Starting phenix.real_space_refine on Sat Jul 20 15:46:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vsp_43501/07_2024/8vsp_43501.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vsp_43501/07_2024/8vsp_43501.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vsp_43501/07_2024/8vsp_43501.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vsp_43501/07_2024/8vsp_43501.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vsp_43501/07_2024/8vsp_43501.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vsp_43501/07_2024/8vsp_43501.cif" } resolution = 3.12 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= 0.001 sd= 0.021 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 42 5.16 5 C 7239 2.51 5 N 1950 2.21 5 O 2157 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 11388 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1609 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 203} Chain breaks: 1 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "B" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1625 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 195} Chain breaks: 2 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 2, 'ARG:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 548 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 5, 'TRANS': 64} Chain: "D" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1609 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 203} Chain breaks: 1 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "E" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1625 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 195} Chain breaks: 2 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 2, 'ARG:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "F" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 548 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 5, 'TRANS': 64} Chain: "G" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1609 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 203} Chain breaks: 1 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "H" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1625 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 195} Chain breaks: 2 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 2, 'ARG:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "I" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 548 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 5, 'TRANS': 64} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.37, per 1000 atoms: 0.56 Number of scatterers: 11388 At special positions: 0 Unit cell: (108.231, 104.456, 139.694, 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 42 16.00 O 2157 8.00 N 1950 7.00 C 7239 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 109 " - pdb=" SG CYS A 165 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 79 " distance=2.03 Simple disulfide: pdb=" SG CYS B 117 " - pdb=" SG CYS B 173 " distance=2.03 Simple disulfide: pdb=" SG CYS D 109 " - pdb=" SG CYS D 165 " distance=2.03 Simple disulfide: pdb=" SG CYS E 15 " - pdb=" SG CYS E 79 " distance=2.03 Simple disulfide: pdb=" SG CYS E 117 " - pdb=" SG CYS E 173 " distance=2.03 Simple disulfide: pdb=" SG CYS G 109 " - pdb=" SG CYS G 165 " distance=2.03 Simple disulfide: pdb=" SG CYS H 15 " - pdb=" SG CYS H 79 " distance=2.03 Simple disulfide: pdb=" SG CYS H 117 " - pdb=" SG CYS H 173 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.98 Conformation dependent library (CDL) restraints added in 2.1 seconds 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2778 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 18 sheets defined 36.2% alpha, 30.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 48 through 52 Processing helix chain 'A' and resid 57 through 79 removed outlier: 3.963A pdb=" N ALA A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS A 77 " --> pdb=" O ASN A 73 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 221 removed outlier: 3.646A pdb=" N ARG A 220 " --> pdb=" O ILE A 216 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N SER A 221 " --> pdb=" O ARG A 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 64 removed outlier: 4.198A pdb=" N TYR B 60 " --> pdb=" O PRO B 56 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN B 64 " --> pdb=" O TYR B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 73 Processing helix chain 'B' and resid 73 through 78 Processing helix chain 'B' and resid 78 through 89 removed outlier: 3.617A pdb=" N GLN B 84 " --> pdb=" O ARG B 80 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU B 85 " --> pdb=" O HIS B 81 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARG B 88 " --> pdb=" O GLN B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 225 removed outlier: 3.874A pdb=" N GLY B 216 " --> pdb=" O PHE B 212 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU B 217 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE B 218 " --> pdb=" O GLY B 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 96 removed outlier: 3.517A pdb=" N ILE C 55 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY C 76 " --> pdb=" O TYR C 72 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG C 77 " --> pdb=" O GLN C 73 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS C 96 " --> pdb=" O ASN C 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 52 Processing helix chain 'D' and resid 57 through 79 removed outlier: 3.963A pdb=" N ALA D 61 " --> pdb=" O ASP D 57 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS D 77 " --> pdb=" O ASN D 73 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG D 78 " --> pdb=" O SER D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 221 removed outlier: 3.646A pdb=" N ARG D 220 " --> pdb=" O ILE D 216 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N SER D 221 " --> pdb=" O ARG D 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 64 removed outlier: 4.199A pdb=" N TYR E 60 " --> pdb=" O PRO E 56 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN E 64 " --> pdb=" O TYR E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 73 Processing helix chain 'E' and resid 73 through 78 Processing helix chain 'E' and resid 78 through 89 removed outlier: 3.618A pdb=" N GLN E 84 " --> pdb=" O ARG E 80 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU E 85 " --> pdb=" O HIS E 81 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG E 88 " --> pdb=" O GLN E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 225 removed outlier: 3.874A pdb=" N GLY E 216 " --> pdb=" O PHE E 212 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU E 217 " --> pdb=" O LEU E 213 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE E 218 " --> pdb=" O GLY E 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 96 removed outlier: 3.517A pdb=" N ILE F 55 " --> pdb=" O THR F 51 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG F 77 " --> pdb=" O GLN F 73 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS F 96 " --> pdb=" O ASN F 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 52 Processing helix chain 'G' and resid 57 through 79 removed outlier: 3.964A pdb=" N ALA G 61 " --> pdb=" O ASP G 57 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS G 77 " --> pdb=" O ASN G 73 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG G 78 " --> pdb=" O SER G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 189 through 221 removed outlier: 3.645A pdb=" N ARG G 220 " --> pdb=" O ILE G 216 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N SER