Starting phenix.real_space_refine on Mon Dec 30 03:43:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6y5h_10697/12_2024/6y5h_10697.cif Found real_map, /net/cci-nas-00/data/ceres_data/6y5h_10697/12_2024/6y5h_10697.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6y5h_10697/12_2024/6y5h_10697.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6y5h_10697/12_2024/6y5h_10697.map" model { file = "/net/cci-nas-00/data/ceres_data/6y5h_10697/12_2024/6y5h_10697.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6y5h_10697/12_2024/6y5h_10697.cif" } resolution = 3.0 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= 0.003 sd= 0.253 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 57 5.16 5 C 7458 2.51 5 N 2055 2.21 5 O 2424 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 11994 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2454 Classifications: {'peptide': 318} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 298} Chain: "B" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1399 Classifications: {'peptide': 172} Link IDs: {'TRANS': 171} Chain: "C" Number of atoms: 2454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2454 Classifications: {'peptide': 318} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 298} Chain: "E" Number of atoms: 2454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2454 Classifications: {'peptide': 318} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 298} Chain: "D" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1399 Classifications: {'peptide': 172} Link IDs: {'TRANS': 171} Chain: "F" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1399 Classifications: {'peptide': 172} Link IDs: {'TRANS': 171} Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 8.76, per 1000 atoms: 0.73 Number of scatterers: 11994 At special positions: 0 Unit cell: (86.11, 87.2, 149.33, 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 57 16.00 O 2424 8.00 N 2055 7.00 C 7458 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS B 137 " distance=2.11 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS D 137 " distance=1.96 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.03 Simple disulfide: pdb=" SG CYS E 14 " - pdb=" SG CYS F 137 " distance=2.01 Simple disulfide: pdb=" SG CYS E 52 " - pdb=" SG CYS E 277 " distance=2.03 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 76 " distance=2.03 Simple disulfide: pdb=" SG CYS E 97 " - pdb=" SG CYS E 139 " distance=2.03 Simple disulfide: pdb=" SG CYS E 281 " - pdb=" SG CYS E 305 " distance=2.03 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 148 " distance=2.03 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 148 " distance=2.03 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 Links applied ALPHA1-3 " BMA G 3 " - " MAN G 4 " " BMA J 3 " - " MAN J 4 " " BMA L 3 " - " MAN L 4 " ALPHA1-6 " BMA G 3 " - " MAN G 5 " " BMA J 3 " - " MAN J 5 " " BMA L 3 " - " MAN L 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 401 " - " ASN A 38 " " NAG A 409 " - " ASN A 81 " " NAG C 401 " - " ASN C 38 " " NAG C 409 " - " ASN C 81 " " NAG E 401 " - " ASN E 38 " " NAG E 409 " - " ASN E 81 " " NAG G 1 " - " ASN A 165 " " NAG H 1 " - " ASN A 285 " " NAG I 1 " - " ASN B 154 " " NAG J 1 " - " ASN C 165 " " NAG K 1 " - " ASN C 285 " " NAG L 1 " - " ASN E 165 " " NAG M 1 " - " ASN E 285 " " NAG N 1 " - " ASN D 154 " " NAG O 1 " - " ASN F 154 " Time building additional restraints: 3.21 Conformation dependent library (CDL) restraints added in 1.6 seconds 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2706 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 33 sheets defined 26.1% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.67 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 76 through 80 removed outlier: 3.816A pdb=" N GLN A 80 " --> pdb=" O ASP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 114 Processing helix chain 'A' and resid 187 through 193 removed outlier: 3.802A pdb=" N GLN A 191 " --> pdb=" O THR A 187 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N THR A 192 " --> pdb=" O ASN A 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 56 removed outlier: 3.867A pdb=" N THR B 41 " --> pdb=" O ASP B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 126 removed outlier: 3.595A pdb=" N TYR B 94 " --> pdb=" O ASP B 90 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN B 95 " --> pdb=" O LEU B 91 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL B 100 " --> pdb=" O ALA B 96 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN B 105 " --> pdb=" O ALA B 101 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N MET B 115 " --> pdb=" O THR B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 154 removed outlier: 3.850A pdb=" N GLU B 150 " --> pdb=" O ASN B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 161 removed outlier: 3.777A pdb=" N VAL B 161 " --> pdb=" O ASP B 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 158 through 161' Processing helix chain 'B' and resid 162 through 172 removed outlier: 3.648A pdb=" N GLN B 172 " --> pdb=" O ASN B 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 76 through 80 removed outlier: 3.816A pdb=" N GLN C 80 " --> pdb=" O ASP C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 114 Processing