Starting phenix.real_space_refine on Fri Jun 13 03:17:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hx1_35071/06_2025/8hx1_35071.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hx1_35071/06_2025/8hx1_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_35071/06_2025/8hx1_35071.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hx1_35071/06_2025/8hx1_35071.map" model { file = "/net/cci-nas-00/data/ceres_data/8hx1_35071/06_2025/8hx1_35071.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hx1_35071/06_2025/8hx1_35071.cif" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.252 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.27, per 1000 atoms: 0.62 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: 3.84 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.39 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: 4.48 Time building geometry restraints manager: 4.55 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: 0.01 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: 0.900 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: 0.020 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 35.630 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.060 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:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.460 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.012 0.002 TRP G 42 HIS 0.006 0.002 HIS F 53 PHE 0.020 0.002 PHE B 19 ARG 0.007 0.001 ARG L 75 Details of bonding type rmsd hydrogen bonds : bond 0.11617 ( 1159) hydrogen bonds : angle 4.04000 ( 3477) covalent geometry : bond 0.00465 (15147) covalent geometry : angle 0.63412 (20592) *********************** 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 : 1.914 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: 0.3661 time to fit residues: 60.7001 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 : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 112 optimal weight: 9.9990 chunk 174 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 HIS C 24 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 = 0.3424 r_free = 0.3424 target = 0.135686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.115171 restraints weight = 16539.106| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.77 r_work: 0.3164 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.0762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 15147 Z= 0.273 Angle : 0.610 4.986 20592 Z= 0.355 Chirality : 0.042 0.168 2415 Planarity : 0.005 0.036 2754 Dihedral : 4.925 68.831 2082 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.63 % Allowed : 3.40 % Favored : 95.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.19), residues: 1902 helix: 2.39 (0.13), residues: 1434 sheet: None (None), residues: 0 loop : -0.55 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP L 152 HIS 0.008 0.002 HIS K 41 PHE 0.020 0.003 PHE B 19 ARG 0.005 0.001 ARG B 73 Details of bonding type rmsd hydrogen bonds : bond 0.11717 ( 1159) hydrogen bonds : angle 4.12794 ( 3477) covalent geometry : bond 0.00642 (15147) covalent geometry : angle 0.61018 (20592) *********************** 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 100 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 1.542 Fit side-chains REVERT: D 157 GLU cc_start: 0.7708 (mp0) cc_final: 0.7464 (mp0) REVERT: F 130 ASP cc_start: 0.8542 (t0) cc_final: 0.8212 (t0) REVERT: J 65 GLU cc_start: 0.7207 (mt-10) cc_final: 0.6862 (mt-10) outliers start: 10 outliers final: 10 residues processed: 99 average time/residue: 0.3295 time to fit residues: 46.9108 Evaluate side-chains 97 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 1.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain I residue 78 ASP Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain F residue 125 VAL 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 189 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 145 optimal weight: 1.9990 chunk 135 optimal weight: 0.9990 chunk 144 optimal weight: 9.9990 chunk 21 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.146943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.125118 restraints weight = 16196.422| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.89 r_work: 0.3296 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.0891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15147 Z= 0.172 Angle : 0.482 6.046 20592 Z= 0.279 Chirality : 0.036 0.148 2415 Planarity : 0.004 0.031 2754 Dihedral : 4.519 60.511 2082 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 0.69 % Allowed : 5.41 % Favored : 93.