G 221 " --> pdb=" O ARG G 217 " (cutoff:3.500A) Processing helix chain 'H' and resid 54 through 64 removed outlier: 4.198A pdb=" N TYR H 60 " --> pdb=" O PRO H 56 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN H 64 " --> pdb=" O TYR H 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 73 Processing helix chain 'H' and resid 73 through 78 Processing helix chain 'H' and resid 78 through 89 removed outlier: 3.617A pdb=" N GLN H 84 " --> pdb=" O ARG H 80 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU H 85 " --> pdb=" O HIS H 81 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARG H 88 " --> pdb=" O GLN H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 197 through 225 removed outlier: 3.874A pdb=" N GLY H 216 " --> pdb=" O PHE H 212 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU H 217 " --> pdb=" O LEU H 213 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE H 218 " --> pdb=" O GLY H 214 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 96 removed outlier: 3.517A pdb=" N ILE I 55 " --> pdb=" O THR I 51 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY I 76 " --> pdb=" O TYR I 72 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG I 77 " --> pdb=" O GLN I 73 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS I 96 " --> pdb=" O ASN I 92 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 46 removed outlier: 6.791A pdb=" N HIS A 27 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N TYR A 36 " --> pdb=" O TYR A 25 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N TYR A 25 " --> pdb=" O TYR A 36 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N ASP A 38 " --> pdb=" O GLY A 23 " (cutoff:3.500A) removed outlier: 10.031A pdb=" N GLY A 23 " --> pdb=" O ASP A 38 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N SER A 22 " --> pdb=" O TYR A 16 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N TYR A 16 " --> pdb=" O SER A 22 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLN A 24 " --> pdb=" O ASN A 14 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ASN A 14 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N THR A 26 " --> pdb=" O GLY A 12 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N GLY A 12 " --> pdb=" O THR A 26 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ALA B 13 " --> pdb=" O TYR A 11 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL A 13 " --> pdb=" O PHE B 11 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N PHE B 11 " --> pdb=" O VAL A 13 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N LEU A 15 " --> pdb=" O TYR B 9 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N TYR B 9 " --> pdb=" O LEU A 15 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG B 23 " --> pdb=" O THR B 18 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA B 38 " --> pdb=" O TYR B 30 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N TYR B 32 " --> pdb=" O GLU B 36 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N GLU B 36 " --> pdb=" O TYR B 32 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 95 removed outlier: 5.108A pdb=" N ILE A 106 " --> pdb=" O LEU A 155 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU A 155 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ILE A 108 " --> pdb=" O LEU A 153 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LEU A 153 " --> pdb=" O ILE A 108 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N LEU A 110 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N SER A 151 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ASP A 112 " --> pdb=" O LYS A 149 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N LYS A 149 " --> pdb=" O ASP A 112 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 95 removed outlier: 5.108A pdb=" N ILE A 106 " --> pdb=" O LEU A 155 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU A 155 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ILE A 108 " --> pdb=" O LEU A 153 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LEU A 153 " --> pdb=" O ILE A 108 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N LEU A 110 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N SER A 151 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ASP A 112 " --> pdb=" O LYS A 149 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N LYS A 149 " --> pdb=" O ASP A 112 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 128 through 130 removed outlier: 4.846A pdb=" N TRP A 123 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 98 through 102 removed outlier: 5.975A pdb=" N PHE B 155 " --> pdb=" O ASP B 121 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLN B 156 " --> pdb=" O LEU B 147 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N LEU B 147 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU B 158 " --> pdb=" O THR B 145 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 128 through 133 Processing sheet with id=AA7, first strand: chain 'D' and resid 43 through 46 removed outlier: 6.791A pdb=" N HIS D 27 " --> pdb=" O GLN D 34 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N TYR D 36 " --> pdb=" O TYR D 25 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N TYR D 25 " --> pdb=" O TYR D 36 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N ASP D 38 " --> pdb=" O GLY D 23 " (cutoff:3.500A) removed outlier: 10.031A pdb=" N GLY D 23 " --> pdb=" O ASP D 38 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N SER D 22 " --> pdb=" O TYR D 16 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N TYR D 16 " --> pdb=" O SER D 22 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLN D 24 " --> pdb=" O ASN D 14 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ASN D 14 " --> pdb=" O GLN D 24 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N THR D 26 " --> pdb=" O GLY D 12 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N GLY D 12 " --> pdb=" O THR D 26 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ALA E 13 " --> pdb=" O TYR D 11 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL D 13 " --> pdb=" O PHE E 11 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N PHE E 11 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N LEU D 15 " --> pdb=" O TYR E 9 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N TYR E 9 " --> pdb=" O LEU D 15 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG E 23 " --> pdb=" O THR E 18 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA E 38 " --> pdb=" O TYR E 30 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N TYR E 32 " --> pdb=" O GLU E 36 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N GLU E 36 " --> pdb=" O TYR E 32 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 90 through 95 removed outlier: 5.108A pdb=" N ILE D 106 " --> pdb=" O LEU D 155 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU D 155 " --> pdb=" O ILE D 106 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ILE D 108 " --> pdb=" O LEU D 153 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LEU D 153 " --> pdb=" O ILE D 108 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N LEU D 110 " --> pdb=" O SER D 151 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N SER D 151 " --> pdb=" O LEU D 110 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ASP D 112 " --> pdb=" O LYS D 149 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N LYS D 149 " --> pdb=" O ASP D 112 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 90 through 95 removed outlier: 5.108A pdb=" N ILE D 106 " --> pdb=" O LEU D 155 