helix chain 'C' and resid 187 through 193 removed outlier: 3.801A pdb=" N GLN C 191 " --> pdb=" O THR C 187 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N THR C 192 " --> pdb=" O ASN C 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 76 through 80 removed outlier: 3.815A pdb=" N GLN E 80 " --> pdb=" O ASP E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 114 Processing helix chain 'E' and resid 187 through 193 removed outlier: 3.802A pdb=" N GLN E 191 " --> pdb=" O THR E 187 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N THR E 192 " --> pdb=" O ASN E 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 56 removed outlier: 3.867A pdb=" N THR D 41 " --> pdb=" O ASP D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 126 removed outlier: 3.595A pdb=" N TYR D 94 " --> pdb=" O ASP D 90 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASN D 95 " --> pdb=" O LEU D 91 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL D 100 " --> pdb=" O ALA D 96 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN D 105 " --> pdb=" O ALA D 101 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N MET D 115 " --> pdb=" O THR D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 154 removed outlier: 3.850A pdb=" N GLU D 150 " --> pdb=" O ASN D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 161 removed outlier: 3.778A pdb=" N VAL D 161 " --> pdb=" O ASP D 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 158 through 161' Processing helix chain 'D' and resid 162 through 172 removed outlier: 3.648A pdb=" N GLN D 172 " --> pdb=" O ASN D 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 56 removed outlier: 3.867A pdb=" N THR F 41 " --> pdb=" O ASP F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 126 removed outlier: 3.595A pdb=" N TYR F 94 " --> pdb=" O ASP F 90 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN F 95 " --> pdb=" O LEU F 91 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL F 100 " --> pdb=" O ALA F 96 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN F 105 " --> pdb=" O ALA F 101 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N MET F 115 " --> pdb=" O THR F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 154 removed outlier: 3.850A pdb=" N GLU F 150 " --> pdb=" O ASN F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 161 removed outlier: 3.777A pdb=" N VAL F 161 " --> pdb=" O ASP F 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 158 through 161' Processing helix chain 'F' and resid 162 through 172 removed outlier: 3.647A pdb=" N GLN F 172 " --> pdb=" O ASN F 168 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 35 through 36 Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 52 removed outlier: 6.064A pdb=" N ILE A 51 " --> pdb=" O ASP A 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 58 through 61 removed outlier: 6.691A pdb=" N LEU A 59 " --> pdb=" O VAL A 88 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 120 through 122 removed outlier: 6.686A pdb=" N GLY A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ILE A 179 " --> pdb=" O GLY A 256 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AA9, first strand: chain 'A' and resid 151 through 153 Processing sheet with id=AB1, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB2, first strand: chain 'A' and resid 286 through 287 Processing sheet with id=AB3, first strand: chain 'D' and resid 35 through 36 removed outlier: 3.517A pdb=" N GLY D 23 " --> pdb=" O GLY C 16 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY C 16 " --> pdb=" O GLY D 23 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 24 through 26 Processing sheet with id=AB5, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AB6, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AB7, first strand: chain 'C' and resid 51 through 52 removed outlier: 6.064A pdb=" N ILE C 51 " --> pdb=" O ASP C 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 58 through 61 removed outlier: 6.691A pdb=" N LEU C 59 " --> pdb=" O VAL C 88 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 120 through 122 removed outlier: 6.686A pdb=" N GLY C 256 " --> pdb=" O ILE C 179 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ILE C 179 " --> pdb=" O GLY C 256 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AC2, first strand: chain 'C' and resid 151 through 153 Processing sheet with id=AC3, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AC4, first strand: chain 'C' and resid 286 through 287 Processing sheet with id=AC5, first strand: chain 'F' and resid 35 through 36 Processing sheet with id=AC6, first strand: chain 'E' and resid 24 through 26 Processing sheet with id=AC7, first strand: chain 'E' and resid 39 through 41 Processing sheet with id=AC8, first strand: chain 'E' and resid 43 through 44 Processing sheet with id=AC9, first strand: chain 'E' and resid 51 through 52 removed outlier: 6.064A pdb=" N ILE E 51 " --> pdb=" O ASP E 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'E' and resid 58 through 61 removed outlier: 6.690A pdb=" N LEU E 59 " --> pdb=" O VAL E 88 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 120 through 122 removed outlier: 6.687A pdb=" N GLY E 256 " --> pdb=" O ILE E 179 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ILE E 179 " --> pdb=" O GLY E 256 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 130 through 131 Processing sheet with id=AD4, first strand: chain 'E' and resid 151 through 153 Processing sheet with id=AD5, first strand: chain 'E' and resid 164 through 169 Processing sheet with id=AD6, first strand: chain 'E' and resid 286 through 287 427 hydrogen bonds defined for protein. 