Starting phenix.real_space_refine on Thu Feb 15 15:28:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fk0_29247/02_2024/8fk0_29247.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fk0_29247/02_2024/8fk0_29247.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fk0_29247/02_2024/8fk0_29247.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fk0_29247/02_2024/8fk0_29247.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fk0_29247/02_2024/8fk0_29247.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fk0_29247/02_2024/8fk0_29247.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.035 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 14 5.16 5 C 8008 2.51 5 N 2016 2.21 5 O 2590 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 122": "OE1" <-> "OE2" Residue "E PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 122": "OE1" <-> "OE2" Residue "G TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12628 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "B" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "C" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "I" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "D" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "J" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "E" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "K" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "F" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "L" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "G" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "M" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "H" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "N" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Time building chain proxies: 6.23, per 1000 atoms: 0.49 Number of scatterers: 12628 At special positions: 0 Unit cell: (90.72, 89.64, 164.16, 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 14 16.00 O 2590 8.00 N 2016 7.00 C 8008 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 4.47 Conformation dependent library (CDL) restraints added in 2.3 seconds 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3220 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 27 sheets defined 28.4% alpha, 37.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'A' and resid 1 through 34 removed outlier: 3.684A pdb=" N GLY A 30 " --> pdb=" O PHE A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 108 removed outlier: 3.741A pdb=" N ARG A 105 " --> pdb=" O THR A 102 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL A 108 " --> pdb=" O ARG A 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 34 Processing helix chain 'B' and resid 102 through 108 removed outlier: 3.695A pdb=" N ARG B 105 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY B 106 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL B 108 " --> pdb=" O ARG B 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 34 removed outlier: 3.758A pdb=" N THR C 6 " --> pdb=" O SER C 2 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY C 34 " --> pdb=" O GLY C 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 34 removed outlier: 3.607A pdb=" N GLY I 30 " --> pdb=" O PHE I 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 34 Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.818A pdb=" N GLY D 106 " --> pdb=" O THR D 103 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 34 removed outlier: 3.760A pdb=" N GLY J 30 " --> pdb=" O PHE J 26 " (cutoff:3.500A) Processing helix chain 'J' and resid 102 through 108 removed outlier: 3.657A pdb=" N GLY J 106 " --> pdb=" O THR J 103 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL J 108 " --> pdb=" O ARG J 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 34 Processing helix chain 'E' and resid 103 through 108 removed outlier: 3.729A pdb=" N GLY E 106 " --> pdb=" O THR E 103 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL E 108 " --> pdb=" O ARG E 105 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 34 Processing helix chain 'K' and resid 102 through 106 removed outlier: 3.579A pdb=" N ARG K 105 " --> pdb=" O THR K 102 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY K 106 " --> pdb=" O THR K 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 102 through 106' Processing helix chain 'F' and resid 2 through 34 removed outlier: 3.535A pdb=" N PHE F 29 " --> pdb=" O ALA F 25 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY F 30 " --> pdb=" O PHE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 108 removed outlier: 3.762A pdb=" N VAL F 108 " --> pdb=" O ARG F 105 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 34 Processing helix chain 'G' and resid 2 through 34 removed outlier: 3.545A pdb=" N PHE G 26 " --> pdb=" O VAL G 22 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY G 27 " --> pdb=" O GLY G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 108 removed outlier: 3.839A pdb=" N VAL G 108 " --> pdb=" O ARG G 105 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 34 removed outlier: 3.831A pdb=" N GLY M 34 " --> pdb=" O GLY M 30 " (cutoff:3.500A) Processing helix chain 'M' and resid 103 through 108 removed outlier: 3.579A pdb=" N GLY M 106 " --> pdb=" O THR M 103 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL M 108 " --> pdb=" O ARG M 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 34 removed outlier: 3.548A pdb=" N PHE H 29 " --> pdb=" O ALA H 25 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLY H 30 " --> pdb=" O PHE H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 108 removed outlier: 3.995A pdb=" N GLY H 106 " --> pdb=" O THR H 103 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL H 108 " --> pdb=" O ARG H 105 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 34 Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 40 removed outlier: 4.118A pdb=" N SER A 77 " --> pdb=" O SER A 96 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N VAL A 78 " --> pdb=" O THR A 67 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N THR A 67 " --> pdb=" O VAL A 78 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ALA