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU D 155 " --> pdb=" O ILE D 106 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ILE D 108 " --> pdb=" O LEU D 153 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LEU D 153 " --> pdb=" O ILE D 108 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N LEU D 110 " --> pdb=" O SER D 151 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N SER D 151 " --> pdb=" O LEU D 110 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ASP D 112 " --> pdb=" O LYS D 149 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N LYS D 149 " --> pdb=" O ASP D 112 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 128 through 130 removed outlier: 4.847A pdb=" N TRP D 123 " --> pdb=" O VAL D 130 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 98 through 102 removed outlier: 5.976A pdb=" N PHE E 155 " --> pdb=" O ASP E 121 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLN E 156 " --> pdb=" O LEU E 147 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N LEU E 147 " --> pdb=" O GLN E 156 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU E 158 " --> pdb=" O THR E 145 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 128 through 133 Processing sheet with id=AB4, first strand: chain 'G' and resid 43 through 46 removed outlier: 6.790A pdb=" N HIS G 27 " --> pdb=" O GLN G 34 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N TYR G 36 " --> pdb=" O TYR G 25 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N TYR G 25 " --> pdb=" O TYR G 36 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N ASP G 38 " --> pdb=" O GLY G 23 " (cutoff:3.500A) removed outlier: 10.031A pdb=" N GLY G 23 " --> pdb=" O ASP G 38 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N SER G 22 " --> pdb=" O TYR G 16 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N TYR G 16 " --> pdb=" O SER G 22 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLN G 24 " --> pdb=" O ASN G 14 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ASN G 14 " --> pdb=" O GLN G 24 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N THR G 26 " --> pdb=" O GLY G 12 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N GLY G 12 " --> pdb=" O THR G 26 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ALA H 13 " --> pdb=" O TYR G 11 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL G 13 " --> pdb=" O PHE H 11 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N PHE H 11 " --> pdb=" O VAL G 13 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N LEU G 15 " --> pdb=" O TYR H 9 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N TYR H 9 " --> pdb=" O LEU G 15 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG H 23 " --> pdb=" O THR H 18 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA H 38 " --> pdb=" O TYR H 30 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N TYR H 32 " --> pdb=" O GLU H 36 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N GLU H 36 " --> pdb=" O TYR H 32 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 90 through 95 removed outlier: 5.109A pdb=" N ILE G 106 " --> pdb=" O LEU G 155 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LEU G 155 " --> pdb=" O ILE G 106 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ILE G 108 " --> pdb=" O LEU G 153 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LEU G 153 " --> pdb=" O ILE G 108 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N LEU G 110 " --> pdb=" O SER G 151 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N SER G 151 " --> pdb=" O LEU G 110 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ASP G 112 " --> pdb=" O LYS G 149 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N LYS G 149 " --> pdb=" O ASP G 112 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 90 through 95 removed outlier: 5.109A pdb=" N ILE G 106 " --> pdb=" O LEU G 155 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LEU G 155 " --> pdb=" O ILE G 106 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ILE G 108 " --> pdb=" O LEU G 153 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LEU G 153 " --> pdb=" O ILE G 108 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N LEU G 110 " --> pdb=" O SER G 151 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N SER G 151 " --> pdb=" O LEU G 110 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ASP G 112 " --> pdb=" O LYS G 149 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N LYS G 149 " --> pdb=" O ASP G 112 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 128 through 130 removed outlier: 4.846A pdb=" N TRP G 123 " --> pdb=" O VAL G 130 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 98 through 102 removed outlier: 5.976A pdb=" N PHE H 155 " --> pdb=" O ASP H 121 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLN H 156 " --> pdb=" O LEU H 147 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N LEU H 147 " --> pdb=" O GLN H 156 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU H 158 " --> pdb=" O THR H 145 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 128 through 133 651 hydrogen bonds defined for protein. 1773 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: 3.28 Time building geometry restraints manager: 4.40 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: 3744 1.34 - 1.46: 2599 1.46 - 1.58: 5246 1.58 - 1.69: 0 1.69 - 1.81: 63 Bond restraints: 11652 Sorted by residual: bond pdb=" N VAL B 46 " pdb=" CA VAL B 46 " ideal model delta sigma weight residual 1.459 1.493 -0.033 1.19e-02 7.06e+03 7.92e+00 bond pdb=" N VAL E 46 " pdb=" CA VAL E 46 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.19e-02 7.06e+03 7.70e+00 bond pdb=" N VAL H 46 " pdb=" CA VAL H 46 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.19e-02 7.06e+03 7.68e+00 bond pdb=" N VAL H 44 " pdb=" CA VAL H 44 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.22e+00 bond pdb=" N VAL B 44 " pdb=" CA VAL B 44 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.25e-02 6.40e+03 6.99e+00 ... (remaining 11647 not shown) Histogram of bond angle deviations from ideal: 100.24 - 107.05: 417 107.05 - 113.87: 6544 113.87 - 120.68: 4839 120.68 - 127.50: 3951 127.50 - 134.31: 137 Bond angle restraints: 15888 Sorted by residual: angle pdb=" CA ASP E 152 " pdb=" C ASP E 152 " pdb=" O ASP E 152 " ideal model delta sigma weight residual 122.38 117.89 4.49 1.49e+00 4.50e-01 9.07e+00 angle pdb=" CA ASP B 152 " pdb=" C ASP B 152 " pdb=" O ASP B 152 " ideal model delta sigma weight residual 122.38 117.91 4.47 1.49e+00 4.50e-01 9.00e+00 angle pdb=" CA ASP H 152 " pdb=" C ASP H 152 " pdb=" O ASP H 152 " ideal model delta sigma weight residual 122.38 117.97 4.41 1.49e+00 4.50e-01 8.76e+00 angle pdb=" C ASN E 19 " pdb=" CA ASN E 19 " pdb=" CB ASN E 19 " ideal model delta sigma weight residual 116.34 112.30 4.04 1.40e+00 5.10e-01 8.33e+00 angle pdb=" C ASN B 19 " pdb=" CA ASN B 19 " pdb=" CB ASN B 19 " ideal model delta sigma weight residual 116.34 112.31 4.03 1.40e+00 5.10e-01 8.30e+00 ... (remaining 15883 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.68: 6411 11.68 - 23.36: 378 23.36 - 35.04: 123 35.04 - 46.73: 54 46.73 - 58.41: 6 Dihedral angle restraints: 6972 sinusoidal: 2673 harmonic: 4299 Sorted by residual: dihedral pdb=" CA LEU A 140 " pdb=" CB LEU A 140 " pdb=" CG LEU A 140 " pdb=" CD1 LEU A 140 " ideal model delta sinusoidal sigma weight residual 60.00 118.41 -58.41 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA LEU D 140 " pdb=" CB LEU D 140 " pdb=" CG LEU D 140 " pdb=" CD1 LEU D 140 " ideal model delta sinusoidal sigma