Starting phenix.real_space_refine on Wed Mar 4 15:36:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hx1_35071/03_2026/8hx1_35071.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hx1_35071/03_2026/8hx1_35071.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hx1_35071/03_2026/8hx1_35071.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hx1_35071/03_2026/8hx1_35071.map" model { file = "/net/cci-nas-00/data/ceres_data/8hx1_35071/03_2026/8hx1_35071.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hx1_35071/03_2026/8hx1_35071.cif" } resolution = 3.29 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= 0.252 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 49 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: 3.69, per 1000 atoms: 0.25 Number of scatterers: 14919 At special positions: 0 Unit cell: (106.8, 105.6, 103.2, 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: 1.09 Conformation dependent library (CDL) restraints added in 691.4 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: 67 helices and 7 sheets defined 76.7% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 16 through 44 Processing helix chain 'A' and resid 48 through 77 removed outlier: 3.558A pdb=" N ASP A 57 " --> pdb=" O HIS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 92 Processing helix chain 'A' and resid 103 through 133 removed outlier: 4.312A pdb=" N ASP A 127 " --> pdb=" O ARG A 123 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N ALA A 128 " --> pdb=" O ARG A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 156 removed outlier: 3.788A pdb=" N LEU A 139 " --> pdb=" O SER A 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 44 removed outlier: 3.640A pdb=" N ASP B 29 " --> pdb=" O LYS B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 77 removed outlier: 4.033A pdb=" N LEU B 52 " --> pdb=" O ASN B 48 " (cutoff:3.500A) removed outlier: 3.865A 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: 4.548A pdb=" N ASP B 127 " --> pdb=" O ARG B 123 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ALA B 128 " --> pdb=" O ARG B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 156 removed outlier: 3.645A pdb=" N LEU B 139 " --> pdb=" O SER B 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 43 removed outlier: 3.700A pdb=" N ASP C 29 " --> pdb=" O LYS C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 77 removed outlier: 3.597A pdb=" N ASP C 57 " --> pdb=" O HIS C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 92 Processing helix chain 'C' and resid 104 through 133 removed outlier: 3.515A pdb=" N ILE C 122 " --> pdb=" O THR C 118 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ASP C 127 " --> pdb=" O ARG C 123 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N ALA C 128 " --> pdb=" O ARG C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 156 removed outlier: 3.780A 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 43 removed outlier: 3.841A pdb=" N VAL D 26 " --> pdb=" O ASN D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 77 removed outlier: 3.902A pdb=" N LEU D 52 " --> pdb=" O ASN D 48 " (cutoff:3.500A) removed outlier: 3.699A 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 104 through 133 removed outlier: 4.281A pdb=" N ASP D 127 " --> pdb=" O ARG D 123 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ALA D 128 " --> pdb=" O ARG D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 156 removed outlier: 3.666A 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 removed outlier: 3.542A pdb=" N ASP E 57 " --> pdb=" O HIS E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 92 Processing helix chain 'E' and resid 103 through 133 removed outlier: 4.291A pdb=" N ASP E 127 " --> pdb=" O ARG E 123 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N ALA E 128 " --> pdb=" O ARG E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 156 removed outlier: 3.692A pdb=" N LEU E 139 " --> pdb=" O SER E 135 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 44 removed outlier: 3.706A pdb=" N ASP G 29 " --> pdb=" O LYS G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 77 removed outlier: 4.054A pdb=" N LEU G 52 " --> pdb=" O ASN G 48 " (cutoff:3.500A) removed outlier: 3.859A 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: 4.528A pdb=" N ASP G 127 " --> pdb=" O ARG G 123 