resid 16 through 64 or (resid 65 and (name N or name CA or name C \ or name O or name CB )) or resid 66 through 159 or (resid 160 and (name N or na \ me CA or name C or name O or name CB )) or resid 161)) selection = (chain 'F' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 5 or (resid 6 and (name N or name CA or name C or \ name O or name CB )) or (resid 7 through 8 and (name N or name CA or name C or \ name O )) or (resid 9 through 10 and (name N or name CA or name C or name O or n \ ame CB )) or resid 11 through 14 or (resid 15 and (name N or name CA or name C o \ r name O )) or resid 16 through 64 or (resid 65 and (name N or name CA or name C \ or name O or name CB )) or resid 66 through 159 or (resid 160 and (name N or na \ me CA or name C or name O or name CB )) or resid 161)) selection = (chain 'G' and (resid 2 through 5 or (resid 6 and (name N or name CA or name C o \ r name O or name CB )) or (resid 7 through 8 and (name N or name CA or name C or \ name O )) or (resid 9 through 10 and (name N or name CA or name C or name O or \ name CB )) or resid 11 through 14 or (resid 15 and (name N or name CA or name C \ or name O )) or resid 16 through 64 or (resid 65 and (name N or name CA or name \ C or name O or name CB )) or resid 66 through 159 or (resid 160 and (name N or n \ ame CA or name C or name O or name CB )) or resid 161)) selection = (chain 'H' and (resid 2 through 5 or (resid 6 and (name N or name CA or name C o \ r name O or name CB )) or (resid 7 through 8 and (name N or name CA or name C or \ name O )) or (resid 9 through 10 and (name N or name CA or name C or name O or \ name CB )) or resid 11 through 14 or (resid 15 and (name N or name CA or name C \ or name O )) or resid 16 through 64 or (resid 65 and (name N or name CA or name \ C or name O or name CB )) or resid 66 through 159 or (resid 160 and (name N or n \ ame CA or name C or name O or name CB )) or resid 161)) selection = (chain 'I' and (resid 2 through 5 or (resid 6 and (name N or name CA or name C o \ r name O or name CB )) or (resid 7 through 8 and (name N or name CA or name C or \ name O )) or (resid 9 through 10 and (name N or name CA or name C or name O or \ name CB )) or resid 11 through 14 or (resid 15 and (name N or name CA or name C \ or name O )) or resid 16 through 64 or (resid 65 and (name N or name CA or name \ C or name O or name CB )) or resid 66 through 159 or (resid 160 and (name N or n \ ame CA or name C or name O or name CB )) or resid 161)) selection = (chain 'J' and (resid 2 through 5 or (resid 6 and (name N or name CA or name C o \ r name O or name CB )) or (resid 7 through 8 and (name N or name CA or name C or \ name O )) or (resid 9 through 10 and (name N or name CA or name C or name O or \ name CB )) or resid 11 through 14 or (resid 15 and (name N or name CA or name C \ or name O )) or resid 16 through 64 or (resid 65 and (name N or name CA or name \ C or name O or name CB )) or resid 66 through 159 or (resid 160 and (name N or n \ ame CA or name C or name O or name CB )) or resid 161)) selection = (chain 'K' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 161)) selection = (chain 'L' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 161)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.330 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: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.810 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15147 Z= 0.163 Angle : 0.545 8.075 20592 Z= 0.335 Chirality : 0.036 0.129 2415 Planarity : 0.004 0.039 2754 Dihedral : 13.324 86.651 5526 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 0.06 % Allowed : 0.00 % Favored : 99.94 % 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 are not related in a simple way. whole: 3.64 (0.19), residues: 1902 helix: 3.09 (0.13), residues: 1434 sheet: None (None), residues: 0 loop : 0.17 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 155 PHE 0.011 0.002 PHE H 19 TRP 0.003 0.001 TRP C 42 HIS 0.008 0.002 HIS J 53 Details of bonding type rmsd covalent geometry : bond 0.00322 (15147) covalent geometry : angle 0.54504 (20592) hydrogen bonds : bond 0.09258 ( 1169) hydrogen bonds : angle 3.63885 ( 3507) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 102 time to evaluate : 0.544 Fit side-chains outliers start: 1 outliers final: 2 residues processed: 103 average time/residue: 0.8948 time to fit residues: 98.6906 Evaluate side-chains 84 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 82 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain L residue 29 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 55 GLN C 150 GLN ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 HIS ** D 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 55 GLN G 150 GLN ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 55 GLN I 150 GLN ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 41 HIS ** K 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 55 GLN K 150 GLN ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 55 GLN J 150 GLN ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 