weight residual 60.00 118.36 -58.36 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" CA LEU G 140 " pdb=" CB LEU G 140 " pdb=" CG LEU G 140 " pdb=" CD1 LEU G 140 " ideal model delta sinusoidal sigma weight residual 60.00 118.34 -58.34 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 6969 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1399 0.048 - 0.095: 286 0.095 - 0.143: 115 0.143 - 0.190: 3 0.190 - 0.238: 3 Chirality restraints: 1806 Sorted by residual: chirality pdb=" CA VAL H 44 " pdb=" N VAL H 44 " pdb=" C VAL H 44 " pdb=" CB VAL H 44 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA VAL B 44 " pdb=" N VAL B 44 " pdb=" C VAL B 44 " pdb=" CB VAL B 44 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA VAL E 44 " pdb=" N VAL E 44 " pdb=" C VAL E 44 " pdb=" CB VAL E 44 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 1803 not shown) Planarity restraints: 2055 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY H 54 " -0.040 5.00e-02 4.00e+02 6.01e-02 5.78e+00 pdb=" N PRO H 55 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO H 55 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO H 55 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 54 " 0.040 5.00e-02 4.00e+02 5.99e-02 5.74e+00 pdb=" N PRO B 55 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO B 55 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 55 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 54 " 0.040 5.00e-02 4.00e+02 5.97e-02 5.70e+00 pdb=" N PRO E 55 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO E 55 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 55 " 0.033 5.00e-02 4.00e+02 ... (remaining 2052 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 100 2.63 - 3.20: 9748 3.20 - 3.77: 16586 3.77 - 4.33: 23682 4.33 - 4.90: 38907 Nonbonded interactions: 89023 Sorted by model distance: nonbonded pdb=" OD1 ASP E 152 " pdb=" OG1 THR E 154 " model vdw 2.066 2.440 nonbonded pdb=" OD1 ASP B 152 " pdb=" OG1 THR B 154 " model vdw 2.066 2.440 nonbonded pdb=" OD1 ASP H 152 " pdb=" OG1 THR H 154 " model vdw 2.067 2.440 nonbonded pdb=" CE1 TYR C 50 " pdb=" CE1 TYR F 50 " model vdw 2.198 3.640 nonbonded pdb=" CE1 TYR F 50 " pdb=" CE1 TYR I 50 " model vdw 2.203 3.640 ... (remaining 89018 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 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: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.220 Process input model: 32.010 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 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 11652 Z= 0.258 Angle : 0.529 5.148 15888 Z= 0.314 Chirality : 0.045 0.238 1806 Planarity : 0.005 0.060 2055 Dihedral : 9.478 58.408 4167 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.51 % Allowed : 4.08 % Favored : 95.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.72 (0.23), residues: 1440 helix: 1.17 (0.22), residues: 504 sheet: 0.70 (0.26), residues: 402 loop : -0.26 (0.29), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 61 HIS 0.003 0.001 HIS H 177 PHE 0.013 0.001 PHE D 148 TYR 0.008 0.001 TYR G 25 ARG 0.002 0.000 ARG E 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 332 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 ASN cc_start: 0.8494 (m110) cc_final: 0.8224 (m110) REVERT: A 43 GLU cc_start: 0.7263 (tp30) cc_final: 0.6944 (tp30) REVERT: A 44 THR cc_start: 0.8565 (m) cc_final: 0.7872 (t) REVERT: A 158 SER cc_start: 0.7735 (t) cc_final: 0.7181 (p) REVERT: A 164 ASP cc_start: 0.8166 (m-30) cc_final: 0.7897 (m-30) REVERT: B 14 MET cc_start: 0.8724 (mtp) cc_final: 0.8514 (mtm) REVERT: C 73 GLN cc_start: 0.8495 (tp40) cc_final: 0.8266 (tp40) REVERT: C 107 MET cc_start: 0.6894 (mmm) cc_final: 0.6427 (mmt) REVERT: C 109 MET cc_start: 0.7907 (ptm) cc_final: 0.7644 (ptm) REVERT: D 14 ASN cc_start: 0.8447 (m110) cc_final: 0.8100 (m-40) REVERT: D 28 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8213 (mt-10) REVERT: D 42 LYS cc_start: 0.8029 (tttt) cc_final: 0.7825 (tttt) REVERT: D 63 THR cc_start: 0.8263 (m) cc_final: 0.8021 (m) REVERT: D 81 SER cc_start: 0.8207 (t) cc_final: 0.7743 (p) REVERT: D 82 THR cc_start: 0.8392 (p) cc_final: 0.7898 (p) REVERT: D 87 GLU cc_start: 0.8424 (mm-30) cc_final: 0.8208 (mm-30) REVERT: D 105 ASN cc_start: 0.8706 (t0) cc_final: 0.8312 (m-40) REVERT: D 118 VAL cc_start: 0.8567 (t) cc_final: 0.8171 (m) REVERT: D 177 LEU cc_start: 0.8152 (mt) cc_final: 0.7890 (mm) REVERT: E 14 MET cc_start: 0.8766 (mtp) cc_final: 0.8494 (mtm) REVERT: E 83 TYR cc_start: 0.8419 (t80) cc_final: 0.7969 (t80) REVERT: E 163 MET cc_start: 0.2647 (mtm) cc_final: 0.1831 (ptt) REVERT: E 176 GLU cc_start: 0.7182 (pt0) cc_final: 0.6971 (pt0) REVERT: E 185 THR cc_start: 0.8391 (m) cc_final: 0.8178 (t) REVERT: G 14 ASN cc_start: 0.8379 (m110) cc_final: 0.8100 (m-40) REVERT: G 82 THR cc_start: 0.8365 (p) cc_final: 0.8154 (p) REVERT: G 106 ILE cc_start: 0.8322 (mt) cc_final: 0.8100 (mt) REVERT: G 125 SER cc_start: 0.8025 (t) cc_final: 0.7422 (p) REVERT: G 144 ASP cc_start: 0.8433 (p0) cc_final: 0.8111 (p0) REVERT: G 176 LEU cc_start: 0.7717 (tt) cc_final: 0.7332 (tp) REVERT: G 179 HIS cc_start: 0.8252 (t70) cc_final: 0.7694 (t70) REVERT: H 6 ASP cc_start: 0.8559 (t0) cc_final: 0.8257 (t0) REVERT: H 22 GLU cc_start: 0.5616 (mt-10) cc_final: 0.5395 (mt-10) REVERT: H 30 TYR cc_start: 0.8657 (m-80) cc_final: 0.8381 (m-80) REVERT: H 93 ARG cc_start: 0.8529 (ttt180) cc_final: 0.8274 (ttt-90) REVERT: H 163 MET cc_start: 0.3111 (mtm) cc_final: 0.2582 (ptt) REVERT: I 72 TYR cc_start: 0.8638 (t80) cc_final: 0.8399 (t80) REVERT: I 73 GLN cc_start: 0.8465 (tp40) cc_final: 0.8256 (mm-40) outliers start: 6 outliers final: 1 residues processed: 338 average time/residue: 0.2493 time to fit residues: 116.4421 Evaluate side-chains 297 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 296 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 91 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 3.9990 chunk 109 optimal weight: 0.0020 chunk 60 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 68 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 130 optimal weight: 0.8980 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 103 GLN A 120 ASN B 64 GLN C 64 GLN C 75 GLN ** C 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 14 ASN D 86 ASN D 103 GLN D 120 ASN D 179 HIS ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 GLN F 75 GLN G 14 ASN G 103 GLN G 120 ASN H 64 GLN ** I 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 75 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11652 Z= 0.246 Angle : 0.536 6.714 15888 Z= 0.284 Chirality : 0.043 0.127 1806 Planarity : 0.005 0.057 2055 Dihedral : 4.574 47.288 1656 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.40 % Allowed : 9.95 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.58 (0.22), residues: 1440 helix: 2.60 (0.22), residues: 498 sheet: 0.86 (0.25), residues: 402 loop : -0.27 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 46 HIS 0.004 0.001 HIS G 7 PHE 0.016 0.002 PHE D 54 TYR 0.016 0.001 TYR B 60 ARG 0.006 0.001 ARG H 48 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 291 time to evaluate : 1.302 Fit side-chains REVERT: A 42 LYS cc_start: 0.7779 (tttt) cc_final: 0.7523 (tttt) REVERT: A 43 GLU cc_start: 0.7262 (tp30) cc_final: 0.7010 (tp30) REVERT: A 44 THR cc_start: 0.8599 (m) cc_final: 0.7574 (t) REVERT: A 158 SER cc_start: 0.7744 (t) cc_final: 0.7206 (p) REVERT: A 164 ASP cc_start: 0.8073 (m-30) cc_final: 0.7801 (m-30) REVERT: B 23 ARG cc_start: 0.7711 (ttt90) cc_final: 0.7372 (tpt170) REVERT: C 53 PHE cc_start: 0.7974 (OUTLIER) cc_final: 0.7199 (t80) REVERT: C 73 GLN cc_start: 0.8434 (tp40) cc_final: 0.8126 (tp40) REVERT: C 107 MET cc_start: 0.6881 (mmm) cc_final: 0.6506 (mmt) REVERT: D 28 GLU cc_start: 0.8408 (mt-10) cc_final: 0.8184 (mt-10) REVERT: D 81 SER cc_start: 0.8236 (t) cc_final: 0.7838 (p) REVERT: D 105 ASN cc_start: 0.8723 (t0) cc_final: 0.8354 (m-40) REVERT: D 118 VAL cc_start: 0.8550 (t) cc_final: 0.8173 (m) REVERT: D 177 LEU cc_start: 0.8143 (mt) cc_final: 0.7904 (mm) REVERT: E 14 MET cc_start: 0.8709 (mtp) cc_final: 0.8473 (mtm) REVERT: E 23 ARG cc_start: 0.7414 (ttt90) cc_final: 0.7172 (tpt170) REVERT: E 39 ARG cc_start: 0.8313 (ttp-170) cc_final: 0.8105 (ttp-110) REVERT: E 77 THR cc_start: 0.7747 (p) cc_final: 0.7449 (t) REVERT: E 163 MET cc_start: 0.2659 (mtm) cc_final: 0.1801 (ptt) REVERT: F 91 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.7035 (mt-10) REVERT: G 14 ASN cc_start: 0.8305 (m-40) cc_final: 0.8096 (m-40) REVERT: G 82 THR cc_start: 0.8288 (p) cc_final: 0.8063 (p) REVERT: G 144 ASP cc_start: 0.8511 (p0) cc_final: 0.8209 (p0) REVERT: G 176 LEU cc_start: 0.7639 (tt) cc_final: 0.7319 (tp) REVERT: G 179 HIS cc_start: 0.8326 (t70) cc_final: 0.7834 (t70) REVERT: H 6 ASP cc_start: 0.8442 (t0) cc_final: 0.8229 (t0) REVERT: H 22 GLU cc_start: 0.6061 (mt-10) cc_final: 0.5821 (mt-10) REVERT: H 46 VAL cc_start: 0.8151 (t) cc_final: 0.7661 (p) REVERT: H 163 MET cc_start: 0.3150 (mtm) cc_final: 0.2571 (ptt) REVERT: I 72 TYR cc_start: 0.8619 (t80) cc_final: 0.8382 (t80) outliers start: 40 outliers final: 23 residues processed: 307 average time/residue: 0.2477 time to fit residues: 106.1055 Evaluate side-chains 296 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 271 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain F residue 53 PHE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 91 GLU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 154 THR Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 160 MET Chi-restraints excluded: chain I residue 53 PHE Chi-restraints excluded: chain I residue 107 MET Chi-restraints excluded: chain I residue 111 THR Chi-restraints excluded: chain I residue 113 LEU 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: 10.0000 chunk 108 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 131 optimal weight: 0.6980 chunk 141 optimal weight: 0.8980 chunk 116 optimal weight: 8.9990 chunk 129 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 92 ASN D 120 ASN ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 HIS G 120 ASN H 64 GLN H 174 HIS ** I 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 92 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 11652 Z= 0.345 Angle : 0.556 6.654 15888 Z= 0.292 Chirality : 0.045 0.134 1806 Planarity : 0.005 0.056 2055 Dihedral : 4.422 48.072 1656 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.57 % Allowed : 12.67 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.59 (0.23), residues: 1440 helix: 2.69 (0.22), residues: 498 sheet: 0.82 (0.25), residues: 402 loop : -0.30 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP D 46 HIS 0.006 0.001 HIS G 27 PHE 0.015 0.002 PHE H 122 TYR 0.015 0.002 TYR B 60 ARG 0.006 0.001 ARG E 94 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 282 time to evaluate : 1.102 Fit side-chains REVERT: A 42 LYS cc_start: 0.7782 (tttt) cc_final: 0.7517 (tttt) REVERT: A 43 GLU cc_start: 0.7143 (tp30) cc_final: 0.6814 (tp30) REVERT: A 44 THR cc_start: 0.8610 (m) cc_final: 0.7786 (t) REVERT: A 51 LEU cc_start: 0.8147 (mt) cc_final: 0.7913 (mp) REVERT: A 132 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6744 (tm-30) REVERT: A 158 SER cc_start: 0.7776 (t) cc_final: 0.7209 (p) REVERT: B 23 ARG cc_start: 0.7741 (ttt90) cc_final: 0.7365 (tpt170) REVERT: B 163 MET cc_start: 0.2576 (ttm) cc_final: 0.1430 (ptt) REVERT: C 53 PHE cc_start: 0.7902 (OUTLIER) cc_final: 0.6990 (t80) REVERT: C 73 GLN cc_start: 0.8475 (tp40) cc_final: 0.8156 (tp40) REVERT: C 107 MET cc_start: 0.6901 (mmm) cc_final: 0.6586 (mmt) REVERT: C 115 MET cc_start: 0.6651 (mtp) cc_final: 0.6402 (mtp) REVERT: D 28 GLU cc_start: 0.8374 (mt-10) cc_final: 0.8127 (mt-10) REVERT: D 105 ASN cc_start: 0.8701 (t0) cc_final: 0.8349 (m-40) REVERT: D 118 VAL cc_start: 0.8546 (t) cc_final: 0.8151 (m) REVERT: D 132 GLU cc_start: 0.6944 (tt0) cc_final: 0.6706 (tt0) REVERT: D 177 LEU cc_start: 0.8153 (mt) cc_final: 0.7897 (mm) REVERT: E 14 MET cc_start: 0.8734 (mtp) cc_final: 0.8429 (mtm) REVERT: E 23 ARG cc_start: 0.7402 (ttt90) cc_final: 0.7169 (tpt170) REVERT: E 39 ARG cc_start: 0.8368 (ttp-170) cc_final: 0.8150 (ttp-110) REVERT: E 69 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7313 (mm-30) REVERT: E 163 MET cc_start: 0.2752 (mtm) cc_final: 0.1744 (ptt) REVERT: F 64 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7989 (tt0) REVERT: F 91 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.7161 (mt-10) REVERT: G 14 ASN cc_start: 0.8319 (m-40) cc_final: 0.8058 (m-40) REVERT: G 144 ASP cc_start: 0.8557 (p0) cc_final: 0.8261 (p0) REVERT: G 176 LEU cc_start: 0.7738 (tt) cc_final: 0.7458 (tp) REVERT: G 179 HIS cc_start: 0.8344 (t70) cc_final: 0.7878 (t70) REVERT: H 23 ARG cc_start: 0.7335 (OUTLIER) cc_final: 0.6608 (ttt-90) REVERT: H 46 VAL cc_start: 0.8293 (t) cc_final: 0.7816 (p) REVERT: H 163 MET cc_start: 0.3063 (mtm) cc_final: 0.2489 (ptt) outliers start: 42 outliers final: 28 residues processed: 298 average time/residue: 0.2510 time to fit residues: 102.7363 Evaluate side-chains 304 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 271 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 176 GLU Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain F residue 53 PHE Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 64 GLN Chi-restraints excluded: chain F residue 91 GLU Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 87 LEU Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 160 MET Chi-restraints excluded: chain I residue 53 PHE Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 107 MET Chi-restraints excluded: chain I residue 111 THR Chi-restraints excluded: chain I residue 113 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN D 120 ASN ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 71 ASN G 120 ASN H 64 GLN ** I 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 11652 Z= 0.425 Angle : 0.576 7.566 15888 Z= 0.305 Chirality : 0.046 0.140 1806 Planarity : 0.005 0.055 2055 Dihedral : 4.531 42.828 1656 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 4.17 % Allowed : 13.27 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.34 (0.22), residues: 1440 helix: 2.47 (0.22), residues: 498 sheet: 0.69 (0.25), residues: 402 loop : -0.44 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP G 123 HIS 0.005 0.001 HIS H 177 PHE 0.018 0.003 PHE H 122 TYR 0.014 0.002 TYR D 11 ARG 0.006 0.001 ARG E 94 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 284 time to evaluate : 1.310 Fit side-chains REVERT: A 42 LYS cc_start: 0.7755 (tttt) cc_final: 0.7510 (tttt) REVERT: A 43 GLU cc_start: 0.7114 (tp30) cc_final: 0.6792 (tp30) REVERT: A 44 THR cc_start: 0.8613 (m) cc_final: 0.7932 (t) REVERT: A 97 SER cc_start: 0.8285 (m) cc_final: 0.7866 (p) REVERT: A 132 GLU cc_start: 0.7072 (tt0) cc_final: 0.6754 (tm-30) REVERT: A 158 SER cc_start: 0.7828 (t) cc_final: 0.7275 (p) REVERT: B 23 ARG cc_start: 0.7770 (ttt90) cc_final: 0.7299 (tpt170) REVERT: C 107 MET cc_start: 0.6861 (mmm) cc_final: 0.6560 (mmt) REVERT: D 28 GLU cc_start: 0.8403 (mt-10) cc_final: 