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N ALA G 128 " --> pdb=" O ARG G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 156 removed outlier: 3.626A pdb=" N LEU G 139 " --> pdb=" O SER G 135 " (cutoff:3.500A) Processing helix chain 'I' and resid 16 through 43 removed outlier: 3.751A pdb=" N ASP I 29 " --> pdb=" O LYS I 25 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 77 removed outlier: 3.597A pdb=" N ASP I 57 " --> pdb=" O HIS I 53 " (cutoff:3.500A) Processing helix chain 'I' and resid 84 through 92 Processing helix chain 'I' and resid 104 through 133 removed outlier: 4.414A pdb=" N ASP I 127 " --> pdb=" O ARG I 123 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N ALA I 128 " --> pdb=" O ARG I 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 133 through 156 removed outlier: 3.679A pdb=" N LEU I 139 " --> pdb=" O SER I 135 " (cutoff:3.500A) Processing helix chain 'I' and resid 157 through 159 No H-bonds generated for 'chain 'I' and resid 157 through 159' Processing helix chain 'K' and resid 16 through 43 removed outlier: 3.816A pdb=" N VAL K 26 " --> pdb=" O ASN K 22 " (cutoff:3.500A) Processing helix chain 'K' and resid 48 through 77 removed outlier: 3.956A pdb=" N LEU K 52 " --> pdb=" O ASN K 48 " (cutoff:3.500A) removed outlier: 3.743A 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 104 through 133 removed outlier: 4.327A pdb=" N ASP K 127 " --> pdb=" O ARG K 123 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ALA K 128 " --> pdb=" O ARG K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 133 through 156 removed outlier: 3.669A 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 43 Processing helix chain 'F' and resid 48 through 77 removed outlier: 3.529A pdb=" N ASP F 57 " --> pdb=" O HIS F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 92 Processing helix chain 'F' and resid 104 through 133 removed outlier: 4.352A pdb=" N ASP F 127 " --> pdb=" O ARG F 123 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ALA F 128 " --> pdb=" O ARG F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 156 removed outlier: 3.733A pdb=" N LEU F 139 " --> pdb=" O SER F 135 " (cutoff:3.500A) Processing helix chain 'H' and resid 16 through 44 removed outlier: 3.706A pdb=" N ASP H 29 " --> pdb=" O LYS H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 77 removed outlier: 4.001A pdb=" N LEU H 52 " --> pdb=" O ASN H 48 " (cutoff:3.500A) removed outlier: 3.879A 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: 4.530A pdb=" N ASP H 127 " --> pdb=" O ARG H 123 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N ALA H 128 " --> pdb=" O ARG H 124 " (cutoff:3.500A) Processing helix chain 'H' and resid 133 through 156 removed outlier: 3.769A 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: 3.744A pdb=" N ASP J 29 " --> pdb=" O LYS J 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 48 through 77 removed outlier: 3.569A pdb=" N ASP J 57 " --> pdb=" O HIS J 53 " (cutoff:3.500A) Processing helix chain 'J' and resid 84 through 92 Processing helix chain 'J' and resid 104 through 133 removed outlier: 4.711A pdb=" N ASP J 127 " --> pdb=" O ARG J 123 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N ALA J 128 " --> pdb=" O ARG J 124 " (cutoff:3.500A) Processing helix chain 'J' and resid 133 through 156 removed outlier: 3.770A 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 43 removed outlier: 3.893A pdb=" N VAL L 26 " --> pdb=" O ASN L 22 " (cutoff:3.500A) Processing helix chain 'L' and resid 48 through 77 removed outlier: 3.996A pdb=" N LEU L 52 " --> pdb=" O ASN L 48 " (cutoff:3.500A) removed outlier: 3.761A 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 104 through 133 removed outlier: 4.352A pdb=" N ASP L 127 " --> pdb=" O ARG L 123 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N ALA L 128 " --> pdb=" O ARG L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 133 through 156 removed outlier: 3.713A 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 'C' and resid 44 through 45 Processing sheet with id=AA2, first strand: chain 'D' 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 'K' and resid 44 through 45 Processing sheet with id=AA5, first strand: chain 'F' and resid 44 through 45 Processing sheet with id=AA6, first strand: chain 'J' and resid 44 through 45 Processing sheet with id=AA7, first strand: chain 'L' and resid 44 through 45 1159 hydrogen bonds defined for protein. 