41 HIS ** L 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 55 GLN L 150 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.127808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.105156 restraints weight = 15573.011| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.63 r_work: 0.3127 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.0868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 15147 Z= 0.209 Angle : 0.536 5.438 20592 Z= 0.304 Chirality : 0.040 0.162 2415 Planarity : 0.004 0.036 2754 Dihedral : 4.641 56.224 2086 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 0.31 % Allowed : 4.03 % Favored : 95.66 % 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 are not related in a simple way. whole: 3.28 (0.19), residues: 1902 helix: 2.80 (0.13), residues: 1434 sheet: None (None), residues: 0 loop : 0.13 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 159 PHE 0.014 0.002 PHE D 19 TRP 0.006 0.001 TRP L 152 HIS 0.013 0.002 HIS J 53 Details of bonding type rmsd covalent geometry : bond 0.00488 (15147) covalent geometry : angle 0.53629 (20592) hydrogen bonds : bond 0.08947 ( 1169) hydrogen bonds : angle 3.69318 ( 3507) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 111 time to evaluate : 0.493 Fit side-chains REVERT: E 82 ASP cc_start: 0.8975 (t70) cc_final: 0.8707 (t70) REVERT: F 86 ASP cc_start: 0.7161 (m-30) cc_final: 0.6614 (m-30) outliers start: 5 outliers final: 1 residues processed: 115 average time/residue: 0.7906 time to fit residues: 98.3463 Evaluate side-chains 99 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 98 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 29 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 61 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 176 optimal weight: 20.0000 chunk 75 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 181 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 156 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 121 optimal weight: 4.9990 chunk 118 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 HIS ** D 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 55 GLN D 150 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 41 HIS ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.136809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.113986 restraints weight = 15393.712| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.67 r_work: 0.3231 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.0936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 15147 Z= 0.130 Angle : 0.436 5.457 20592 Z= 0.247 Chirality : 0.035 0.150 2415 Planarity : 0.003 0.032 2754 Dihedral : 4.278 55.149 2084 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Rotamer: Outliers : 0.50 % Allowed : 5.35 % Favored : 94.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.72 (0.19), residues: 1902 helix: 3.15 (0.13), residues: 1434 sheet: None (None), residues: 0 loop : 0.18 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 114 PHE 0.011 0.002 PHE H 49 TRP 0.004 0.001 TRP F 42 HIS 0.011 0.002 HIS J 53 Details of bonding type rmsd covalent geometry : bond 0.00246 (15147) covalent geometry : angle 0.43611 (20592) hydrogen bonds : bond 0.06444 ( 1169) hydrogen bonds : angle 3.44080 ( 3507) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 0.690 Fit side-chains REVERT: J 148 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7410 (mt-10) outliers start: 8 outliers final: 5 residues processed: 90 average time/residue: 0.9442 time to fit residues: 91.0128 Evaluate side-chains 87 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain I residue 29 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 74 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 151 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 150 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 166 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 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 = 0.3524 r_free = 0.3524 target = 0.132523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.109708 restraints weight = 15589.144| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.64 r_work: 0.3198 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.0987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 15147 Z= 0.148 Angle : 0.450 5.700 20592 Z= 0.253 Chirality : 0.035 0.154 2415 Planarity : 0.003 0.034 2754 Dihedral : 4.303 55.333 2082 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 0.63 % Allowed : 6.35 % Favored : 93.02 % 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 are not related in a simple way. whole: 3.67 (0.19), residues: 1902 helix: 3.10 (0.13), residues: 1434 sheet: None (None), residues: 0 loop : 0.21 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 159 PHE 0.011 0.002 PHE H 49 TRP 0.003 0.001 TRP F 42 HIS 0.010 0.002 HIS J 53 Details of bonding type rmsd covalent geometry : bond 0.00308 (15147) covalent geometry : angle 0.45046 (20592) hydrogen bonds : bond 0.07090 ( 1169) hydrogen bonds : angle 3.44598 ( 