0.8151 (mt-10) REVERT: D 105 ASN cc_start: 0.8638 (t0) cc_final: 0.8320 (m-40) REVERT: D 118 VAL cc_start: 0.8525 (t) cc_final: 0.8135 (m) REVERT: D 177 LEU cc_start: 0.8238 (mt) cc_final: 0.7909 (mm) REVERT: E 10 GLN cc_start: 0.9038 (OUTLIER) cc_final: 0.8699 (pt0) REVERT: E 14 MET cc_start: 0.8752 (mtp) cc_final: 0.8416 (mtm) REVERT: E 23 ARG cc_start: 0.7411 (ttt90) cc_final: 0.7158 (tpt170) REVERT: E 30 TYR cc_start: 0.8640 (m-80) cc_final: 0.8391 (m-80) REVERT: E 39 ARG cc_start: 0.8369 (ttp-170) cc_final: 0.8120 (ttp-170) REVERT: E 48 ARG cc_start: 0.7487 (mtt-85) cc_final: 0.7287 (mtt-85) REVERT: E 70 ARG cc_start: 0.7231 (ttt180) cc_final: 0.7028 (ttt-90) REVERT: G 14 ASN cc_start: 0.8285 (m-40) cc_final: 0.8058 (m-40) REVERT: G 63 THR cc_start: 0.7934 (t) cc_final: 0.7700 (p) REVERT: G 144 ASP cc_start: 0.8581 (p0) cc_final: 0.8280 (p0) REVERT: G 176 LEU cc_start: 0.7802 (tt) cc_final: 0.7570 (tp) REVERT: G 179 HIS cc_start: 0.8320 (t70) cc_final: 0.7903 (t70) REVERT: H 23 ARG cc_start: 0.7310 (OUTLIER) cc_final: 0.6638 (ttt-90) REVERT: H 163 MET cc_start: 0.3050 (mtm) cc_final: 0.2559 (ptt) REVERT: I 77 ARG cc_start: 0.8410 (mtp180) cc_final: 0.8176 (mtp180) outliers start: 49 outliers final: 37 residues processed: 303 average time/residue: 0.2514 time to fit residues: 104.2682 Evaluate side-chains 316 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 277 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain B residue 176 GLU Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain E residue 10 GLN Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 176 GLU Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 87 LEU Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 139 THR Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 160 MET Chi-restraints excluded: chain I residue 55 ILE Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 107 MET Chi-restraints excluded: chain I residue 111 THR Chi-restraints excluded: chain I residue 113 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 118 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 124 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 120 ASN ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 ASN ** I 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11652 Z= 0.267 Angle : 0.511 7.977 15888 Z= 0.269 Chirality : 0.043 0.126 1806 Planarity : 0.005 0.053 2055 Dihedral : 4.028 15.226 1653 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.74 % Allowed : 14.54 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.59 (0.22), residues: 1440 helix: 2.78 (0.22), residues: 501 sheet: 0.77 (0.25), residues: 402 loop : -0.38 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 188 HIS 0.003 0.001 HIS H 177 PHE 0.017 0.002 PHE D 54 TYR 0.011 0.001 TYR G 152 ARG 0.009 0.000 ARG H 48 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 285 time to evaluate : 1.246 Fit side-chains REVERT: A 42 LYS cc_start: 0.7731 (tttt) cc_final: 0.7500 (tttt) REVERT: A 43 GLU cc_start: 0.7097 (tp30) cc_final: 0.6771 (tp30) REVERT: A 44 THR cc_start: 0.8630 (m) cc_final: 0.7812 (t) REVERT: A 132 GLU cc_start: 0.7064 (tt0) cc_final: 0.6738 (tm-30) REVERT: A 158 SER cc_start: 0.7802 (t) cc_final: 0.7244 (p) REVERT: B 23 ARG cc_start: 0.7783 (ttt90) cc_final: 0.7390 (tpt-90) REVERT: C 107 MET cc_start: 0.6880 (mmm) cc_final: 0.6655 (mmt) REVERT: D 28 GLU cc_start: 0.8401 (mt-10) cc_final: 0.8144 (mt-10) REVERT: D 51 LEU cc_start: 0.8233 (mt) cc_final: 0.7935 (mp) REVERT: D 105 ASN cc_start: 0.8636 (t0) cc_final: 0.8304 (m-40) REVERT: D 177 LEU cc_start: 0.8199 (mt) cc_final: 0.7908 (mm) REVERT: E 10 GLN cc_start: 0.9054 (OUTLIER) cc_final: 0.8722 (pt0) REVERT: E 14 MET cc_start: 0.8703 (mtp) cc_final: 0.8437 (mtm) REVERT: E 39 ARG cc_start: 0.8331 (ttp-170) cc_final: 0.8122 (ttp-110) REVERT: E 70 ARG cc_start: 0.7217 (ttt180) cc_final: 0.6998 (ttt-90) REVERT: E 163 MET cc_start: 0.2837 (mtm) cc_final: 0.2039 (pmm) REVERT: G 14 ASN cc_start: 0.8229 (m-40) cc_final: 0.8006 (m-40) REVERT: G 144 ASP cc_start: 0.8553 (p0) cc_final: 0.8240 (p0) REVERT: G 176 LEU cc_start: 0.7794 (tt) cc_final: 0.7532 (tp) REVERT: G 179 HIS cc_start: 0.8291 (t70) cc_final: 0.7896 (t70) REVERT: H 23 ARG cc_start: 0.7322 (OUTLIER) cc_final: 0.6565 (ttt-90) REVERT: H 163 MET cc_start: 0.3014 (mtm) cc_final: 0.2581 (ptt) REVERT: I 77 ARG cc_start: 0.8417 (mtp180) cc_final: 0.8208 (mtp180) outliers start: 44 outliers final: 36 residues processed: 303 average time/residue: 0.2446 time to fit residues: 101.9745 Evaluate side-chains 312 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 274 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain B residue 176 GLU Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain E residue 10 GLN Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 139 THR Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 160 MET Chi-restraints excluded: chain I residue 53 PHE Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 111 THR Chi-restraints excluded: chain I residue 113 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 3.9990 chunk 125 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 73 optimal weight: 0.4980 chunk 134 optimal weight: 0.0270 overall best weight: 0.6242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 ASN ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 ASN ** I 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11652 Z= 0.224 Angle : 0.497 7.050 15888 Z= 0.261 Chirality : 0.042 0.125 1806 Planarity : 0.005 0.052 2055 Dihedral : 3.907 14.452 1653 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.83 % Allowed : 14.88 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.85 (0.23), residues: 1440 helix: 3.08 (0.22), residues: 501 sheet: 0.92 (0.25), residues: 399 loop : -0.34 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 180 HIS 0.003 0.001 HIS H 177 PHE 0.018 0.002 PHE D 54 TYR 0.010 0.001 TYR G 152 ARG 0.010 0.000 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 280 time to evaluate : 1.249 Fit side-chains REVERT: A 42 LYS cc_start: 0.7731 (tttt) cc_final: 0.7491 (tttt) REVERT: A 43 GLU cc_start: 0.7065 (tp30) cc_final: 0.6752 (tp30) REVERT: A 44 THR cc_start: 0.8631 (m) cc_final: 0.7819 (t) REVERT: A 132 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.6745 (tm-30) REVERT: A 158 SER cc_start: 0.7804 (t) cc_final: 0.7252 (p) REVERT: B 23 ARG cc_start: 0.7769 (ttt90) cc_final: 0.7427 (tpt-90) REVERT: B 82 ASN cc_start: 0.8412 (m-40) cc_final: 0.7761 (m-40) REVERT: B 163 MET cc_start: 0.3195 (ptt) cc_final: 0.2869 (ptt) REVERT: D 28 GLU cc_start: 0.8381 (mt-10) cc_final: 0.8123 (mt-10) REVERT: D 77 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.8076 (mttm) REVERT: D 105 ASN cc_start: 0.8626 (t0) cc_final: 0.8310 (m-40) REVERT: D 177 LEU cc_start: 0.8164 (mt) cc_final: 0.7873 (mm) REVERT: E 10 GLN cc_start: 0.9074 (OUTLIER) cc_final: 0.8743 (pt0) REVERT: E 14 MET cc_start: 0.8682 (mtp) cc_final: 0.8463 (mtm) REVERT: E 70 ARG cc_start: 0.7248 (ttt180) cc_final: 0.7019 (ttt-90) REVERT: E 86 GLU cc_start: 0.7108 (mm-30) cc_final: 0.6466 (mm-30) REVERT: E 163 MET cc_start: 0.2574 (mtm) cc_final: 0.2123 (ptt) REVERT: G 14 ASN cc_start: 0.8208 (m-40) cc_final: 0.8006 (m-40) REVERT: G 87 GLU cc_start: 0.8399 (mm-30) cc_final: 0.8130 (mm-30) REVERT: G 144 ASP cc_start: 0.8544 (p0) cc_final: 0.8226 (p0) REVERT: G 176 LEU cc_start: 0.7798 (tt) cc_final: 0.7507 (tp) REVERT: G 179 HIS cc_start: 0.8275 (t70) cc_final: 0.7895 (t70) REVERT: H 23 ARG cc_start: 0.7342 (OUTLIER) cc_final: 