1173 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: 3.84 Time building geometry restraints manager: 3.71 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: 3868 1.34 - 1.46: 2158 1.46 - 1.58: 6130 1.58 - 1.70: 0 1.70 - 1.81: 78 Bond restraints: 12234 Sorted by residual: bond pdb=" N PHE E 79 " pdb=" CA PHE E 79 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.10e-02 8.26e+03 7.76e+00 bond pdb=" N PHE A 79 " pdb=" CA PHE A 79 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.10e-02 8.26e+03 7.75e+00 bond pdb=" N GLN E 80 " pdb=" CA GLN E 80 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.25e-02 6.40e+03 7.55e+00 bond pdb=" N ILE C 214 " pdb=" CA ILE C 214 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.23e-02 6.61e+03 7.53e+00 bond pdb=" N GLN A 80 " pdb=" CA GLN A 80 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.25e-02 6.40e+03 7.48e+00 ... (remaining 12229 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.24: 15655 1.24 - 2.47: 710 2.47 - 3.71: 168 3.71 - 4.95: 27 4.95 - 6.18: 30 Bond angle restraints: 16590 Sorted by residual: angle pdb=" CA ASN E 81 " pdb=" C ASN E 81 " pdb=" O ASN E 81 " ideal model delta sigma weight residual 121.28 117.58 3.70 1.19e+00 7.06e-01 9.68e+00 angle pdb=" CA ASN C 81 " pdb=" C ASN C 81 " pdb=" O ASN C 81 " ideal model delta sigma weight residual 121.28 117.60 3.68 1.19e+00 7.06e-01 9.58e+00 angle pdb=" CA ASN A 81 " pdb=" C ASN A 81 " pdb=" O ASN A 81 " ideal model delta sigma weight residual 121.28 117.60 3.68 1.19e+00 7.06e-01 9.55e+00 angle pdb=" C VAL A 78 " pdb=" N PHE A 79 " pdb=" CA PHE A 79 " ideal model delta sigma weight residual 122.83 118.65 4.18 1.54e+00 4.22e-01 7.38e+00 angle pdb=" C VAL C 78 " pdb=" N PHE C 79 " pdb=" CA PHE C 79 " ideal model delta sigma weight residual 122.83 118.66 4.17 1.54e+00 4.22e-01 7.34e+00 ... (remaining 16585 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.03: 7103 22.03 - 44.07: 529 44.07 - 66.10: 75 66.10 - 88.14: 39 88.14 - 110.17: 18 Dihedral angle restraints: 7764 sinusoidal: 3546 harmonic: 4218 Sorted by residual: dihedral pdb=" CB CYS D 144 " pdb=" SG CYS D 144 " pdb=" SG CYS D 148 " pdb=" CB CYS D 148 " ideal model delta sinusoidal sigma weight residual 93.00 3.54 89.46 1 1.00e+01 1.00e-02 9.51e+01 dihedral pdb=" CB CYS B 144 " pdb=" SG CYS B 144 " pdb=" SG CYS B 148 " pdb=" CB CYS B 148 " ideal model delta sinusoidal sigma weight residual 93.00 3.60 89.40 1 1.00e+01 1.00e-02 9.50e+01 dihedral pdb=" CB CYS F 144 " pdb=" SG CYS F 144 " pdb=" SG CYS F 148 " pdb=" CB CYS F 148 " ideal model delta sinusoidal sigma weight residual 93.00 3.62 89.38 1 1.00e+01 1.00e-02 9.50e+01 ... (remaining 7761 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.236: 1905 0.236 - 0.472: 6 0.472 - 0.708: 6 0.708 - 0.943: 0 0.943 - 1.179: 3 Chirality restraints: 1920 Sorted by residual: chirality pdb=" C1 MAN J 4 " pdb=" O3 BMA J 3 " pdb=" C2 MAN J 4 " pdb=" O5 MAN J 4 " both_signs ideal model delta sigma weight residual False 2.40 1.22 1.18 2.00e-02 2.50e+03 3.48e+03 chirality pdb=" C1 MAN G 4 " pdb=" O3 BMA G 3 " pdb=" C2 MAN G 4 " pdb=" O5 MAN G 4 " both_signs ideal model delta sigma weight residual False 2.40 1.22 1.18 2.00e-02 2.50e+03 3.48e+03 chirality pdb=" C1 MAN L 4 " pdb=" O3 BMA L 3 " pdb=" C2 MAN L 4 " pdb=" O5 MAN L 4 " both_signs ideal model delta sigma weight residual False 2.40 1.22 1.18 2.00e-02 2.50e+03 3.46e+03 ... (remaining 1917 not shown) Planarity restraints: 2142 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 409 " -0.167 2.00e-02 2.50e+03 1.38e-01 2.38e+02 pdb=" C7 NAG E 409 " 0.045 2.00e-02 2.50e+03 pdb=" C8 NAG E 409 " -0.123 2.00e-02 2.50e+03 pdb=" N2 NAG E 409 " 0.223 2.00e-02 2.50e+03 pdb=" O7 NAG E 409 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 409 " -0.167 2.00e-02 2.50e+03 1.38e-01 2.37e+02 pdb=" C7 NAG A 409 " 0.045 2.00e-02 2.50e+03 pdb=" C8 NAG A 409 " -0.123 2.00e-02 2.50e+03 pdb=" N2 NAG A 409 " 0.222 2.00e-02 2.50e+03 pdb=" O7 NAG A 409 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 409 " -0.167 2.00e-02 2.50e+03 1.38e-01 2.37e+02 pdb=" C7 NAG C 409 " 0.045 2.00e-02 2.50e+03 pdb=" C8 NAG C 409 " -0.123 2.00e-02 2.50e+03 pdb=" N2 NAG C 409 " 0.222 2.00e-02 2.50e+03 pdb=" O7 NAG C 409 " 0.022 2.00e-02 2.50e+03 ... (remaining 2139 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1954 2.77 - 3.30: 9864 3.30 - 3.84: 18906 3.84 - 4.37: 22571 4.37 - 4.90: 40324 Nonbonded interactions: 93619 Sorted by model distance: nonbonded pdb=" N GLY F 1 " pdb=" OD2 ASP F 112 " model vdw 2.238 3.120 nonbonded pdb=" N GLY B 1 " pdb=" OD2 ASP B 112 " model vdw 2.238 3.120 nonbonded pdb=" N GLY D 1 " pdb=" OD2 ASP D 112 " model vdw 2.239 3.120 nonbonded pdb=" OD1 ASP C 68 " pdb=" OH TYR C 100 " model vdw 2.337 3.040 nonbonded pdb=" OD1 ASP E 68 " pdb=" OH TYR E 100 " model vdw 2.337 3.040 ... (remaining 93614 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' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' } 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: 3.770 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: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 31.670 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.070 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:13.