3507) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.478 Fit side-chains REVERT: A 148 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7645 (mt-10) REVERT: E 82 ASP cc_start: 0.8825 (t0) cc_final: 0.8465 (t70) REVERT: J 148 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7459 (mt-10) outliers start: 10 outliers final: 9 residues processed: 87 average time/residue: 0.8949 time to fit residues: 83.3983 Evaluate side-chains 87 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain I residue 29 ASP Chi-restraints excluded: chain K residue 29 ASP Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain L residue 29 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 113 optimal weight: 4.9990 chunk 104 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 161 optimal weight: 5.9990 chunk 126 optimal weight: 0.7980 chunk 166 optimal weight: 5.9990 chunk 116 optimal weight: 0.6980 chunk 129 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 HIS ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 41 HIS ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.127568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.104769 restraints weight = 15775.417| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.65 r_work: 0.3068 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 15147 Z= 0.197 Angle : 0.508 5.878 20592 Z= 0.285 Chirality : 0.038 0.157 2415 Planarity : 0.004 0.036 2754 Dihedral : 4.569 55.354 2082 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 0.94 % Allowed : 6.86 % Favored : 92.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.28 (0.19), residues: 1902 helix: 2.80 (0.13), residues: 1434 sheet: None (None), residues: 0 loop : 0.11 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 102 PHE 0.012 0.002 PHE L 19 TRP 0.005 0.001 TRP L 152 HIS 0.011 0.002 HIS J 53 Details of bonding type rmsd covalent geometry : bond 0.00454 (15147) covalent geometry : angle 0.50827 (20592) hydrogen bonds : bond 0.08646 ( 1169) hydrogen bonds : angle 3.61329 ( 3507) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.511 Fit side-chains REVERT: A 45 VAL cc_start: 0.7731 (OUTLIER) cc_final: 0.7422 (m) REVERT: A 148 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7727 (mt-10) REVERT: C 157 GLU cc_start: 0.7548 (tp30) cc_final: 0.7244 (tp30) REVERT: F 101 GLU cc_start: 0.7645 (mt-10) cc_final: 0.7401 (mt-10) REVERT: J 127 ASP cc_start: 0.6692 (m-30) cc_final: 0.6416 (t70) REVERT: J 148 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7561 (mt-10) outliers start: 15 outliers final: 9 residues processed: 122 average time/residue: 0.7694 time to fit residues: 101.5788 Evaluate side-chains 113 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain I residue 29 ASP Chi-restraints excluded: chain I residue 65 GLU Chi-restraints excluded: chain H residue 29 ASP Chi-restraints excluded: chain L residue 29 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 107 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 129 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 GLN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.128339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.105644 restraints weight = 15648.136| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.64 r_work: 0.3122 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 15147 Z= 0.181 Angle : 0.490 5.852 20592 Z= 0.276 Chirality : 0.037 0.155 2415 Planarity : 0.004 0.034 2754 Dihedral : 4.545 55.253 2082 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.01 % Allowed : 7.86 % Favored : 91.13 % 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 are not related in a simple way. whole: 3.28 (0.19), residues: 1902 helix: 2.80 (0.13), residues: 1434 sheet: None (None), residues: 0 loop : 0.11 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 102 PHE 0.012 0.002 PHE H 49 TRP 0.004 0.001 TRP L 152 HIS 0.011 0.002 HIS J 53 Details of bonding type rmsd covalent geometry : bond 0.00407 (15147) covalent geometry : angle 0.48960 (20592) hydrogen bonds : bond 0.08200 ( 1169) hydrogen bonds : angle 3.58616 ( 3507) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.598 Fit side-chains REVERT: A 45 VAL cc_start: 0.7785 (OUTLIER) cc_final: 0.7502 (m) REVERT: A 148 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7854 (mt-10) REVERT: C 157 GLU cc_start: 0.7632 (tp30) cc_final: 0.7342 (tp30) REVERT: F 101 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7412 (mt-10) REVERT: H 150 GLN cc_start: 0.8034 (OUTLIER) cc_final: 0.7816 (mm-40) REVERT: J 148 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7646 (mt-10) outliers start: 16 outliers final: 13 residues processed: 105 average time/residue: 0.8517 time to fit residues: 96.1297 Evaluate side-chains 106 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain I residue 29 ASP Chi-restraints excluded: chain I residue 65 GLU Chi-restraints excluded: chain I residue 127 ASP Chi-restraints excluded: chain K residue 29 ASP Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain H residue 150 GLN Chi-restraints excluded: chain L residue 29 