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.05 (0.19), residues: 1902 helix: 2.79 (0.13), residues: 1434 sheet: None (None), residues: 0 loop : -0.56 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP L 152 HIS 0.005 0.001 HIS I 53 PHE 0.015 0.002 PHE G 19 ARG 0.003 0.000 ARG L 114 Details of bonding type rmsd hydrogen bonds : bond 0.08854 ( 1159) hydrogen bonds : angle 3.76753 ( 3477) covalent geometry : bond 0.00333 (15147) covalent geometry : angle 0.48198 (20592) *********************** 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 125 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 1.630 Fit side-chains REVERT: D 157 GLU cc_start: 0.7504 (mp0) cc_final: 0.7181 (mp0) REVERT: F 130 ASP cc_start: 0.8308 (t0) cc_final: 0.7997 (t0) REVERT: H 127 ASP cc_start: 0.7298 (m-30) cc_final: 0.6950 (m-30) outliers start: 11 outliers final: 6 residues processed: 120 average time/residue: 0.3112 time to fit residues: 54.4249 Evaluate side-chains 111 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 105 time to evaluate : 1.712 ------------------------------------------------------------------------------- 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 K 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 34 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 = 0.3443 r_free = 0.3443 target = 0.135798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.114745 restraints weight = 16554.747| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.82 r_work: 0.3163 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 15147 Z= 0.266 Angle : 0.589 5.155 20592 Z= 0.341 Chirality : 0.041 0.157 2415 Planarity : 0.005 0.034 2754 Dihedral : 4.972 70.156 2082 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.13 % Allowed : 7.86 % Favored : 91.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.19), residues: 1902 helix: 2.29 (0.13), residues: 1434 sheet: None (None), residues: 0 loop : -0.83 (0.25), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP L 152 HIS 0.008 0.002 HIS K 41 PHE 0.019 0.003 PHE B 19 ARG 0.005 0.001 ARG B 73 Details of bonding type rmsd hydrogen bonds : bond 0.11576 ( 1159) hydrogen bonds : angle 4.10206 ( 3477) covalent geometry : bond 0.00622 (15147) covalent geometry : angle 0.58895 (20592) *********************** 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 111 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 1.533 Fit side-chains REVERT: D 157 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.6730 (mp0) REVERT: I 157 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7446 (mp0) REVERT: F 130 ASP cc_start: 0.8521 (t0) cc_final: 0.8190 (t0) REVERT: H 39 GLN cc_start: 0.9039 (OUTLIER) cc_final: 0.8275 (tp40) REVERT: H 111 ILE cc_start: 0.7871 (OUTLIER) cc_final: 0.7656 (tp) REVERT: J 65 GLU cc_start: 0.7253 (mt-10) cc_final: 0.6895 (mt-10) outliers start: 18 outliers final: 12 residues processed: 107 average time/residue: 0.3208 time to fit residues: 49.4645 Evaluate side-chains 107 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 1.646 ------------------------------------------------------------------------------- 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 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 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 125 VAL Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain L residue 125 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 105 optimal weight: 0.0770 chunk 22 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 135 optimal weight: 0.7980 chunk 108 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 112 optimal weight: 9.9990 chunk 145 optimal weight: 2.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- 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 = 0.3712 r_free = 0.3712 target = 0.157553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.135129 restraints weight = 16080.485| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.94 r_work: 0.3384 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 15147 Z= 0.136 Angle : 0.440 7.735 20592 Z= 0.249 Chirality : 0.035 0.134 2415 Planarity : 0.003 0.028 2754 Dihedral : 4.221 56.591 2082 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.94 % Allowed : 8.87 % Favored : 90.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.33 (0.19), residues: 1902 helix: 3.05 (0.13), residues: 1434 sheet: None (None), residues: 0 loop : -0.67 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 42 HIS 0.006 0.001 HIS I 53 PHE 0.014 0.002 PHE G 49 ARG 0.002 0.000 ARG F 102 Details of bonding type rmsd hydrogen bonds : bond 0.06882 ( 1159) hydrogen bonds : angle 3.52394 ( 3477) covalent geometry : bond 0.00241 (15147) covalent geometry : angle 0.44004 (20592) *********************** 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 151 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 1.477 Fit side-chains REVERT: A 156 SER cc_start: 0.8940 (t) cc_final: 0.8615 (t) REVERT: D 148 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7413 (mt-10) REVERT: D 157 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.6914 (mp0) REVERT: I 157 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7260 (mp0) REVERT: H 39 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.7416 (tp40) outliers start: 15 outliers final: 10 residues processed: 145 average time/residue: 0.2899 time to fit residues: 61.6135 Evaluate side-chains 142 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 129 time to evaluate : 1.833 ------------------------------------------------------------------------------- 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 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 G residue 45 VAL Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain I residue 157 GLU Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 45 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 21 optimal weight: 2.9990 chunk 