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5413 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 : 0.004 0.034 12234 Z= 0.230 Angle : 0.655 6.184 16590 Z= 0.351 Chirality : 0.076 1.179 1920 Planarity : 0.007 0.138 2127 Dihedral : 16.337 110.171 5004 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.70 % Allowed : 16.39 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -2.50 (0.18), residues: 1458 helix: -0.26 (0.26), residues: 348 sheet: -0.34 (0.31), residues: 243 loop : -2.83 (0.15), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 84 HIS 0.004 0.001 HIS F 142 PHE 0.007 0.001 PHE F 9 TYR 0.005 0.001 TYR C 161 ARG 0.004 0.000 ARG D 124 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 267 time to evaluate : 1.425 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 274 average time/residue: 1.0468 time to fit residues: 315.6492 Evaluate side-chains 140 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 139 time to evaluate : 1.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 295 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 68 optimal weight: 0.3980 chunk 84 optimal weight: 0.4980 chunk 130 optimal weight: 0.3980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN A 216 ASN B 27 GLN B 142 HIS C 18 HIS C 54 ASN C 132 GLN C 197 GLN C 211 GLN C 295 GLN E 54 ASN E 132 GLN D 142 HIS D 146 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.6986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 12234 Z= 0.416 Angle : 1.013 10.791 16590 Z= 0.499 Chirality : 0.064 0.746 1920 Planarity : 0.007 0.062 2127 Dihedral : 9.544 70.280 2262 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 6.32 % Allowed : 18.19 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.81 (0.19), residues: 1458 helix: -0.22 (0.25), residues: 360 sheet: -0.05 (0.33), residues: 258 loop : -2.13 (0.17), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP E 153 HIS 0.011 0.002 HIS C 75 PHE 0.029 0.004 PHE F 138 TYR 0.041 0.003 TYR B 162 ARG 0.014 0.001 ARG F 153 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 240 time to evaluate : 1.440 Fit side-chains revert: symmetry clash REVERT: A 307 LYS cc_start: 0.8353 (mtmm) cc_final: 0.7899 (mtpt) REVERT: B 65 GLN cc_start: 0.8115 (mt0) cc_final: 0.7813 (mt0) REVERT: B 121 LYS cc_start: 0.8005 (ttmt) cc_final: 0.7687 (ttpt) REVERT: B 123 ARG cc_start: 0.8392 (ttp80) cc_final: 0.8160 (ttp-170) REVERT: C 295 GLN cc_start: 0.9245 (OUTLIER) cc_final: 0.8804 (pp30) REVERT: E 104 ASP cc_start: 0.7277 (OUTLIER) cc_final: 0.7062 (OUTLIER) REVERT: E 168 MET cc_start: 0.7825 (OUTLIER) cc_final: 0.7372 (tpt) REVERT: E 207 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.7213 (mtt180) REVERT: E 241 ASP cc_start: 0.8001 (OUTLIER) cc_final: 0.7677 (t0) REVERT: E 292 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8384 (mttm) REVERT: D 62 LYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7035 (mtpp) REVERT: D 65 GLN cc_start: 0.8452 (mt0) cc_final: 0.8167 (mt0) REVERT: D 111 THR cc_start: 0.7616 (p) cc_final: 0.7414 (p) REVERT: F 17 MET cc_start: 0.8361 (tpp) cc_final: 0.8123 (ttm) REVERT: F 45 ILE cc_start: 0.8225 (tt) cc_final: 0.7757 (pp) REVERT: F 59 THR cc_start: 0.4167 (OUTLIER) cc_final: 0.3883 (p) REVERT: F 139 LYS cc_start: 0.8103 (tttp) cc_final: 0.7823 (tptm) outliers start: 81 outliers final: 18 residues processed: 303 average time/residue: 1.2542 time to fit residues: 412.2879 Evaluate side-chains 182 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 157 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 295 GLN Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 168 MET Chi-restraints excluded: chain E residue 201 ARG Chi-restraints excluded: chain E residue 207 ARG Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 292 LYS Chi-restraints excluded: chain D residue 62 LYS Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain F residue 59 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 1.9990 chunk 40 optimal weight: 0.4980 chunk 108 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 131 optimal weight: 0.5980 chunk 141 optimal weight: 0.9980 chunk 116 optimal weight: 0.6980 chunk 129 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN B 28 ASN B 34 GLN C 18 HIS C 44 GLN C 295 GLN C 312 ASN E 18 HIS E 191 GLN E 246 ASN D 47 GLN D 105 GLN D 125 GLN D 146 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.8561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 12234 Z= 0.306 Angle : 0.657 8.992 16590 Z= 0.337 Chirality : 0.049 0.350 1920 Planarity : 0.005 0.053 2127 Dihedral : 9.040 76.471 2262 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 5.15 % Allowed : 21.78 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.16 (0.20), residues: 1458 helix: 1.16 (0.28), residues: 357 sheet: 0.27 (0.33), residues: 234 loop : -2.05 (0.17), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 84 HIS 0.007 0.002 HIS C 18 PHE 0.020 0.002 PHE B 24 TYR 