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 84 optimal weight: 0.9980 chunk 48 optimal weight: 20.0000 chunk 129 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 4 optimal weight: 0.6980 chunk 148 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 47 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 157 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 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 = 0.3559 r_free = 0.3559 target = 0.135412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.112658 restraints weight = 15309.811| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.65 r_work: 0.3188 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 15147 Z= 0.133 Angle : 0.430 5.618 20592 Z= 0.243 Chirality : 0.034 0.148 2415 Planarity : 0.003 0.032 2754 Dihedral : 4.288 55.010 2082 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 1.38 % Allowed : 7.55 % Favored : 91.07 % 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 are not related in a simple way. whole: 3.72 (0.19), residues: 1902 helix: 3.14 (0.13), residues: 1434 sheet: None (None), residues: 0 loop : 0.20 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 114 PHE 0.012 0.002 PHE H 49 TRP 0.004 0.001 TRP A 42 HIS 0.010 0.002 HIS J 53 Details of bonding type rmsd covalent geometry : bond 0.00263 (15147) covalent geometry : angle 0.43004 (20592) hydrogen bonds : bond 0.06501 ( 1169) hydrogen bonds : angle 3.41231 ( 3507) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 73 time to evaluate : 0.605 Fit side-chains REVERT: A 45 VAL cc_start: 0.7558 (OUTLIER) cc_final: 0.7275 (m) REVERT: A 148 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7718 (mt-10) REVERT: C 157 GLU cc_start: 0.7588 (tp30) cc_final: 0.7302 (tp30) REVERT: H 157 GLU cc_start: 0.7648 (tp30) cc_final: 0.7291 (tp30) REVERT: J 148 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7449 (mt-10) outliers start: 22 outliers final: 11 residues processed: 92 average time/residue: 0.8858 time to fit residues: 87.5591 Evaluate side-chains 81 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain I residue 65 GLU Chi-restraints excluded: chain I residue 127 ASP Chi-restraints excluded: chain H residue 45 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 1 optimal weight: 8.9990 chunk 82 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 chunk 74 optimal weight: 0.0000 chunk 137 optimal weight: 10.0000 chunk 79 optimal weight: 0.0770 chunk 16 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 135 optimal weight: 3.9990 chunk 169 optimal weight: 0.9990 overall best weight: 1.8148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 48 ASN ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 55 GLN ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.130705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.107921 restraints weight = 15647.948| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.68 r_work: 0.3097 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 15147 Z= 0.171 Angle : 0.476 5.850 20592 Z= 0.267 Chirality : 0.037 0.152 2415 Planarity : 0.004 0.035 2754 Dihedral : 4.486 55.365 2082 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.26 % Allowed : 7.92 % Favored : 90.82 % 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 are not related in a simple way. whole: 3.43 (0.19), residues: 1902 helix: 2.92 (0.13), residues: 1434 sheet: None (None), residues: 0 loop : 0.15 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 102 PHE 0.011 0.002 PHE H 49 TRP 0.004 0.001 TRP L 152 HIS 0.010 0.002 HIS J 53 Details of bonding type rmsd covalent geometry : bond 0.00378 (15147) covalent geometry : angle 0.47633 (20592) hydrogen bonds : bond 0.07864 ( 1169) hydrogen bonds : angle 3.51940 ( 3507) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 0.521 Fit side-chains REVERT: A 45 VAL cc_start: 0.7688 (OUTLIER) cc_final: 0.7399 (m) REVERT: A 148 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7750 (mt-10) REVERT: C 157 GLU cc_start: 0.7594 (tp30) cc_final: 0.7300 (tp30) REVERT: H 157 GLU cc_start: 0.7678 (tp30) cc_final: 0.7304 (tp30) REVERT: J 148 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7545 (mt-10) outliers start: 20 outliers final: 13 residues processed: 107 average time/residue: 0.7412 time to fit residues: 85.7286 Evaluate side-chains 106 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain I residue 29 ASP Chi-restraints excluded: chain I residue 65 GLU Chi-restraints excluded: chain I residue 127 ASP Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain H residue 29 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 53 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 176 optimal weight: 7.9990 chunk 4 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 chunk 172 optimal weight: 1.9990 chunk 182 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 ASN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.129438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.110273 restraints weight = 15589.425| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.18 