128 optimal weight: 10.0000 chunk 118 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 chunk 165 optimal weight: 4.9990 chunk 117 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 190 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 = 0.3479 r_free = 0.3479 target = 0.140502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.119820 restraints weight = 16461.078| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.77 r_work: 0.3285 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 15147 Z= 0.204 Angle : 0.510 6.271 20592 Z= 0.293 Chirality : 0.037 0.142 2415 Planarity : 0.004 0.030 2754 Dihedral : 4.611 66.093 2082 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.57 % Allowed : 9.62 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.86 (0.19), residues: 1902 helix: 2.70 (0.13), residues: 1434 sheet: None (None), residues: 0 loop : -0.81 (0.25), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 152 HIS 0.006 0.001 HIS K 41 PHE 0.017 0.002 PHE G 19 ARG 0.003 0.000 ARG B 73 Details of bonding type rmsd hydrogen bonds : bond 0.09682 ( 1159) hydrogen bonds : angle 3.80287 ( 3477) covalent geometry : bond 0.00446 (15147) covalent geometry : angle 0.50972 (20592) *********************** 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 136 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 1.571 Fit side-chains REVERT: A 156 SER cc_start: 0.9261 (t) cc_final: 0.9033 (t) REVERT: D 157 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.6541 (mp0) REVERT: G 111 ILE cc_start: 0.7683 (OUTLIER) cc_final: 0.7473 (tp) REVERT: I 157 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7383 (mp0) REVERT: F 45 VAL cc_start: 0.8056 (OUTLIER) cc_final: 0.7530 (m) REVERT: F 157 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.7486 (tm-30) REVERT: H 39 GLN cc_start: 0.9025 (OUTLIER) cc_final: 0.8020 (tp40) REVERT: J 157 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.7677 (tp30) outliers start: 25 outliers final: 12 residues processed: 126 average time/residue: 0.3028 time to fit residues: 56.0092 Evaluate side-chains 128 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 1.663 ------------------------------------------------------------------------------- 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 C residue 125 VAL 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 G residue 45 VAL Chi-restraints excluded: chain G residue 111 ILE 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 F residue 45 VAL Chi-restraints excluded: chain F residue 157 GLU 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 J residue 157 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 95 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 171 optimal weight: 0.9980 chunk 189 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 134 optimal weight: 0.9990 chunk 163 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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 = 0.3504 r_free = 0.3504 target = 0.142536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.121115 restraints weight = 16442.643| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.86 r_work: 0.3262 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1227 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= 0.183 Angle : 0.484 7.010 20592 Z= 0.278 Chirality : 0.036 0.139 2415 Planarity : 0.004 0.030 2754 Dihedral : 4.525 62.924 2082 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.76 % Allowed : 9.94 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.91 (0.19), residues: 1902 helix: 2.76 (0.13), residues: 1434 sheet: None (None), residues: 0 loop : -0.85 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 152 HIS 0.006 0.001 HIS I 53 PHE 0.015 0.002 PHE G 19 ARG 0.003 0.000 ARG B 73 Details of bonding type rmsd hydrogen bonds : bond 0.09055 ( 1159) hydrogen bonds : angle 3.73934 ( 3477) covalent geometry : bond 0.00376 (15147) covalent geometry : angle 0.48380 (20592) *********************** 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 141 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 113 time to evaluate : 1.688 Fit side-chains REVERT: A 156 SER cc_start: 0.9199 (t) cc_final: 0.8951 (t) REVERT: D 111 ILE cc_start: 0.7786 (OUTLIER) cc_final: 0.7552 (tp) REVERT: D 157 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.6546 (mp0) REVERT: E 157 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7376 (mp0) REVERT: I 52 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.7278 (mp) REVERT: I 157 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7392 (mp0) REVERT: F 45 VAL cc_start: 0.7976 (OUTLIER) cc_final: 0.7426 (m) REVERT: F 157 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.7461 (tm-30) REVERT: H 39 GLN cc_start: 0.8981 (OUTLIER) cc_final: 0.7804 (tp40) REVERT: J 157 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.7840 (tp30) outliers start: 28 outliers final: 18 residues processed: 132 average time/residue: 0.3418 time to fit residues: 65.8402 Evaluate side-chains 140 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 113 time to evaluate : 1.464 ------------------------------------------------------------------------------- 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 69 THR Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain D residue 111 ILE 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 157 GLU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain I residue 52 LEU 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 F residue 157 GLU 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 J residue 157 GLU Chi-restraints excluded: chain L residue 101 GLU Chi-restraints excluded: chain L residue 125 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 176 optimal weight: 20.0000 chunk 188 optimal weight: 1.9990 chunk 135 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 172 optimal weight: 0.9980 chunk 140 optimal weight: 0.8980 chunk 174 optimal weight: 4.9990 chunk 109 optimal weight: 0.0270 chunk 54 optimal weight: 0.6980 overall best weight: 0.7238 ------------------------------------------------------------------------------- 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 = 0.3698 r_free = 0.3698 target = 0.156035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.133729 restraints weight = 16047.818| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 1.93 r_work: 0.3381 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 15147 Z= 0.139 Angle : 0.434 7.411 20592 Z= 0.246 Chirality : 0.034 0.134 2415 Planarity : 0.003 0.029 2754 Dihedral : 4.235 59.702 2082 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.19 % Allowed : 10.50 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.36 (0.19), residues: 1902 helix: 3.10 (0.13), residues: 1434 sheet: None (None), residues: 0 loop : -0.76 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 42 HIS 0.006 0.001 HIS I 53 PHE 0.014 0.002 PHE G 49 ARG 0.002 0.000 ARG F 102 Details of bonding type rmsd hydrogen bonds : bond 0.07136 ( 1159) hydrogen bonds : angle 3.50115 ( 3477) covalent geometry : bond 0.00246 (15147) covalent geometry : angle 0.43359 (20592) *********************** 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 142 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 1.715 Fit side-chains REVERT: A 156 SER cc_start: 0.9032 (t) cc_final: 0.8756 (t) REVERT: A 157 GLU cc_start: 0.7920 (mp0) cc_final: 0.7371 (mp0) REVERT: D 111 ILE cc_start: 0.7473 (OUTLIER) cc_final: 0.7213 (tp) REVERT: D 148 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7542 (mt-10) REVERT: D 157 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.6266 (mp0) REVERT: I 157 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7342 (mp0) REVERT: F 157 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.7350 (tm-30) REVERT: H 39 GLN cc_start: 0.8859 (OUTLIER) cc_final: 0.7460 (tp40) outliers start: 19 outliers final: 13 residues processed: 134 average time/residue: 0.3115 time to fit residues: 63.2157 Evaluate side-chains 140 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 1.695 ------------------------------------------------------------------------------- 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 111 ILE Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 125 VAL 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 157 GLU Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 157 GLU Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain J residue 125 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 83 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 128 optimal weight: 20.0000 chunk 177 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 164 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 113 optimal weight: 0.7980 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 = 0.3432 r_free = 0.3432 target = 0.136627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.115981 restraints weight = 16428.184| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.78 r_work: 0.3288 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 15147 Z= 0.235 Angle : 0.547 6.021 20592 Z= 0.314 Chirality : 0.039 0.141 2415 Planarity : 0.004 0.031 2754 Dihedral : 4.764 67.940 2082 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.95 % Allowed : 10.19 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.64 (0.19), residues: 1902 helix: 2.55 (0.13), residues: 1434 sheet: None (None), residues: 0 loop : -0.91 (0.25), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP F 42 HIS 0.008 0.002 HIS K 41 PHE 0.017 0.002 PHE B 19 ARG 0.003 0.001 ARG L 50 Details of bonding type rmsd hydrogen bonds : bond 0.10618 ( 1159) hydrogen bonds : angle 3.92158 ( 3477) covalent geometry : bond 0.00535 (15147) covalent geometry : angle 0.54685 (20592) *********************** 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 128 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 97 time to evaluate : 1.629 Fit side-chains REVERT: A 157 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7083 (mp0) REVERT: D 111 ILE cc_start: 0.7956 (OUTLIER) cc_final: 0.7742 (tp) REVERT: D 157 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.6541 (mp0) REVERT: E 157 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7397 (mp0) REVERT: I 157 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7410 (mp0) REVERT: F 45 VAL cc_start: 0.7950 (OUTLIER) cc_final: 0.7449 (m) REVERT: F 130 ASP cc_start: 0.8376 (t0) cc_final: 0.8009 (t0) REVERT: F 157 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.7491 (tm-30) REVERT: H 39 GLN cc_start: 0.9017 (OUTLIER) cc_final: 0.8216 (tp40) REVERT: J 65 GLU cc_start: 0.7240 (mt-10) cc_final: 0.6870 (mt-10) REVERT: J 130 ASP cc_start: 0.8577 (t0) cc_final: 0.8193 (t0) REVERT: J 157 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.7750 (tp30) outliers start: 31 outliers final: 19 residues processed: 120 average time/residue: 0.3032 time to fit residues: 53.1971 Evaluate side-chains 121 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 93 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 111 ILE 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 157 GLU 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 F residue 157 GLU 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 J residue 157 GLU Chi-restraints excluded: chain L residue 101 GLU Chi-restraints excluded: chain L residue 125 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 155 optimal weight: 0.6980 chunk 166 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 152 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 160 optimal weight: 9.9990 chunk 58 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3702 r_free = 0.3702 target = 0.156436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.134043 restraints weight = 16156.484| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 1.93 r_work: 0.3366 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 15147 Z= 0.141 Angle : 0.436 7.849 20592 Z= 0.248 Chirality : 0.034 0.133 2415 Planarity : 0.004 0.029 2754 Dihedral : 4.215 57.771 2082 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.57 % Allowed : 10.44 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.30 (0.19), residues: 1902 helix: 3.07 (0.13), residues: 1434 sheet: None (None), residues: 0 loop : -0.82 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 42 HIS 0.007 0.001 HIS I 53 PHE 0.014 0.002 PHE G 49 ARG 0.003 0.000 ARG L 114 Details of bonding type rmsd hydrogen bonds : bond 0.07035 ( 1159) hydrogen bonds : angle 3.48625 ( 3477) covalent geometry : bond 0.00259 (15147) covalent geometry : angle 0.43559 (20592) ********************** 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 150 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 1.541 Fit side-chains REVERT: A 156 SER cc_start: 0.9011 (t) cc_final: 0.8710 (t) REVERT: A 157 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7226 (mp0) REVERT: D 111 ILE cc_start: 0.7494 (OUTLIER) cc_final: 0.7240 (tp) REVERT: D 148 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7625 (mt-10) REVERT: D 157 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.6984 (mp0) REVERT: E 6 THR cc_start: 0.8082 (m) cc_final: 0.7601 (t) REVERT: E 157 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.7235 (mp0) REVERT: I 78 ASP cc_start: 0.7286 (OUTLIER) cc_final: 0.6863 (m-30) REVERT: I 157 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7389 (mp0) REVERT: H 39 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.7430 (tp40) REVERT: J 157 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.7784 (tp30) REVERT: L 148 GLU cc_start: 0.8380 (mt-10) cc_final: 0.8005 (mt-10) outliers start: 25 outliers final: 15 residues processed: 140 average time/residue: 0.2902 time to fit residues: 59.2223 Evaluate side-chains 145 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 111 ILE 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 111 ILE 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 157 GLU 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 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 J residue 157 GLU Chi-restraints excluded: chain L residue 101 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 65 optimal weight: 0.7980 chunk 81 optimal weight: 0.0170 chunk 0 optimal weight: 20.0000 chunk 25 optimal weight: 0.0170 chunk 137 optimal weight: 0.6980 chunk 86 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 chunk 94 optimal weight: 0.5980 chunk 16 optimal weight: 0.0670 chunk 32 optimal weight: 0.1980 chunk 113 optimal weight: 0.5980 overall best weight: 0.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS B 14 HIS C 41 HIS E 41 HIS F 41 HIS J 24 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.178632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.155981 restraints weight = 15679.694| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 1.93 r_work: 0.3693 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 15147 Z= 0.100 Angle : 0.391 6.859 20592 Z= 0.215 Chirality : 0.033 0.128 2415 Planarity : 0.003 0.030 2754 Dihedral : 3.859 57.631 2082 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.63 % Allowed : 11.51 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.87 (0.20), residues: 1902 helix: 3.49 (0.13), residues: 1434 sheet: None (None), residues: 0 loop : -0.64 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 152 HIS 0.007 0.002 HIS I 53 PHE 0.010 0.001 PHE D 19 ARG 0.002 0.000 ARG F 102 Details of bonding type rmsd hydrogen bonds : bond 0.04381 ( 1159) hydrogen bonds : angle 3.17310 ( 3477) covalent geometry : bond 0.00163 (15147) covalent geometry : angle 0.39079 (20592) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5944.70 seconds wall clock time: 103 minutes 50.38 seconds (6230.38 seconds total)