A 44 " --> pdb=" O ILE A 129 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N THR A 131 " --> pdb=" O ALA A 44 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N LEU A 46 " --> pdb=" O THR A 131 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR A 52 " --> pdb=" O SER A 47 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 38 through 40 removed outlier: 6.207A pdb=" N ALA B 44 " --> pdb=" O ILE B 129 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N THR B 131 " --> pdb=" O ALA B 44 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N LEU B 46 " --> pdb=" O THR B 131 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 38 through 40 removed outlier: 3.650A pdb=" N ASN B 89 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER B 96 " --> pdb=" O SER B 77 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N SER B 77 " --> pdb=" O SER B 96 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N VAL B 78 " --> pdb=" O THR B 67 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N THR B 67 " --> pdb=" O VAL B 78 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR B 115 " --> pdb=" O LEU B 70 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLU B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 38 through 40 removed outlier: 3.533A pdb=" N ALA C 39 " --> pdb=" O LYS C 58 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ALA C 44 " --> pdb=" O ILE C 129 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N THR C 131 " --> pdb=" O ALA C 44 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N LEU C 46 " --> pdb=" O THR C 131 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER C 110 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 38 through 40 removed outlier: 3.533A pdb=" N ALA C 39 " --> pdb=" O LYS C 58 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU C 57 " --> pdb=" O ASN C 89 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 38 through 40 removed outlier: 6.452A pdb=" N ALA I 44 " --> pdb=" O ILE I 129 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N THR I 131 " --> pdb=" O ALA I 44 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N LEU I 46 " --> pdb=" O THR I 131 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU I 122 " --> pdb=" O LEU I 118 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR I 64 " --> pdb=" O ILE I 84 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 38 through 40 removed outlier: 3.573A pdb=" N ASN I 89 " --> pdb=" O LEU I 57 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER I 77 " --> pdb=" O SER I 96 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N VAL I 78 " --> pdb=" O THR I 67 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N THR I 67 " --> pdb=" O VAL I 78 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR I 64 " --> pdb=" O ILE I 84 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 38 through 40 removed outlier: 3.699A pdb=" N THR D 52 " --> pdb=" O SER D 47 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR D 115 " --> pdb=" O LEU D 70 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR D 64 " --> pdb=" O ILE D 84 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 38 through 40 removed outlier: 3.867A pdb=" N ASN D 89 " --> pdb=" O LEU D 57 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER D 77 " --> pdb=" O SER D 96 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N VAL D 78 " --> pdb=" O THR D 67 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N THR D 67 " --> pdb=" O VAL D 78 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR D 64 " --> pdb=" O ILE D 84 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 38 through 40 removed outlier: 6.604A pdb=" N ALA J 44 " --> pdb=" O ILE J 129 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N THR J 131 " --> pdb=" O ALA J 44 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU J 46 " --> pdb=" O THR J 131 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU J 122 " --> pdb=" O LEU J 118 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR J 64 " --> pdb=" O ILE J 84 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 38 through 40 removed outlier: 3.825A pdb=" N ASN J 89 " --> pdb=" O LEU J 57 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER J 96 " --> pdb=" O SER J 77 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER J 77 " --> pdb=" O SER J 96 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL J 78 " --> pdb=" O THR J 67 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N THR J 67 " --> pdb=" O VAL J 78 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR J 64 " --> pdb=" O ILE J 84 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 38 through 40 Processing sheet with id=AB4, first strand: chain 'E' and resid 38 through 40 Processing sheet with id=AB5, first strand: chain 'K' and resid 38 through 40 removed outlier: 3.603A pdb=" N ASN K 89 " --> pdb=" O LEU K 57 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER K 77 " --> pdb=" O SER K 96 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY K 68 " --> pdb=" O ILE K 117 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU K 122 " --> pdb=" O LEU K 118 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ALA K 44 " --> pdb=" O ILE K 129 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N THR K 131 " --> pdb=" O ALA K 44 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N LEU K 46 " --> pdb=" O THR K 131 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR K 52 " --> pdb=" O SER K 47 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 64 through 65 Processing sheet with id=AB7, first strand: chain 'F' and resid 38 through 40 removed outlier: 3.779A pdb=" N LEU F 57 " --> pdb=" O ASN F 89 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASN F 89 " --> pdb=" O LEU F 57 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER F 77 " --> pdb=" O SER F 96 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N VAL F 78 " --> pdb=" O THR F 67 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N THR F 67 " --> pdb=" O VAL F 78 