3477 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: 2.28 Time building geometry restraints manager: 1.62 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: 5294 1.34 - 1.45: 1279 1.45 - 1.57: 8550 1.57 - 1.68: 0 1.68 - 1.80: 24 Bond restraints: 15147 Sorted by residual: bond pdb=" CB MET A 74 " pdb=" CG MET A 74 " ideal model delta sigma weight residual 1.520 1.478 0.042 3.00e-02 1.11e+03 1.94e+00 bond pdb=" C VAL F 125 " pdb=" O VAL F 125 " ideal model delta sigma weight residual 1.237 1.254 -0.017 1.29e-02 6.01e+03 1.67e+00 bond pdb=" C VAL E 125 " pdb=" O VAL E 125 " ideal model delta sigma weight residual 1.236 1.254 -0.017 1.35e-02 5.49e+03 1.59e+00 bond pdb=" C VAL A 125 " pdb=" O VAL A 125 " ideal model delta sigma weight residual 1.237 1.253 -0.015 1.29e-02 6.01e+03 1.43e+00 bond pdb=" C VAL K 125 " pdb=" O VAL K 125 " ideal model delta sigma weight residual 1.236 1.252 -0.016 1.35e-02 5.49e+03 1.40e+00 ... (remaining 15142 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 20165 1.91 - 3.81: 402 3.81 - 5.72: 24 5.72 - 7.62: 0 7.62 - 9.53: 1 Bond angle restraints: 20592 Sorted by residual: angle pdb=" N HIS H 126 " pdb=" CA HIS H 126 " pdb=" C HIS H 126 " ideal model delta sigma weight residual 111.28 115.17 -3.89 1.09e+00 8.42e-01 1.27e+01 angle pdb=" N HIS B 126 " pdb=" CA HIS B 126 " pdb=" C HIS B 126 " ideal model delta sigma weight residual 111.28 115.07 -3.79 1.09e+00 8.42e-01 1.21e+01 angle pdb=" N HIS J 126 " pdb=" CA HIS J 126 " pdb=" C HIS J 126 " ideal model delta sigma weight residual 111.28 114.75 -3.47 1.09e+00 8.42e-01 1.01e+01 angle pdb=" CB MET A 74 " pdb=" CG MET A 74 " pdb=" SD MET A 74 " ideal model delta sigma weight residual 112.70 103.17 9.53 3.00e+00 1.11e-01 1.01e+01 angle pdb=" N VAL J 80 " pdb=" CA VAL J 80 " pdb=" C VAL J 80 " ideal model delta sigma weight residual 107.60 110.96 -3.36 1.07e+00 8.73e-01 9.88e+00 ... (remaining 20587 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 8417 17.98 - 35.97: 555 35.97 - 53.95: 109 53.95 - 71.93: 40 71.93 - 89.91: 23 Dihedral angle restraints: 9144 sinusoidal: 3612 harmonic: 5532 Sorted by residual: dihedral pdb=" CA TRP L 42 " pdb=" C TRP L 42 " pdb=" N ASN L 43 " pdb=" CA ASN L 43 " ideal model delta harmonic sigma weight residual 180.00 -159.87 -20.13 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA TRP K 42 " pdb=" C TRP K 42 " pdb=" N ASN K 43 " pdb=" CA ASN K 43 " ideal model delta harmonic sigma weight residual -180.00 -160.57 -19.43 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA PRO B 98 " pdb=" C PRO B 98 " pdb=" N ALA B 99 " pdb=" CA ALA B 99 " ideal model delta harmonic sigma weight residual -180.00 -160.58 -19.42 0 5.00e+00 4.00e-02 1.51e+01 ... (remaining 9141 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1315 0.028 - 0.056: 738 0.056 - 0.084: 263 0.084 - 0.111: 82 0.111 - 0.139: 17 Chirality restraints: 2415 Sorted by residual: 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 2.37 0.14 2.00e-01 2.50e+01 4.84e-01 chirality pdb=" CA ASP A 145 " pdb=" N ASP A 145 " pdb=" C ASP A 145 " pdb=" CB ASP A 145 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.64e-01 chirality pdb=" CA GLU G 157 " pdb=" N GLU G 157 " pdb=" C GLU G 157 " pdb=" CB GLU G 157 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.55e-01 ... (remaining 2412 not shown) Planarity restraints: 2754 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 97 " -0.024 5.00e-02 4.00e+02 3.57e-02 2.04e+00 pdb=" N PRO C 98 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO C 98 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 98 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE I 97 " -0.023 5.00e-02 4.00e+02 3.43e-02 1.88e+00 pdb=" N PRO I 98 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO I 98 " -0.018 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 J 97 " 0.019 5.00e-02 4.00e+02 2.88e-02 1.32e+00 pdb=" N PRO J 98 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO J 98 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO J 98 " 0.016 5.00e-02 4.00e+02 ... (remaining 2751 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 682 2.73 - 3.27: 15180 3.27 - 3.81: 24365 3.81 - 4.36: 27533 4.36 - 4.90: 50837 Nonbonded interactions: 118597 Sorted by model distance: nonbonded pdb=" O THR G 87 " pdb=" OG1 THR G 91 " model vdw 2.182 3.040 nonbonded pdb=" OE1 GLU D 72 " pdb=" NZ LYS F 149 " model vdw 2.216 3.120 nonbonded pdb=" NZ LYS B 149 " pdb=" OE1 GLU H 72 " model vdw 2.219 3.120 nonbonded pdb=" O THR D 87 " pdb=" OG1 THR D 91 " model vdw 2.242 3.040 nonbonded pdb=" NH1 ARG D 4 " pdb=" O LEU F 94 " model vdw 2.243 3.120 ... (remaining 118592 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: 1.