0.6516 (ttt-90) REVERT: H 163 MET cc_start: 0.2959 (mtm) cc_final: 0.2533 (ptt) REVERT: I 77 ARG cc_start: 0.8461 (mtp180) cc_final: 0.8260 (mtp180) outliers start: 45 outliers final: 37 residues processed: 298 average time/residue: 0.2520 time to fit residues: 102.9244 Evaluate side-chains 315 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 274 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 176 GLU Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain E residue 10 GLN Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 176 GLU Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain G residue 173 ASP Chi-restraints excluded: chain H residue 22 GLU Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 160 MET Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain I residue 53 PHE Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 113 LEU 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: 0.4980 chunk 101 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 117 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 138 optimal weight: 0.5980 chunk 86 optimal weight: 0.0980 chunk 84 optimal weight: 0.1980 chunk 64 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 64 GLN D 120 ASN ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 ASN H 156 GLN ** I 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11652 Z= 0.169 Angle : 0.474 6.743 15888 Z= 0.248 Chirality : 0.042 0.126 1806 Planarity : 0.005 0.051 2055 Dihedral : 3.754 13.745 1653 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.83 % Allowed : 16.07 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 2.08 (0.23), residues: 1440 helix: 3.36 (0.22), residues: 501 sheet: 1.02 (0.25), residues: 399 loop : -0.28 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 180 HIS 0.003 0.001 HIS H 177 PHE 0.017 0.001 PHE D 54 TYR 0.009 0.001 TYR G 152 ARG 0.010 0.001 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 285 time to evaluate : 1.244 Fit side-chains REVERT: A 42 LYS cc_start: 0.7717 (tttt) cc_final: 0.7483 (tttt) REVERT: A 43 GLU cc_start: 0.7049 (tp30) cc_final: 0.6731 (tp30) REVERT: A 44 THR cc_start: 0.8633 (m) cc_final: 0.7862 (t) REVERT: A 132 GLU cc_start: 0.7039 (OUTLIER) cc_final: 0.6731 (tm-30) REVERT: A 158 SER cc_start: 0.7800 (t) cc_final: 0.7241 (p) REVERT: B 23 ARG cc_start: 0.7649 (ttt90) cc_final: 0.7181 (tpt170) REVERT: B 82 ASN cc_start: 0.8349 (m-40) cc_final: 0.7722 (m-40) REVERT: B 163 MET cc_start: 0.3087 (ptt) cc_final: 0.2702 (ptt) REVERT: C 73 GLN cc_start: 0.8426 (tp40) cc_final: 0.8208 (tp40) REVERT: D 26 THR cc_start: 0.8514 (p) cc_final: 0.8276 (m) REVERT: D 28 GLU cc_start: 0.8367 (mt-10) cc_final: 0.8116 (mt-10) REVERT: D 77 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.8036 (mttm) REVERT: D 177 LEU cc_start: 0.8103 (mt) cc_final: 0.7859 (mm) REVERT: E 10 GLN cc_start: 0.9064 (OUTLIER) cc_final: 0.8713 (pt0) REVERT: E 70 ARG cc_start: 0.7241 (ttt180) cc_final: 0.6993 (ttt-90) REVERT: E 86 GLU cc_start: 0.7077 (mm-30) cc_final: 0.6443 (mm-30) REVERT: E 163 MET cc_start: 0.2755 (mtm) cc_final: 0.2397 (ptt) REVERT: G 14 ASN cc_start: 0.8177 (m-40) cc_final: 0.7974 (m-40) REVERT: G 87 GLU cc_start: 0.8396 (mm-30) cc_final: 0.8137 (mm-30) REVERT: G 144 ASP cc_start: 0.8526 (p0) cc_final: 0.8202 (p0) REVERT: G 176 LEU cc_start: 0.7882 (tt) cc_final: 0.7531 (tp) REVERT: G 179 HIS cc_start: 0.8255 (t70) cc_final: 0.7880 (t70) REVERT: H 23 ARG cc_start: 0.7361 (OUTLIER) cc_final: 0.6460 (ttt-90) REVERT: H 163 MET cc_start: 0.2992 (mtm) cc_final: 0.2502 (ptt) outliers start: 45 outliers final: 30 residues processed: 304 average time/residue: 0.2464 time to fit residues: 102.4763 Evaluate side-chains 314 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 280 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 176 GLU Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain E residue 10 GLN Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 176 GLU Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain G residue 173 ASP Chi-restraints excluded: chain H residue 22 GLU Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 160 MET Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 95 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 26 optimal weight: 0.0980 chunk 88 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 120 ASN ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 ASN H 156 GLN ** I 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11652 Z= 0.253 Angle : 0.507 6.584 15888 Z= 0.265 Chirality : 0.043 0.168 1806 Planarity : 0.005 0.051 2055 Dihedral : 3.851 14.890 1653 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.40 % Allowed : 16.41 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 2.00 (0.23), residues: 1440 helix: 3.30 (0.22), residues: 501 sheet: 0.95 (0.25), residues: 399 loop : -0.31 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 180 HIS 0.004 0.001 HIS H 177 PHE 0.021 0.002 PHE D 54 TYR 0.010 0.001 TYR G 152 ARG 0.010 0.001 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 275 time to evaluate : 1.398 Fit side-chains REVERT: A 42 LYS cc_start: 0.7746 (tttt) cc_final: 0.7502 (tttt) REVERT: A 43 GLU cc_start: 0.7213 (tp30) cc_final: 0.6709 (tp30) REVERT: A 44 THR cc_start: 0.8637 (m) cc_final: 0.7833 (t) REVERT: A 132 GLU cc_start: 0.7046 (OUTLIER) cc_final: 0.6739 (tm-30) REVERT: A 158 SER cc_start: 0.7826 (t) cc_final: 0.7266 (p) REVERT: B 23 ARG cc_start: 0.7776 (ttt90) cc_final: 0.7468 (tpt-90) REVERT: B 82 ASN cc_start: 0.8347 (m-40) cc_final: 0.7756 (m-40) REVERT: B 163 MET cc_start: 0.3187 (ptt) cc_final: 0.2781 (ptt) REVERT: D 28 GLU cc_start: 0.8365 (mt-10) cc_final: 0.8101 (mt-10) REVERT: D 77 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.8056 (mttm) REVERT: D 177 LEU cc_start: 0.8188 (mt) cc_final: 0.7892 (mm) REVERT: E 10 GLN cc_start: 0.9079 (OUTLIER) cc_final: 0.8530 (pt0) REVERT: E 70 ARG cc_start: 0.7236 (ttt180) cc_final: 0.6992 (ttt-90) REVERT: E 86 GLU cc_start: 0.7114 (mm-30) cc_final: 0.6504 (mm-30) REVERT: E 163 MET cc_start: 0.2613 (mtm) cc_final: 0.2292 (ptt) REVERT: F 77 ARG cc_start: 0.8610 (mtp180) cc_final: 0.8405 (mtp180) REVERT: F 115 MET cc_start: 0.6459 (mtp) cc_final: 0.6158 (mtp) REVERT: G 14 ASN cc_start: 0.8197 (m-40) cc_final: 0.7996 (m-40) REVERT: G 87 GLU cc_start: 0.8400 (mm-30) cc_final: 0.8128 (mm-30) REVERT: G 144 ASP cc_start: 0.8465 (p0) cc_final: 0.8198 (p0) REVERT: G 176 LEU cc_start: 0.7915 (tt) cc_final: 0.7615 (tp) REVERT: G 179 HIS cc_start: 0.8282 (t70) cc_final: 0.7909 (t70) REVERT: H 14 MET cc_start: 0.8359 (mtp) cc_final: 0.8099 (mtt) REVERT: H 23 ARG cc_start: 0.7361 (OUTLIER) cc_final: 0.6497 (ttt-90) REVERT: H 163 MET cc_start: 0.2973 (mtm) cc_final: 0.2461 (ptt) outliers start: 40 outliers final: 34 residues processed: 290 average time/residue: 0.2408 time to fit residues: 96.8602 Evaluate side-chains 315 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 277 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 176 GLU Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain E residue 10 GLN Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 176 GLU Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain G residue 173 ASP Chi-restraints excluded: chain H residue 22 GLU Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 160 MET Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 95 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 0.2980 chunk 121 optimal weight: 0.0010 chunk 129 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 101 optimal weight: 0.3980 