Starting phenix.real_space_refine on Tue Dec 31 02:48:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hx1_35071/12_2024/8hx1_35071.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hx1_35071/12_2024/8hx1_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_35071/12_2024/8hx1_35071.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hx1_35071/12_2024/8hx1_35071.map" model { file = "/net/cci-nas-00/data/ceres_data/8hx1_35071/12_2024/8hx1_35071.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hx1_35071/12_2024/8hx1_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-5532/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: 8.83, per 1000 atoms: 0.59 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: 3.45 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: 1.37 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: 4.27 Time building geometry restraints manager: 4.08 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: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 33.610 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.050 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.890 ------------------------------------------------------------------------------- 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= 0.309 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 *********************** 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 : 1.551 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: 0.3339 time to fit residues: 53.6673 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 : 1.691 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 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= 0.428 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 *********************** 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 : 1.646 Fit side-chains REVERT: F 130 ASP cc_start: 0.8565 (t0) cc_final: 0.8218 (t0) REVERT: J 65 GLU cc_start: 0.6506 (mt-10) cc_final: 0.6269 (mt-10) outliers start: 10 outliers final: 10 residues processed: 99 average time/residue: 0.3447 time to fit residues: 48.8484 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 : 1.549 ------------------------------------------------------------------------------- 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 96 optimal weight: 8.9990 chunk 54 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 48 optimal weight: 20.0000 chunk 174 optimal weight: 3.9990 chunk 188 optimal weight: 1.9990 chunk 155 optimal weight: 0.8980 chunk 173 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 140 optimal weight: 3.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.0835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 15147 Z= 0.305 Angle : 0.528 5.540 20592 Z= 0.308 Chirality : 0.038 0.154 2415 Planarity : 0.004 0.033 2754 Dihedral : 4.749 65.472 2082 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.88 % Allowed : 5.91 % Favored : 93.21 % 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: 2.66 (0.19), residues: 1902 helix: 2.51 (0.13), residues: 1434 sheet: None (None), residues: 0 loop : -0.69 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 152 HIS 0.006 0.002 HIS A 53 PHE 0.016 0.002 PHE B 19 ARG 0.004 0.001 ARG B 73 *********************** 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 115 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 1.878 Fit side-chains REVERT: F 130 ASP cc_start: 0.8485 (t0) cc_final: 0.8149 (t0) REVERT: H 39 GLN cc_start: 0.9127 (OUTLIER) cc_final: 0.7812 (tp40) outliers start: 14 outliers final: 8 residues processed: 110 average time/residue: 0.3450 time to fit residues: 54.0216 Evaluate side-chains 107 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 1.620 ------------------------------------------------------------------------------- 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 G residue 45 VAL Chi-restraints excluded: chain I residue 78 ASP Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain H residue 39 GLN 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 172 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 chunk 175 optimal weight: 2.9990 chunk 185 optimal weight: 0.0970 chunk 91 optimal weight: 2.9990 chunk 166 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 15147 Z= 0.226 Angle : 0.476 6.616 20592 Z= 0.274 Chirality : 0.036 0.144 2415 Planarity : 0.004 0.030 2754 Dihedral : 4.511 61.159 2082 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.57 % Allowed : 7.92 % Favored : 91.51 % 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: 3.00 (0.19), residues: 1902 helix: 2.78 (0.13), residues: 1434 sheet: None (None), residues: 0 loop : -0.68 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 42 HIS 0.006 0.001 HIS I 53 PHE 0.014 0.002 PHE G 19 ARG 0.003 0.000 ARG F 102 *********************** 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: 9 poor density : 122 time to evaluate : 1.743 Fit side-chains REVERT: I 157 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7553 (mp0) REVERT: F 130 ASP cc_start: 0.8328 (t0) cc_final: 0.8007 (t0) REVERT: H 127 ASP cc_start: 0.6922 (m-30) cc_final: 0.6710 (m-30) REVERT: J 65 GLU cc_start: 0.6424 (mt-10) cc_final: 0.6221 (mt-10) outliers start: 9 outliers final: 7 residues processed: 125 average time/residue: 0.3193 time to fit residues: 57.9415 Evaluate side-chains 119 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 111 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain C residue 101 GLU 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 I residue 157 GLU Chi-restraints excluded: chain K residue 125 VAL 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 154 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 158 optimal weight: 3.9990 chunk 128 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 94 optimal weight: 5.9990 chunk 166 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 15147 Z= 0.386 Angle : 0.568 5.715 20592 Z= 0.328 Chirality : 0.040 0.150 2415 Planarity : 0.005 0.033 2754 Dihedral : 4.915 70.059 2082 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.82 % Allowed : 8.93 % Favored : 89.25 % 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: 2.39 (0.19), residues: 1902 helix: 2.34 (0.13), residues: 1434 sheet: None (None), residues: 0 loop : -0.89 (0.25), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP L 152 HIS 0.008 0.002 HIS K 41 PHE 0.018 0.003 PHE B 19 ARG 0.004 0.001 ARG B 73 *********************** 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 126 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 97 time to evaluate : 1.620 Fit side-chains REVERT: I 157 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7599 (mp0) REVERT: F 45 VAL cc_start: 0.8120 (OUTLIER) cc_final: 0.7785 (m) REVERT: F 130 ASP cc_start: 0.8552 (t0) cc_final: 0.8211 (t0) REVERT: F 157 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.7548 (tm-30) REVERT: H 39 GLN cc_start: 0.9142 (OUTLIER) cc_final: 0.8113 (tp40) REVERT: H 111 ILE cc_start: 0.7771 (OUTLIER) cc_final: 0.7548 (tp) REVERT: H 132 GLU cc_start: 0.7048 (tt0) cc_final: 0.6750 (tt0) REVERT: J 65 GLU cc_start: 0.6541 (mt-10) cc_final: 0.6294 (mt-10) REVERT: J 157 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7735 (tp30) outliers start: 29 outliers final: 17 residues processed: 120 average time/residue: 0.3272 time to fit residues: 56.8198 Evaluate side-chains 117 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 1.590 ------------------------------------------------------------------------------- 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 101 GLU 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 45 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 10 ILE 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 H residue 111 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 62 optimal weight: 3.9990 chunk 167 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 108 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 185 optimal weight: 5.9990 chunk 154 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 15 optimal weight: 0.0770 chunk 61 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 overall best weight: 1.1542 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 15147 Z= 0.218 Angle : 0.469 7.440 20592 Z= 0.270 Chirality : 0.036 0.138 2415 Planarity : 0.004 0.030 2754 Dihedral : 4.480 61.485 2082 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.57 % Allowed : 10.19 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.94 (0.19), residues: 1902 helix: 2.78 (0.13), residues: 1434 sheet: None (None), residues: 0 loop : -0.83 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 42 HIS 0.006 0.001 HIS I 53 PHE 0.015 0.002 PHE G 49 ARG 0.002 0.000 ARG F 102 *********************** 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 141 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 116 time to evaluate : 1.630 Fit side-chains REVERT: A 157 GLU cc_start: 0.8170 (mp0) cc_final: 0.7654 (mp0) REVERT: D 148 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7879 (mt-10) REVERT: D 157 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.6928 (mp0) REVERT: I 157 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7571 (mp0) REVERT: F 130 ASP cc_start: 0.8357 (t0) cc_final: 0.8050 (t0) REVERT: H 39 GLN cc_start: 0.9119 (OUTLIER) cc_final: 0.7637 (tp40) REVERT: H 111 ILE cc_start: 0.7460 (OUTLIER) cc_final: 0.7229 (tp) REVERT: L 130 ASP cc_start: 0.8434 (t0) cc_final: 0.8208 (t0) outliers start: 25 outliers final: 18 residues processed: 133 average time/residue: 0.2984 time to fit residues: 58.5157 Evaluate side-chains 136 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 111 ILE 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 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 10 ILE Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain L residue 125 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 179 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 135 optimal weight: 0.8980 chunk 156 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 185 optimal weight: 0.9980 chunk 115 optimal weight: 0.7980 chunk 112 optimal weight: 9.9990 chunk 85 optimal weight: 0.8980 chunk 114 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 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 0.018 15147 Z= 0.180 Angle : 0.439 7.187 20592 Z= 0.251 Chirality : 0.035 0.132 2415 Planarity : 0.003 0.030 2754 Dihedral : 4.303 61.621 2082 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.64 % Allowed : 9.81 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.27 (0.19), residues: 1902 helix: 3.03 (0.13), residues: 1434 sheet: None (None), residues: 0 loop : -0.78 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 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 G 73 *********************** 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 154 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 1.635 Fit side-chains REVERT: A 157 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7506 (mp0) REVERT: D 148 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7842 (mt-10) REVERT: I 157 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7524 (mp0) REVERT: H 39 GLN cc_start: 0.9088 (OUTLIER) cc_final: 0.7591 (tp40) REVERT: H 111 ILE cc_start: 0.7449 (OUTLIER) cc_final: 0.7199 (tp) outliers start: 26 outliers final: 18 residues processed: 147 average time/residue: 0.3281 time to fit residues: 71.3622 Evaluate side-chains 142 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 1.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 157 GLU 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 111 ILE 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 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 78 ASP Chi-restraints excluded: chain I residue 157 GLU Chi-restraints excluded: chain F residue 10 ILE 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 H residue 111 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 73 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 126 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 17 optimal weight: 0.4980 chunk 145 optimal weight: 0.7980 chunk 168 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1310 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= 0.255 Angle : 0.486 6.593 20592 Z= 0.279 Chirality : 0.036 0.136 2415 Planarity : 0.004 0.030 2754 Dihedral : 4.532 64.601 2082 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.01 % Allowed : 10.00 % 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: 2.98 (0.19), residues: 1902 helix: 2.81 (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 0.004 0.001 TRP H 152 HIS 0.006 0.001 HIS I 53 PHE 0.015 0.002 PHE F 19 ARG 0.002 0.000 ARG K 4 *********************** 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 147 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 115 time to evaluate : 1.665 Fit side-chains REVERT: A 157 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7599 (mp0) REVERT: C 130 ASP cc_start: 0.8568 (t70) cc_final: 0.8319 (t0) REVERT: D 157 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.6988 (mp0) REVERT: I 157 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7559 (mp0) REVERT: F 45 VAL cc_start: 0.7976 (OUTLIER) cc_final: 0.7516 (m) REVERT: F 157 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.7497 (tm-30) REVERT: H 39 GLN cc_start: 0.9113 (OUTLIER) cc_final: 0.7759 (tp40) REVERT: H 111 ILE cc_start: 0.7542 (OUTLIER) cc_final: 0.7308 (tp) REVERT: H 127 ASP cc_start: 0.7732 (t0) cc_final: 0.7308 (m-30) REVERT: J 157 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.7824 (tp30) outliers start: 32 outliers final: 21 residues processed: 136 average time/residue: 0.3223 time to fit residues: 63.9247 Evaluate side-chains 142 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 113 time to evaluate : 1.