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.340 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 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 : 0.005 0.042 15147 Z= 0.225 Angle : 0.634 9.529 20592 Z= 0.391 Chirality : 0.039 0.139 2415 Planarity : 0.004 0.036 2754 Dihedral : 13.930 89.915 5526 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.33 (0.19), residues: 1902 helix: 2.97 (0.13), residues: 1428 sheet: None (None), residues: 0 loop : -0.33 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 75 PHE 0.020 0.002 PHE B 19 TRP 0.012 0.002 TRP G 42 HIS 0.006 0.002 HIS F 53 Details of bonding type rmsd covalent geometry : bond 0.00465 (15147) covalent geometry : angle 0.63412 (20592) hydrogen bonds : bond 0.11617 ( 1159) hydrogen bonds : angle 4.04000 ( 3477) *********************** 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 113 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.451 Fit side-chains REVERT: F 130 ASP cc_start: 0.8439 (t0) cc_final: 0.8118 (t0) REVERT: J 65 GLU cc_start: 0.6484 (mt-10) cc_final: 0.6247 (mt-10) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.1535 time to fit residues: 24.5433 Evaluate side-chains 91 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 HIS C 150 GLN H 11 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.150927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.130434 restraints weight = 15909.646| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.74 r_work: 0.3385 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.0945 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= 0.155 Angle : 0.467 6.057 20592 Z= 0.269 Chirality : 0.036 0.151 2415 Planarity : 0.003 0.032 2754 Dihedral : 4.304 56.494 2082 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 0.38 % Allowed : 2.83 % Favored : 96.79 % 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: 3.59 (0.19), residues: 1902 helix: 3.17 (0.13), residues: 1434 sheet: None (None), residues: 0 loop : -0.30 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 102 PHE 0.014 0.002 PHE G 19 TRP 0.003 0.001 TRP L 152 HIS 0.005 0.001 HIS I 53 Details of bonding type rmsd covalent geometry : bond 0.00283 (15147) covalent geometry : angle 0.46731 (20592) hydrogen bonds : bond 0.07902 ( 1159) hydrogen bonds : angle 3.60628 ( 3477) *********************** 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 134 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 128 time to evaluate : 0.544 Fit side-chains REVERT: A 156 SER cc_start: 0.8837 (t) cc_final: 0.8514 (t) REVERT: H 127 ASP cc_start: 0.7279 (m-30) cc_final: 0.6926 (m-30) outliers start: 6 outliers final: 5 residues processed: 130 average time/residue: 0.1342 time to fit residues: 25.3914 Evaluate side-chains 121 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 116 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain I residue 78 ASP Chi-restraints excluded: chain L residue 125 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 61 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 176 optimal weight: 20.0000 chunk 75 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 181 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 156 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 HIS B 158 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.147557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.126914 restraints weight = 16214.210| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.76 r_work: 0.3314 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.0949 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= 0.168 Angle : 0.471 5.671 20592 Z= 0.271 Chirality : 0.036 0.149 2415 Planarity : 0.004 0.032 2754 Dihedral : 4.356 58.777 2082 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.57 % Allowed : 5.03 % Favored : 94.40 % 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: 3.44 (0.19), residues: 1902 helix: 3.07 (0.13), residues: 1434 sheet: None (None), residues: 0 loop : -0.37 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 73 PHE 0.016 0.002 PHE B 19 TRP 0.004 0.001 TRP L 152 HIS 0.005 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00330 (15147) covalent geometry : angle 0.47122 (20592) hydrogen bonds : bond 0.08433 ( 1159) hydrogen bonds : angle 3.63386 ( 3477) *********************** 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 128 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 119 time to evaluate : 0.461 Fit side-chains REVERT: A 156 SER cc_start: 0.8958 (t) cc_final: 0.8660 (t) REVERT: H 127 ASP cc_start: 0.7334 (m-30) cc_final: 0.6922 (m-30) outliers start: 9 outliers final: 7 residues processed: 121 average time/residue: 0.1391 time to fit residues: 24.3123 Evaluate side-chains 121 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 114 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain I residue 78 ASP Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain L residue 125 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 74 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 150 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 166 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 HIS B 158 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.144613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.124017 restraints weight = 16290.160| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.76 r_work: 0.3289 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.0980 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= 0.179 Angle : 0.481 5.708 20592 Z= 0.277 Chirality : 0.036 0.148 2415 Planarity : 0.004 0.032 2754 Dihedral : 4.427 59.423 2082 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.01 % Allowed : 6.23 % Favored : 92.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.30 (0.19), residues: 1902 helix: 2.96 (0.13), residues: 1434 sheet: None (None), residues: 0 loop : -0.41 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 73 PHE 0.014 0.002 PHE B 19 TRP 0.005 0.001 TRP B 42 HIS 0.005 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00366 (15147) covalent geometry : angle 0.48120 (20592) hydrogen bonds : bond 0.08903 ( 1159) hydrogen bonds : angle 3.68580 ( 3477) *********************** 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 131 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.541 Fit side-chains REVERT: A 156 SER cc_start: 0.9063 (t) cc_final: 0.8788 (t) REVERT: G 158 ASN cc_start: 0.8591 (m-40) cc_final: 0.8315 (m110) REVERT: H 127 ASP cc_start: 0.7398 (m-30) cc_final: 0.7040 (m-30) REVERT: J 130 ASP cc_start: 0.8417 (t0) cc_final: 0.8105 (t0) outliers start: 16 outliers final: 11 residues processed: 126 average time/residue: 0.1268 time to fit residues: 23.2540 Evaluate side-chains 125 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain I residue 78 ASP Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 156 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 113 optimal weight: 5.9990 chunk 104 optimal weight: 0.5980 chunk 103 optimal weight: 0.8980 chunk 161 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 166 optimal weight: 6.9990 chunk 116 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 HIS B 158 ASN C 24 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.139825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.118650 restraints weight = 16514.083| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.83 r_work: 0.3312 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.0970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 15147 Z= 0.218 Angle : 0.530 5.375 20592 Z= 0.306 Chirality : 0.038 0.151 2415 Planarity : 0.004 0.032 2754 Dihedral : 4.671 63.174 2082 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.07 % Allowed : 7.86 % 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: 2.89 (0.19), residues: 1902 helix: 2.68 (0.13), residues: 1434 sheet: None (None), residues: 0 loop : -0.61 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 73 PHE 0.016 0.002 PHE B 19 TRP 0.007 0.002 TRP F 42 HIS 0.006 0.002 HIS K 41 Details of bonding type rmsd covalent geometry : bond 0.00481 (15147) covalent geometry : angle 0.52962 (20592) hydrogen bonds : bond 0.10244 ( 1159) hydrogen bonds : angle 3.87898 ( 