chunk 39 optimal weight: 9.9990 chunk 116 optimal weight: 8.9990 chunk 122 optimal weight: 0.7980 chunk 128 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 120 ASN ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 ASN H 156 GLN ** I 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11652 Z= 0.178 Angle : 0.481 6.357 15888 Z= 0.251 Chirality : 0.042 0.176 1806 Planarity : 0.005 0.050 2055 Dihedral : 3.719 13.679 1653 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.23 % Allowed : 17.09 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 2.20 (0.23), residues: 1440 helix: 3.49 (0.22), residues: 504 sheet: 1.04 (0.25), residues: 399 loop : -0.23 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 180 HIS 0.003 0.001 HIS H 177 PHE 0.018 0.001 PHE D 54 TYR 0.009 0.001 TYR G 152 ARG 0.011 0.001 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 280 time to evaluate : 1.255 Fit side-chains revert: symmetry clash REVERT: A 42 LYS cc_start: 0.7717 (tttt) cc_final: 0.7493 (tttt) REVERT: A 43 GLU cc_start: 0.7037 (tp30) cc_final: 0.6726 (tp30) REVERT: A 44 THR cc_start: 0.8630 (m) cc_final: 0.7822 (t) REVERT: A 132 GLU cc_start: 0.7023 (tt0) cc_final: 0.6719 (tm-30) REVERT: A 158 SER cc_start: 0.7824 (t) cc_final: 0.7248 (p) REVERT: B 23 ARG cc_start: 0.7689 (ttt90) cc_final: 0.7313 (tpt-90) REVERT: B 82 ASN cc_start: 0.8379 (m-40) cc_final: 0.7751 (m-40) REVERT: B 163 MET cc_start: 0.3002 (ptt) cc_final: 0.2625 (ptt) REVERT: C 73 GLN cc_start: 0.8446 (tp40) cc_final: 0.8212 (tp40) REVERT: D 26 THR cc_start: 0.8546 (p) cc_final: 0.8286 (m) REVERT: D 28 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8179 (mt-10) REVERT: D 77 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7939 (mttm) REVERT: D 177 LEU cc_start: 0.8118 (mt) cc_final: 0.7873 (mm) REVERT: E 10 GLN cc_start: 0.9044 (OUTLIER) cc_final: 0.8694 (pt0) REVERT: E 70 ARG cc_start: 0.7221 (ttt180) cc_final: 0.6978 (ttt-90) REVERT: E 163 MET cc_start: 0.2725 (mtm) cc_final: 0.2488 (ptt) REVERT: F 115 MET cc_start: 0.6443 (mtp) cc_final: 0.6138 (mtp) REVERT: G 87 GLU cc_start: 0.8394 (mm-30) cc_final: 0.8130 (mm-30) REVERT: G 144 ASP cc_start: 0.8520 (p0) cc_final: 0.8196 (p0) REVERT: G 176 LEU cc_start: 0.7889 (tt) cc_final: 0.7523 (tp) REVERT: G 179 HIS cc_start: 0.8255 (t70) cc_final: 0.7877 (t70) REVERT: H 14 MET cc_start: 0.8272 (mtp) cc_final: 0.7997 (mtm) REVERT: H 23 ARG cc_start: 0.7372 (OUTLIER) cc_final: 0.6409 (ttt-90) REVERT: H 163 MET cc_start: 0.2843 (mtm) cc_final: 0.2497 (ptt) outliers start: 38 outliers final: 33 residues processed: 296 average time/residue: 0.2607 time to fit residues: 106.0740 Evaluate side-chains 315 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 279 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 176 GLU Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain E residue 10 GLN Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 176 GLU Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain G residue 173 ASP Chi-restraints excluded: chain H residue 22 GLU Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 160 MET Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 95 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 0.1980 chunk 83 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 143 optimal weight: 0.0870 chunk 132 optimal weight: 0.0970 chunk 114 optimal weight: 0.0870 chunk 11 optimal weight: 0.0470 chunk 88 optimal weight: 0.8980 chunk 70 optimal weight: 0.2980 chunk 90 optimal weight: 1.9990 overall best weight: 0.1032 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN D 120 ASN ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 ASN I 64 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11652 Z= 0.122 Angle : 0.460 6.074 15888 Z= 0.239 Chirality : 0.041 0.153 1806 Planarity : 0.005 0.050 2055 Dihedral : 3.520 12.768 1653 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.04 % Allowed : 18.20 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 2.47 (0.23), residues: 1440 helix: 3.70 (0.22), residues: 510 sheet: 1.19 (0.26), residues: 399 loop : -0.10 (0.28), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 180 HIS 0.003 0.001 HIS E 174 PHE 0.011 0.001 PHE A 148 TYR 0.007 0.001 TYR G 152 ARG 0.011 0.001 ARG B 48 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 285 time to evaluate : 1.255 Fit side-chains revert: symmetry clash REVERT: A 42 LYS cc_start: 0.7671 (tttt) cc_final: 0.7448 (tttt) REVERT: A 43 GLU cc_start: 0.7169 (tp30) cc_final: 0.6836 (tp30) REVERT: A 44 THR cc_start: 0.8564 (m) cc_final: 0.7982 (t) REVERT: A 97 SER cc_start: 0.8253 (m) cc_final: 0.7814 (p) REVERT: A 132 GLU cc_start: 0.7026 (tt0) cc_final: 0.6704 (tm-30) REVERT: B 23 ARG cc_start: 0.7884 (ttt90) cc_final: 0.7544 (tpt170) REVERT: B 82 ASN cc_start: 0.8397 (m-40) cc_final: 0.7723 (m-40) REVERT: C 73 GLN cc_start: 0.8350 (tp40) cc_final: 0.8124 (tp40) REVERT: C 77 ARG cc_start: 0.8639 (mmm-85) cc_final: 0.8436 (mtm180) REVERT: D 28 GLU cc_start: 0.8377 (mt-10) cc_final: 0.8143 (mt-10) REVERT: D 77 LYS cc_start: 0.8089 (mttm) cc_final: 0.7829 (mttm) REVERT: D 87 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8179 (mm-30) REVERT: D 105 ASN cc_start: 0.8583 (t0) cc_final: 0.8242 (m-40) REVERT: E 70 ARG cc_start: 0.7236 (ttt180) cc_final: 0.6983 (ttt-90) REVERT: F 115 MET cc_start: 0.6425 (mtp) cc_final: 0.6088 (mtp) REVERT: G 25 TYR cc_start: 0.8835 (t80) cc_final: 0.8294 (t80) REVERT: G 87 GLU cc_start: 0.8441 (mm-30) cc_final: 0.8180 (mm-30) REVERT: G 144 ASP cc_start: 0.8401 (p0) cc_final: 0.8080 (p0) REVERT: G 176 LEU cc_start: 0.7832 (tt) cc_final: 0.7423 (tp) REVERT: G 179 HIS cc_start: 0.8233 (t70) cc_final: 0.7864 (t70) REVERT: H 23 ARG cc_start: 0.7398 (OUTLIER) cc_final: 0.6435 (ttt-90) REVERT: H 163 MET cc_start: 0.2530 (mtm) cc_final: 0.2188 (ptt) outliers start: 24 outliers final: 16 residues processed: 297 average time/residue: 0.2571 time to fit residues: 103.8582 Evaluate side-chains 297 residues out of total 1332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 280 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 176 GLU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 173 ASP Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 160 MET Chi-restraints excluded: chain I residue 59 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 0.9990 chunk 34 optimal weight: 0.4980 chunk 105 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 31 optimal weight: 0.3980 chunk 114 optimal weight: 0.0470 chunk 47 optimal weight: 0.8980 chunk 117 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN D 120 ASN ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.140490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.115525 restraints weight = 16560.331| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.21 r_work: 0.3253 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11652 Z= 0.185 Angle : 0.483 7.114 15888 Z= 0.251 Chirality : 0.042 0.188 1806 Planarity : 0.005 0.050 2055 Dihedral : 3.622 14.144 1653 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.79 % Allowed : 18.11 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 2.45 (0.23), residues: 1440 helix: 3.73 (0.22), residues: 504 sheet: 1.15 (0.25), residues: 399 loop : -0.10 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 180 HIS 0.003 0.001 HIS H 177 PHE 0.011 0.001 PHE G 148 TYR 0.009 0.001 TYR G 152 ARG 0.010 0.001 ARG B 48 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2978.20 seconds wall clock time: 53 minutes 47.27 seconds (3227.27 seconds total)