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 157 GLU 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 B residue 156 SER Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 111 ILE 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 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 10 ILE 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 H residue 111 ILE Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 157 GLU 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 177 optimal weight: 0.5980 chunk 161 optimal weight: 4.9990 chunk 172 optimal weight: 0.4980 chunk 103 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 135 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 163 optimal weight: 3.9990 chunk 171 optimal weight: 0.7980 chunk 113 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.1739 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= 0.156 Angle : 0.426 7.292 20592 Z= 0.242 Chirality : 0.034 0.129 2415 Planarity : 0.003 0.029 2754 Dihedral : 4.174 58.864 2082 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.26 % Allowed : 10.94 % Favored : 87.80 % 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: 3.45 (0.19), residues: 1902 helix: 3.18 (0.14), residues: 1434 sheet: None (None), residues: 0 loop : -0.75 (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 0.013 0.002 PHE D 19 ARG 0.002 0.000 ARG F 102 *********************** 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 145 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 1.553 Fit side-chains REVERT: D 148 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7799 (mt-10) REVERT: D 157 GLU cc_start: 0.7556 (mp0) cc_final: 0.7254 (mp0) REVERT: I 157 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7579 (mp0) REVERT: H 39 GLN cc_start: 0.9049 (OUTLIER) cc_final: 0.7572 (tp40) REVERT: J 157 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.7795 (tp30) REVERT: L 149 LYS cc_start: 0.8300 (tttt) cc_final: 0.7920 (tttt) outliers start: 20 outliers final: 13 residues processed: 141 average time/residue: 0.3176 time to fit residues: 64.9401 Evaluate side-chains 138 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 156 SER 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 B residue 156 SER Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain D 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 H residue 39 GLN Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain J residue 157 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 182 optimal weight: 4.9990 chunk 111 optimal weight: 0.7980 chunk 86 optimal weight: 4.9990 chunk 126 optimal weight: 0.6980 chunk 191 optimal weight: 1.9990 chunk 176 optimal weight: 20.0000 chunk 152 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 117 optimal weight: 0.9980 chunk 93 optimal weight: 0.0370 chunk 120 optimal weight: 6.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1790 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= 0.157 Angle : 0.422 6.823 20592 Z= 0.239 Chirality : 0.034 0.130 2415 Planarity : 0.003 0.031 2754 Dihedral : 4.160 61.521 2082 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.38 % Allowed : 11.13 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.55 (0.19), residues: 1902 helix: 3.24 (0.13), residues: 1434 sheet: None (None), residues: 0 loop : -0.69 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 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 ********************** 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 146 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 1.361 Fit side-chains REVERT: A 157 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7609 (mp0) REVERT: D 148 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7832 (mt-10) REVERT: D 157 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.6742 (mp0) REVERT: I 157 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7567 (mp0) REVERT: H 39 GLN cc_start: 0.9052 (OUTLIER) cc_final: 0.7600 (tp40) REVERT: J 157 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.7779 (tp30) REVERT: L 149 LYS cc_start: 0.8315 (tttt) cc_final: 0.7940 (tttt) outliers start: 22 outliers final: 16 residues processed: 138 average time/residue: 0.2986 time to fit residues: 60.5585 Evaluate side-chains 140 residues out of total 1626 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 119 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 157 GLU 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 B residue 156 SER Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C 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 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 H residue 39 GLN Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain J residue 157 GLU Chi-restraints excluded: chain L residue 111 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 140 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 152 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 = 0.3438 r_free = 0.3438 target = 0.136843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.116163 restraints weight = 16469.054| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.77 r_work: 0.3207 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 15147 Z= 0.365 Angle : 0.552 6.127 20592 Z= 0.317 Chirality : 0.039 0.138 2415 Planarity : 0.004 0.033 2754 Dihedral : 4.760 68.684 2082 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.64 % Allowed : 11.01 % Favored : 87.36 % 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: 2.73 (0.19), residues: 1902 helix: 2.61 (0.13), residues: 1434 sheet: None (None), residues: 0 loop : -0.84 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP L 152 HIS 0.008 0.002 HIS K 41 PHE 0.017 0.002 PHE L 19 ARG 0.004 0.001 ARG D 75 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2507.24 seconds wall clock time: 47 minutes 19.30 seconds (2839.30 seconds total)