3477) *********************** 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 116 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.522 Fit side-chains REVERT: F 130 ASP cc_start: 0.8220 (t0) cc_final: 0.7986 (t0) REVERT: H 39 GLN cc_start: 0.8979 (OUTLIER) cc_final: 0.7689 (tp40) REVERT: J 130 ASP cc_start: 0.8523 (t0) cc_final: 0.8233 (t0) outliers start: 17 outliers final: 14 residues processed: 113 average time/residue: 0.1378 time to fit residues: 22.3772 Evaluate side-chains 113 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain I residue 78 ASP Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 156 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 107 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 129 optimal weight: 0.2980 chunk 125 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.146329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.124060 restraints weight = 16240.562| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.96 r_work: 0.3270 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 15147 Z= 0.170 Angle : 0.470 6.450 20592 Z= 0.270 Chirality : 0.036 0.143 2415 Planarity : 0.004 0.030 2754 Dihedral : 4.430 59.811 2082 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.13 % Allowed : 8.49 % Favored : 90.38 % 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: 3.16 (0.19), residues: 1902 helix: 2.90 (0.13), residues: 1434 sheet: None (None), residues: 0 loop : -0.60 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 73 PHE 0.014 0.002 PHE G 19 TRP 0.003 0.001 TRP F 42 HIS 0.005 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00334 (15147) covalent geometry : angle 0.46994 (20592) hydrogen bonds : bond 0.08613 ( 1159) hydrogen bonds : angle 3.67473 ( 3477) *********************** 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 132 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.603 Fit side-chains REVERT: A 156 SER cc_start: 0.9021 (t) cc_final: 0.8709 (t) REVERT: G 158 ASN cc_start: 0.8673 (m-40) cc_final: 0.8435 (m110) REVERT: I 157 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7367 (mp0) REVERT: H 127 ASP cc_start: 0.7188 (m-30) cc_final: 0.6808 (m-30) REVERT: J 130 ASP cc_start: 0.8204 (t0) cc_final: 0.7931 (t0) outliers start: 18 outliers final: 16 residues processed: 126 average time/residue: 0.1240 time to fit residues: 23.5438 Evaluate side-chains 129 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain I residue 78 ASP Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 157 GLU Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 156 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 84 optimal weight: 2.9990 chunk 48 optimal weight: 20.0000 chunk 129 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 47 optimal weight: 0.3980 chunk 56 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 157 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.145557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.124459 restraints weight = 16254.443| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.80 r_work: 0.3262 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.1139 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= 0.187 Angle : 0.490 6.319 20592 Z= 0.282 Chirality : 0.036 0.145 2415 Planarity : 0.004 0.030 2754 Dihedral : 4.533 62.248 2082 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.19 % Allowed : 8.93 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.01 (0.19), residues: 1902 helix: 2.80 (0.13), residues: 1434 sheet: None (None), residues: 0 loop : -0.68 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 73 PHE 0.014 0.002 PHE B 19 TRP 0.005 0.001 TRP F 42 HIS 0.005 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00391 (15147) covalent geometry : angle 0.48957 (20592) hydrogen bonds : bond 0.09222 ( 1159) hydrogen bonds : angle 3.73759 ( 3477) *********************** 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 130 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 0.519 Fit side-chains REVERT: G 158 ASN cc_start: 0.8716 (m-40) cc_final: 0.8439 (m110) REVERT: I 157 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.6662 (mp0) REVERT: F 45 VAL cc_start: 0.7906 (OUTLIER) cc_final: 0.7401 (m) REVERT: H 39 GLN cc_start: 0.8971 (OUTLIER) cc_final: 0.7677 (tp40) REVERT: H 127 ASP cc_start: 0.7424 (m-30) cc_final: 0.7047 (m-30) REVERT: J 130 ASP cc_start: 0.8356 (t0) cc_final: 0.8104 (t0) outliers start: 19 outliers final: 16 residues processed: 124 average time/residue: 0.1384 time to fit residues: 24.7108 Evaluate side-chains 129 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain I residue 78 ASP Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 157 GLU Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 156 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 1 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 16 optimal weight: 0.0370 chunk 65 optimal weight: 1.9990 chunk 135 optimal weight: 4.9990 chunk 169 optimal weight: 2.9990 overall best weight: 0.9460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.150705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.128811 restraints weight = 16251.764| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.89 r_work: 0.3334 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.1379 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= 0.151 Angle : 0.446 7.009 20592 Z= 0.255 Chirality : 0.035 0.140 2415 Planarity : 0.004 0.029 2754 Dihedral : 4.291 59.134 2082 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.13 % Allowed : 9.25 % Favored : 89.62 % 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: 3.37 (0.19), residues: 1902 helix: 3.07 (0.13), residues: 1434 sheet: None (None), residues: 0 loop : -0.62 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 73 PHE 0.014 0.002 PHE G 49 TRP 0.004 0.001 TRP C 42 HIS 0.006 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00285 (15147) covalent geometry : angle 0.44570 (20592) hydrogen bonds : bond 0.07720 ( 1159) hydrogen bonds : angle 3.54764 ( 3477) *********************** 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 141 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 0.509 Fit side-chains REVERT: A 156 SER cc_start: 0.9034 (t) cc_final: 0.8737 (t) REVERT: D 148 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7558 (mt-10) REVERT: G 158 ASN cc_start: 0.8611 (m-40) cc_final: 0.8403 (m110) REVERT: I 157 GLU cc_start: 0.7806 (mp0) cc_final: 0.7438 (mp0) REVERT: H 39 GLN cc_start: 0.8892 (OUTLIER) cc_final: 0.7492 (tp40) outliers start: 18 outliers final: 17 residues processed: 138 average time/residue: 0.1256 time to fit residues: 25.6325 Evaluate side-chains 138 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 156 SER 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 G residue 125 VAL Chi-restraints excluded: chain I residue 78 ASP Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 156 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 53 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 25 optimal weight: 0.1980 chunk 103 optimal weight: 2.9990 chunk 176 optimal weight: 20.0000 chunk 4 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 172 optimal weight: 0.9980 chunk 182 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.146581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.125285 restraints weight = 16313.573| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.83 r_work: 0.3342 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 15147 Z= 0.181 Angle : 0.478 6.282 20592 Z= 0.275 Chirality : 0.036 0.141 2415 Planarity : 0.004 0.030 2754 Dihedral : 4.472 62.433 2082 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.32 % Allowed : 9.25 % Favored : 89.43 % 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: 3.13 (0.19), residues: 1902 helix: 2.89 (0.13), residues: 1434 sheet: None (None), residues: 0 loop : -0.68 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 73 PHE 0.014 0.002 PHE B 19 TRP 0.005 0.001 TRP B 42 HIS 0.005 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00376 (15147) covalent geometry : angle 0.47836 (20592) hydrogen bonds : bond 0.08926 ( 1159) hydrogen bonds : angle 3.68252 ( 3477) *********************** 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 134 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 0.460 Fit side-chains REVERT: A 156 SER cc_start: 0.9163 (t) cc_final: 0.8903 (t) REVERT: A 157 GLU cc_start: 0.7850 (mp0) cc_final: 0.7477 (mp0) REVERT: G 158 ASN cc_start: 0.8695 (m-40) cc_final: 0.8431 (m110) REVERT: I 157 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.6693 (mp0) REVERT: F 45 VAL cc_start: 0.7847 (OUTLIER) cc_final: 0.7301 (m) REVERT: H 39 GLN cc_start: 0.8967 (OUTLIER) cc_final: 0.7650 (tp40) outliers start: 21 outliers final: 16 residues processed: 127 average time/residue: 0.1377 time to fit residues: 25.2945 Evaluate side-chains 130 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 156 SER 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 G residue 125 VAL Chi-restraints excluded: chain I residue 78 ASP Chi-restraints excluded: chain I residue 157 GLU Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 156 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 187 optimal weight: 0.9980 chunk 124 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 119 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 155 optimal weight: 0.8980 chunk 162 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 121 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.153941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.132251 restraints weight = 16052.547| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 1.85 r_work: 0.3348 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 15147 Z= 0.145 Angle : 0.439 6.995 20592 Z= 0.250 Chirality : 0.035 0.139 2415 Planarity : 0.004 0.029 2754 Dihedral : 4.226 58.727 2082 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.32 % Allowed : 9.25 % Favored : 89.43 % 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: 3.45 (0.19), residues: 1902 helix: 3.14 (0.13), residues: 1434 sheet: None (None), residues: 0 loop : -0.62 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 73 PHE 0.014 0.002 PHE G 49 TRP 0.005 0.001 TRP C 42 HIS 0.006 0.001 HIS I 53 Details of bonding type rmsd covalent geometry : bond 0.00270 (15147) covalent geometry : angle 0.43884 (20592) hydrogen bonds : bond 0.07383 ( 1159) hydrogen bonds : angle 3.49008 ( 3477) ********************** 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 142 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 0.369 Fit side-chains REVERT: A 156 SER cc_start: 0.9027 (t) cc_final: 0.8728 (t) REVERT: D 148 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7578 (mt-10) REVERT: D 157 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.6296 (mp0) REVERT: I 157 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7449 (mp0) REVERT: H 39 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.7481 (tp40) REVERT: L 14 HIS cc_start: 0.6816 (m170) cc_final: 0.6553 (m-70) REVERT: L 74 MET cc_start: 0.8846 (ttm) cc_final: 0.8608 (ttp) outliers start: 21 outliers final: 17 residues processed: 135 average time/residue: 0.1263 time to fit residues: 25.0993 Evaluate side-chains 137 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 157 GLU 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 G residue 125 VAL Chi-restraints excluded: chain I residue 78 ASP Chi-restraints excluded: chain I residue 157 GLU Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain L residue 156 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 6.9990 chunk 139 optimal weight: 0.9980 chunk 189 optimal weight: 2.9990 chunk 185 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 137 optimal weight: 0.6980 chunk 97 optimal weight: 0.8980 chunk 170 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 HIS G 158 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.153628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.131898 restraints weight = 16057.105| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 1.86 r_work: 0.3415 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 15147 Z= 0.146 Angle : 0.436 6.580 20592 Z= 0.249 Chirality : 0.035 0.138 2415 Planarity : 0.003 0.029 2754 Dihedral : 4.231 60.486 2082 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.32 % Allowed : 9.50 % Favored : 89.18 % 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: 3.50 (0.19), residues: 1902 helix: 3.17 (0.13), residues: 1434 sheet: None (None), residues: 0 loop : -0.60 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 73 PHE 0.012 0.002 PHE K 19 TRP 0.005 0.001 TRP L 42 HIS 0.005 0.001 HIS I 53 Details of bonding type rmsd covalent geometry : bond 0.00270 (15147) covalent geometry : angle 0.43611 (20592) hydrogen bonds : bond 0.07440 ( 1159) hydrogen bonds : angle 3.48166 ( 3477) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2519.31 seconds wall clock time: 44 minutes 2.26 seconds (2642.26 seconds total)