0.020 0.002 TYR A 308 ARG 0.009 0.001 ARG C 141 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 175 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8470 (tp) REVERT: B 46 ASP cc_start: 0.7322 (m-30) cc_final: 0.7107 (m-30) REVERT: B 65 GLN cc_start: 0.8469 (mt0) cc_final: 0.8175 (mt0) REVERT: B 67 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.6728 (mp0) REVERT: B 121 LYS cc_start: 0.8010 (ttmt) cc_final: 0.7707 (ttpt) REVERT: C 168 MET cc_start: 0.7952 (OUTLIER) cc_final: 0.7731 (mmp) REVERT: C 210 GLN cc_start: 0.8980 (OUTLIER) cc_final: 0.8721 (tt0) REVERT: C 245 ILE cc_start: 0.8480 (OUTLIER) cc_final: 0.7955 (mt) REVERT: E 168 MET cc_start: 0.8187 (mmt) cc_final: 0.7951 (mmt) REVERT: F 17 MET cc_start: 0.8520 (tpp) cc_final: 0.8123 (ttm) REVERT: F 151 SER cc_start: 0.7142 (t) cc_final: 0.6555 (p) outliers start: 66 outliers final: 23 residues processed: 225 average time/residue: 1.0639 time to fit residues: 263.0943 Evaluate side-chains 170 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 142 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain F residue 30 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 87 optimal weight: 0.0050 chunk 131 optimal weight: 0.5980 chunk 139 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 124 optimal weight: 0.5980 chunk 37 optimal weight: 0.0770 overall best weight: 0.4152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 HIS C 18 HIS E 18 HIS E 197 GLN D 47 GLN D 105 GLN D 142 HIS F 28 ASN F 78 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.9096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12234 Z= 0.198 Angle : 0.547 9.224 16590 Z= 0.287 Chirality : 0.045 0.282 1920 Planarity : 0.004 0.044 2127 Dihedral : 7.711 66.070 2259 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 4.14 % Allowed : 22.72 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.82 (0.21), residues: 1458 helix: 1.51 (0.28), residues: 360 sheet: -0.17 (0.31), residues: 276 loop : -1.71 (0.18), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 92 HIS 0.006 0.001 HIS C 18 PHE 0.012 0.002 PHE B 138 TYR 0.011 0.001 TYR B 162 ARG 0.008 0.000 ARG C 141 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 160 time to evaluate : 1.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 CYS cc_start: 0.6907 (m) cc_final: 0.6440 (m) REVERT: B 46 ASP cc_start: 0.7243 (m-30) cc_final: 0.6990 (m-30) REVERT: B 47 GLN cc_start: 0.7731 (tt0) cc_final: 0.7385 (mt0) REVERT: B 65 GLN cc_start: 0.8552 (mt0) cc_final: 0.8177 (mt0) REVERT: B 67 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.6684 (mp0) REVERT: B 121 LYS cc_start: 0.7992 (ttmt) cc_final: 0.7700 (tttt) REVERT: C 118 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8323 (mp) REVERT: C 168 MET cc_start: 0.8126 (mmp) cc_final: 0.7882 (tpt) REVERT: C 210 GLN cc_start: 0.8924 (OUTLIER) cc_final: 0.8574 (tt0) REVERT: E 195 TYR cc_start: 0.7807 (OUTLIER) cc_final: 0.5608 (m-80) REVERT: D 65 GLN cc_start: 0.8578 (mt0) cc_final: 0.8359 (mt0) REVERT: F 17 MET cc_start: 0.8507 (tpp) cc_final: 0.8287 (ttm) REVERT: F 151 SER cc_start: 0.7486 (t) cc_final: 0.6894 (p) outliers start: 53 outliers final: 22 residues processed: 204 average time/residue: 1.0858 time to fit residues: 244.4851 Evaluate side-chains 174 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 148 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain C residue 18 HIS Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 150 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 57 optimal weight: 0.0980 chunk 118 optimal weight: 0.3980 chunk 96 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 18 HIS E 18 HIS E 295 GLN D 47 GLN F 78 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.9837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 12234 Z= 0.344 Angle : 0.655 9.916 16590 Z= 0.339 Chirality : 0.049 0.293 1920 Planarity : 0.005 0.052 2127 Dihedral : 7.978 67.202 2259 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 5.31 % Allowed : 22.25 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.84 (0.20), residues: 1458 helix: 1.58 (0.28), residues: 357 sheet: 0.35 (0.33), residues: 234 loop : -1.87 (0.17), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 234 HIS 0.039 0.002 HIS C 18 PHE 0.019 0.002 PHE C 125 TYR 0.018 0.002 TYR A 308 ARG 0.005 0.001 ARG C 150 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 157 time to evaluate : 1.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ILE cc_start: 0.8677 (OUTLIER) cc_final: 0.8426 (mp) REVERT: A 243 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8543 (tp) REVERT: B 47 GLN cc_start: 0.7915 (tt0) cc_final: 0.7566 (mt0) REVERT: B 65 GLN cc_start: 0.8656 (mt0) cc_final: 0.8336 (mt0) REVERT: B 67 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.6884 (mp0) REVERT: B 121 LYS cc_start: 0.8063 (ttmt) cc_final: 0.7772 (tttt) REVERT: C 168 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.8072 (tpt) REVERT: C 210 GLN cc_start: 0.9001 (OUTLIER) cc_final: 0.8597 (tt0) REVERT: C 261 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7453 (mtp85) REVERT: E 62 ILE cc_start: 0.8436 (OUTLIER) cc_final: 0.8108 (mp) REVERT: E 179 ILE cc_start: 0.8948 (OUTLIER) cc_final: 0.8638 (mp) REVERT: E 261 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7137 (mmm-85) REVERT: D 74 GLU cc_start: 0.6941 (mm-30) cc_final: 0.6654 (tt0) REVERT: F 146 ASN cc_start: 0.7630 (m110) cc_final: 0.7292 (m110) REVERT: F 151 SER cc_start: 0.8082 (t) cc_final: 0.7456 (p) outliers start: 68 outliers final: 36 residues processed: 210 average time/residue: 1.1038 time to fit residues: 254.8586 Evaluate side-chains 192 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 147 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 261 ARG Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 179 ILE Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 261 ARG Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain F residue 18 ILE Chi-restraints excluded: chain F residue 30 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 chunk 27 optimal weight: 0.3980 chunk 81 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 11 optimal weight: 0.3980 chunk 73 optimal weight: 1.9990 chunk 134 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 GLN E 18 HIS E 33 GLN E 246 ASN E 312 ASN D 34 GLN D 47 GLN D 105 GLN D 146 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 1.0174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12234 Z= 0.235 Angle : 0.566 9.143 16590 Z= 0.295 Chirality : 0.045 0.242 1920 Planarity : 0.004 0.042 2127 Dihedral : 7.388 61.318 2259 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 4.61 % Allowed : 21.78 % Favored : 73.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.65 (0.20), residues: 1458 helix: 1.82 (0.28), residues: 357 sheet: 0.33 (0.33), residues: 234 loop : -1.75 (0.17), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 234 HIS 0.008 0.001 HIS C 18 PHE 0.013 0.002 PHE B 24 TYR 0.011 0.001 TYR A 308 ARG 0.005 0.000 ARG C 141 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 151 time to evaluate : 1.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7698 (mt-10) REVERT: A 121 ILE cc_start: 0.8632 (OUTLIER) cc_final: 0.8385 (mp) REVERT: B 34 GLN cc_start: 0.8284 (tt0) cc_final: 0.7967 (tt0) REVERT: B 47 GLN cc_start: 0.7837 (tt0) cc_final: 0.7598 (mt0) REVERT: B 65 GLN cc_start: 0.8599 (mt0) cc_final: 0.8245 (mt0) REVERT: B 67 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.6785 (mp0) REVERT: C 118 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8352 (mp) REVERT: C 119 GLU cc_start: 0.8406 (tt0) cc_final: 0.8161 (tt0) REVERT: C 168 MET cc_start: 0.8359 (mmp) cc_final: 0.8114 (tpt) REVERT: C 245 ILE cc_start: 0.8711 (OUTLIER) cc_final: 0.8100 (mt) REVERT: E 62 ILE cc_start: 0.8428 (OUTLIER) cc_final: 0.8157 (mp) REVERT: E 168 MET cc_start: 0.8460 (mmt) cc_final: 0.7985 (tpt) REVERT: E 179 ILE cc_start: 0.8933 (OUTLIER) cc_final: 0.8623 (mp) REVERT: E 195 TYR cc_start: 0.8068 (OUTLIER) cc_final: 0.6032 (m-80) REVERT: F 47 GLN cc_start: 0.7741 (mt0) cc_final: 0.7529 (mt0) REVERT: F 151 SER cc_start: 0.8246 (t) cc_final: 0.7574 (p) outliers start: 59 outliers final: 31 residues processed: 201 average time/residue: 1.1876 time to fit residues: 261.1718 Evaluate side-chains 177 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 139 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 224 ARG Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 179 ILE Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain F residue 143 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 117 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 138 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 85 optimal weight: 0.3980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 GLN C 312 ASN E 18 HIS E 33 GLN D 34 GLN D 47 GLN F 28 ASN F 105 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 1.0463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12234 Z= 0.266 Angle : 0.597 10.434 16590 Z= 0.309 Chirality : 0.046 0.260 1920 Planarity : 0.005 0.041 2127 Dihedral : 7.302 59.521 2259 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 5.00 % Allowed : 21.70 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.59 (0.21), residues: 1458 helix: 1.93 (0.28), residues: 357 sheet: 0.35 (0.33), residues: 234 loop : -1.73 (0.18), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 234 HIS 0.005 0.001 HIS E 75 PHE 0.016 0.002 PHE F 24 TYR 0.015 0.002 TYR A 308 ARG 0.005 0.000 ARG C 141 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 143 time to evaluate : 1.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ILE cc_start: 0.8463 (pt) cc_final: 0.7816 (tt) REVERT: A 35 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7757 (mt-10) REVERT: A 121 ILE cc_start: 0.8612 (OUTLIER) cc_final: 0.8389 (mp) REVERT: B 34 GLN cc_start: 0.8432 (tt0) cc_final: 0.8116 (tt0) REVERT: B 47 GLN cc_start: 0.7863 (tt0) cc_final: 0.7600 (mt0) REVERT: B 65 GLN cc_start: 0.8661 (mt0) cc_final: 0.8457 (mt0) REVERT: B 67 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.6831 (mp0) REVERT: B 121 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7917 (tttt) REVERT: B 128 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.7092 (tp30) REVERT: C 118 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8349 (mp) REVERT: C 119 GLU cc_start: 0.8377 (tt0) cc_final: 0.8154 (tt0) REVERT: C 168 MET cc_start: 0.8358 (OUTLIER) cc_final: 0.8143 (tpt) REVERT: C 214 ILE cc_start: 0.8693 (tt) cc_final: 0.8479 (mt) REVERT: C 245 ILE