r_work: 0.3113 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15147 Z= 0.139 Angle : 0.439 5.933 20592 Z= 0.248 Chirality : 0.035 0.149 2415 Planarity : 0.003 0.033 2754 Dihedral : 4.321 54.888 2082 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 1.26 % Allowed : 8.05 % Favored : 90.69 % 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 are not related in a simple way. whole: 3.68 (0.19), residues: 1902 helix: 3.12 (0.13), residues: 1434 sheet: None (None), residues: 0 loop : 0.17 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 102 PHE 0.012 0.002 PHE H 49 TRP 0.004 0.001 TRP A 42 HIS 0.010 0.002 HIS J 53 Details of bonding type rmsd covalent geometry : bond 0.00275 (15147) covalent geometry : angle 0.43945 (20592) hydrogen bonds : bond 0.06824 ( 1169) hydrogen bonds : angle 3.42589 ( 3507) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 69 time to evaluate : 0.591 Fit side-chains REVERT: H 157 GLU cc_start: 0.8032 (tp30) cc_final: 0.7703 (tp30) REVERT: J 148 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8129 (mt-10) outliers start: 20 outliers final: 16 residues processed: 86 average time/residue: 0.9683 time to fit residues: 89.0549 Evaluate side-chains 84 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain I residue 29 ASP Chi-restraints excluded: chain I residue 65 GLU Chi-restraints excluded: chain I residue 127 ASP Chi-restraints excluded: chain K residue 29 ASP Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain L residue 127 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 187 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 119 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 65 optimal weight: 0.0070 chunk 155 optimal weight: 3.9990 chunk 162 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 121 optimal weight: 0.0570 overall best weight: 0.9720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 24 GLN ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 ASN ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 41 HIS ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.131897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.112791 restraints weight = 15463.158| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.17 r_work: 0.3147 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 15147 Z= 0.128 Angle : 0.423 5.549 20592 Z= 0.239 Chirality : 0.034 0.147 2415 Planarity : 0.003 0.033 2754 Dihedral : 4.224 54.453 2082 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 1.01 % Allowed : 8.36 % Favored : 90.63 % 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 are not related in a simple way. whole: 3.84 (0.19), residues: 1902 helix: 3.23 (0.13), residues: 1434 sheet: None (None), residues: 0 loop : 0.25 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 50 PHE 0.012 0.002 PHE H 49 TRP 0.005 0.001 TRP A 42 HIS 0.009 0.002 HIS J 53 Details of bonding type rmsd covalent geometry : bond 0.00248 (15147) covalent geometry : angle 0.42322 (20592) hydrogen bonds : bond 0.06249 ( 1169) hydrogen bonds : angle 3.35084 ( 3507) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.450 Fit side-chains REVERT: J 148 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8143 (mt-10) outliers start: 16 outliers final: 14 residues processed: 78 average time/residue: 0.9864 time to fit residues: 82.3477 Evaluate side-chains 75 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain I residue 29 ASP Chi-restraints excluded: chain I residue 65 GLU Chi-restraints excluded: chain I residue 127 ASP Chi-restraints excluded: chain K residue 29 ASP Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain L residue 127 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 189 optimal weight: 0.9990 chunk 185 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 65 optimal weight: 0.3980 chunk 137 optimal weight: 8.9990 chunk 97 optimal weight: 9.9990 chunk 170 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 41 HIS ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.125182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.106121 restraints weight = 15680.914| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.17 r_work: 0.3073 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 15147 Z= 0.174 Angle : 0.481 5.596 20592 Z= 0.270 Chirality : 0.037 0.153 2415 Planarity : 0.004 0.035 2754 Dihedral : 4.488 54.884 2082 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.07 % Allowed : 8.43 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.47 (0.19), residues: 1902 helix: 2.94 (0.13), residues: 1434 sheet: None (None), residues: 0 loop : 0.20 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 114 PHE 0.012 0.002 PHE G 49 TRP 0.004 0.001 TRP L 152 HIS 0.010 0.002 HIS J 53 Details of bonding type rmsd covalent geometry : bond 0.00389 (15147) covalent geometry : angle 0.48075 (20592) hydrogen bonds : bond 0.07934 ( 1169) hydrogen bonds : angle 3.51103 ( 3507) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3922.20 seconds wall clock time: 67 minutes 37.51 seconds (4057.51 seconds total)