cc_start: 0.8752 (OUTLIER) cc_final: 0.8138 (mt) REVERT: E 62 ILE cc_start: 0.8540 (OUTLIER) cc_final: 0.8283 (mp) REVERT: E 168 MET cc_start: 0.8419 (mmt) cc_final: 0.7939 (tpt) REVERT: E 179 ILE cc_start: 0.8941 (OUTLIER) cc_final: 0.8629 (mp) REVERT: E 280 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7320 (mm-30) REVERT: D 128 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.6689 (tp30) REVERT: F 47 GLN cc_start: 0.7814 (mt0) cc_final: 0.7577 (mt0) REVERT: F 151 SER cc_start: 0.8364 (t) cc_final: 0.7766 (p) outliers start: 64 outliers final: 31 residues processed: 194 average time/residue: 1.1220 time to fit residues: 238.9248 Evaluate side-chains 181 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 140 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 179 ILE Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain F residue 18 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 0.9990 chunk 82 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 27 optimal weight: 0.2980 chunk 26 optimal weight: 0.7980 chunk 88 optimal weight: 0.2980 chunk 94 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 chunk 126 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 GLN C 33 GLN E 18 HIS E 33 GLN D 34 GLN F 105 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 1.0555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12234 Z= 0.229 Angle : 0.561 9.814 16590 Z= 0.292 Chirality : 0.045 0.229 1920 Planarity : 0.004 0.037 2127 Dihedral : 7.058 56.480 2259 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 4.22 % Allowed : 22.87 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.44 (0.21), residues: 1458 helix: 1.98 (0.28), residues: 360 sheet: 0.10 (0.31), residues: 264 loop : -1.55 (0.18), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 234 HIS 0.004 0.001 HIS E 75 PHE 0.014 0.002 PHE F 24 TYR 0.011 0.001 TYR A 308 ARG 0.005 0.000 ARG C 141 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 141 time to evaluate : 1.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ILE cc_start: 0.8466 (OUTLIER) cc_final: 0.7752 (tt) REVERT: A 35 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7745 (tt0) REVERT: A 121 ILE cc_start: 0.8619 (OUTLIER) cc_final: 0.8402 (mp) REVERT: B 34 GLN cc_start: 0.8465 (tt0) cc_final: 0.8161 (tt0) REVERT: B 47 GLN cc_start: 0.7857 (OUTLIER) cc_final: 0.7609 (mt0) REVERT: B 65 GLN cc_start: 0.8645 (mt0) cc_final: 0.8434 (mt0) REVERT: B 67 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.6815 (mp0) REVERT: B 121 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7841 (tttt) REVERT: C 118 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8370 (mp) REVERT: C 119 GLU cc_start: 0.8356 (tt0) cc_final: 0.8144 (tt0) REVERT: C 245 ILE cc_start: 0.8722 (OUTLIER) cc_final: 0.8145 (mt) REVERT: E 62 ILE cc_start: 0.8521 (OUTLIER) cc_final: 0.8268 (mp) REVERT: E 168 MET cc_start: 0.8391 (mmt) cc_final: 0.7919 (tpt) REVERT: E 179 ILE cc_start: 0.8930 (OUTLIER) cc_final: 0.8616 (mp) REVERT: E 195 TYR cc_start: 0.8159 (OUTLIER) cc_final: 0.6265 (m-80) REVERT: E 280 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7318 (mm-30) REVERT: F 47 GLN cc_start: 0.7744 (mt0) cc_final: 0.7477 (mt0) REVERT: F 151 SER cc_start: 0.8398 (t) cc_final: 0.7779 (p) outliers start: 54 outliers final: 28 residues processed: 182 average time/residue: 1.1628 time to fit residues: 231.8936 Evaluate side-chains 177 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 139 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 47 GLN Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 179 ILE Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain F residue 18 ILE Chi-restraints excluded: chain F residue 143 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 129 optimal weight: 0.3980 chunk 77 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 101 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 116 optimal weight: 0.1980 chunk 122 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 chunk 84 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 248 ASN C 312 ASN E 18 HIS E 33 GLN D 34 GLN F 105 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 1.0646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12234 Z= 0.227 Angle : 0.563 9.971 16590 Z= 0.293 Chirality : 0.045 0.243 1920 Planarity : 0.004 0.039 2127 Dihedral : 6.887 54.445 2259 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.83 % Allowed : 23.42 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.34 (0.21), residues: 1458 helix: 2.14 (0.28), residues: 357 sheet: 0.17 (0.31), residues: 264 loop : -1.50 (0.18), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 234 HIS 0.005 0.001 HIS B 106 PHE 0.014 0.002 PHE F 24 TYR 0.011 0.001 TYR C 308 ARG 0.005 0.000 ARG C 141 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 143 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ILE cc_start: 0.8448 (OUTLIER) cc_final: 0.7792 (tt) REVERT: A 35 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7712 (tt0) REVERT: A 121 ILE cc_start: 0.8587 (OUTLIER) cc_final: 0.8378 (mp) REVERT: B 34 GLN cc_start: 0.8452 (tt0) cc_final: 0.8150 (tt0) REVERT: B 47 GLN cc_start: 0.7855 (OUTLIER) cc_final: 0.7606 (mt0) REVERT: B 67 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.6869 (mp0) REVERT: B 121 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7860 (tttt) REVERT: B 125 GLN cc_start: 0.7795 (tt0) cc_final: 0.7514 (mt0) REVERT: C 118 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8360 (mp) REVERT: C 245 ILE cc_start: 0.8720 (OUTLIER) cc_final: 0.8164 (mt) REVERT: E 62 ILE cc_start: 0.8479 (OUTLIER) cc_final: 0.8263 (mp) REVERT: E 168 MET cc_start: 0.8393 (mmt) cc_final: 0.7900 (tpt) REVERT: E 179 ILE cc_start: 0.8923 (OUTLIER) cc_final: 0.8608 (mp) REVERT: E 280 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7318 (mm-30) REVERT: F 47 GLN cc_start: 0.7838 (mt0) cc_final: 0.7578 (mt0) REVERT: F 143 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.8220 (ttpt) REVERT: F 151 SER cc_start: 0.8393 (t) cc_final: 0.7818 (p) outliers start: 49 outliers final: 28 residues processed: 182 average time/residue: 1.2205 time to fit residues: 242.7939 Evaluate side-chains 175 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 137 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 47 GLN Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 179 ILE Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain F residue 18 ILE Chi-restraints excluded: chain F residue 143 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 143 optimal weight: 3.9990 chunk 132 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 chunk 11 optimal weight: 0.0870 chunk 88 optimal weight: 0.0670 chunk 70 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 GLN D 34 GLN F 105 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 1.0694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12234 Z= 0.189 Angle : 0.536 9.501 16590 Z= 0.279 Chirality : 0.044 0.227 1920 Planarity : 0.004 0.036 2127 Dihedral : 6.622 51.958 2259 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.12 % Allowed : 23.97 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.24 (0.21), residues: 1458 helix: 2.21 (0.28), residues: 360 sheet: 0.21 (0.31), residues: 264 loop : -1.45 (0.19), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 92 HIS 0.005 0.001 HIS B 106 PHE 0.012 0.001 PHE F 24 TYR 0.010 0.001 TYR B 162 ARG 0.004 0.000 ARG C 141 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 139 time to evaluate : 1.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ILE cc_start: 0.8434 (OUTLIER) cc_final: 0.7825 (tt) REVERT: A 35 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7707 (tt0) REVERT: B 34 GLN cc_start: 0.8468 (tt0) cc_final: 0.8166 (tt0) REVERT: B 47 GLN cc_start: 0.7824 (OUTLIER) cc_final: 0.7616 (mt0) REVERT: B 67 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.6733 (mp0) REVERT: B 121 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7882 (tttt) REVERT: B 125 GLN cc_start: 0.7752 (tt0) cc_final: 0.7515 (mt0) REVERT: C 118 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8378 (mp) REVERT: C 245 ILE cc_start: 0.8679 (OUTLIER) cc_final: 0.8152 (mt) REVERT: E 62 ILE cc_start: 0.8501 (OUTLIER) cc_final: 0.8280 (mp) REVERT: E 168 MET cc_start: 0.8375 (mmt) cc_final: 0.7928 (tpt) REVERT: E 179 ILE cc_start: 0.8937 (OUTLIER) cc_final: 0.8632 (mp) REVERT: E 280 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7320 (mm-30) REVERT: D 34 GLN cc_start: 0.8474 (tt0) cc_final: 0.8237 (tt0) REVERT: F 47 GLN cc_start: 0.7804 (mt0) cc_final: 0.7557 (mt0) REVERT: F 143 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.8260 (ttpt) REVERT: F 151 SER cc_start: 0.8413 (t) cc_final: 0.7829 (p) outliers start: 40 outliers final: 25 residues processed: 172 average time/residue: 1.1653 time to fit residues: 219.6061 Evaluate side-chains 169 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 135 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 47 GLN Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 179 ILE Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain F residue 18 ILE Chi-restraints excluded: chain F residue 143 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 1.9990 chunk 34 optimal weight: 0.0070 chunk 105 optimal weight: 0.9990 chunk 16 optimal weight: 0.2980 chunk 31 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 117 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 100 optimal weight: 0.6980 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 312 ASN E 18 HIS E 33 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.130004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.108214 restraints weight = 13401.924| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 1.81 r_work: 0.2954 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 1.0739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12234 Z= 0.209 Angle : 0.549 9.523 16590 Z= 0.286 Chirality : 0.045 0.222 1920 Planarity : 0.004 0.036 2127 Dihedral : 6.576 51.149 2259 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.28 % Allowed : 23.89 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.21 (0.21), residues: 1458 helix: 2.24 (0.28), residues: 360 sheet: 0.24 (0.32), residues: 264 loop : -1.44 (0.19), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 92 HIS 0.007 0.001 HIS B 106 PHE 0.013 0.002 PHE F 24 TYR 0.010 0.001 TYR D 157 ARG 0.004 0.000 ARG C 141 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4593.18 seconds wall clock time: 83 minutes 19.97 seconds (4999.97 seconds total)