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY F 68 " --> pdb=" O ILE F 117 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ALA F 44 " --> pdb=" O ILE F 129 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N THR F 131 " --> pdb=" O ALA F 44 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N LEU F 46 " --> pdb=" O THR F 131 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR F 52 " --> pdb=" O SER F 47 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 38 through 40 removed outlier: 3.558A pdb=" N ALA L 39 " --> pdb=" O LYS L 58 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ALA L 44 " --> pdb=" O ILE L 129 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N THR L 131 " --> pdb=" O ALA L 44 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N LEU L 46 " --> pdb=" O THR L 131 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLY L 68 " --> pdb=" O ILE L 117 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 38 through 40 removed outlier: 3.558A pdb=" N ALA L 39 " --> pdb=" O LYS L 58 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU L 57 " --> pdb=" O ASN L 89 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASN L 89 " --> pdb=" O LEU L 57 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 64 through 65 removed outlier: 3.631A pdb=" N THR L 64 " --> pdb=" O ILE L 84 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 38 through 40 Processing sheet with id=AC3, first strand: chain 'G' and resid 75 through 77 removed outlier: 3.672A pdb=" N THR G 115 " --> pdb=" O LEU G 70 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ALA G 44 " --> pdb=" O ILE G 129 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N THR G 131 " --> pdb=" O ALA G 44 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N LEU G 46 " --> pdb=" O THR G 131 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR G 45 " --> pdb=" O THR G 54 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR G 54 " --> pdb=" O THR G 45 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER G 47 " --> pdb=" O THR G 52 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N THR G 52 " --> pdb=" O SER G 47 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'M' and resid 38 through 40 removed outlier: 3.586A pdb=" N ALA M 39 " --> pdb=" O LYS M 58 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL M 55 " --> pdb=" O TYR M 91 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N TYR M 91 " --> pdb=" O VAL M 55 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER M 96 " --> pdb=" O SER M 77 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N SER M 77 " --> pdb=" O SER M 96 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N VAL M 78 " --> pdb=" O THR M 67 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N THR M 67 " --> pdb=" O VAL M 78 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLY M 68 " --> pdb=" O ILE M 117 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE M 117 " --> pdb=" O GLY M 68 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU M 122 " --> pdb=" O LEU M 118 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ALA M 44 " --> pdb=" O ILE M 129 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N THR M 131 " --> pdb=" O ALA M 44 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N LEU M 46 " --> pdb=" O THR M 131 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR M 52 " --> pdb=" O SER M 47 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 38 through 40 Processing sheet with id=AC6, first strand: chain 'H' and resid 75 through 76 removed outlier: 3.729A pdb=" N THR H 64 " --> pdb=" O ILE H 84 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 75 through 76 removed outlier: 6.640A pdb=" N ALA H 44 " --> pdb=" O ILE H 129 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N THR H 131 " --> pdb=" O ALA H 44 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N LEU H 46 " --> pdb=" O THR H 131 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N THR H 52 " --> pdb=" O SER H 47 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'N' and resid 38 through 40 removed outlier: 6.645A pdb=" N ALA N 44 " --> pdb=" O ILE N 129 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N THR N 131 " --> pdb=" O ALA N 44 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N LEU N 46 " --> pdb=" O THR N 131 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU N 116 " --> pdb=" O VAL N 124 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 38 through 40 removed outlier: 3.935A pdb=" N LEU N 57 " --> pdb=" O ASN N 89 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASN N 89 " --> pdb=" O LEU N 57 " (cutoff:3.500A) 751 hydrogen bonds defined for protein. 2157 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: 3.73 Time building geometry restraints manager: 4.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3990 1.34 - 1.46: 2823 1.46 - 1.58: 5843 1.58 - 1.70: 0 1.70 - 1.82: 28 Bond restraints: 12684 Sorted by residual: bond pdb=" N VAL K 66 " pdb=" CA VAL K 66 " ideal model delta sigma weight residual 1.460 1.474 -0.014 1.23e-02 6.61e+03 1.38e+00 bond pdb=" N VAL N 66 " pdb=" CA VAL N 66 " ideal model delta sigma weight residual 1.460 1.474 -0.014 1.23e-02 6.61e+03 1.38e+00 bond pdb=" CG1 ILE N 16 " pdb=" CD1 ILE N 16 " ideal model delta sigma weight residual 1.513 1.471 0.042 3.90e-02 6.57e+02 1.15e+00 bond pdb=" CA GLY G 76 " pdb=" C GLY G 76 " ideal model delta sigma weight residual 1.514 1.523 -0.008 8.20e-03 1.49e+04 1.06e+00 bond pdb=" CG ARG A 105 " pdb=" CD ARG A 105 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 6.75e-01 ... (remaining 12679 not shown) Histogram of bond angle deviations from ideal: 100.67 - 106.20: 29 106.20 - 111.73: 7617 111.73 - 117.26: 2711 117.26 - 122.79: 5763 122.79 - 128.33: 1268 Bond angle restraints: 17388 Sorted by residual: angle pdb=" C SER C 101 " pdb=" N THR C 102 " pdb=" CA THR C 102 " ideal model delta sigma weight residual 121.54 128.33 -6.79 1.91e+00 2.74e-01 1.26e+01 angle pdb=" N ILE A 100 " pdb=" CA ILE A 100 " pdb=" C ILE A 100 " ideal model delta sigma weight residual 111.91 109.16 2.75 8.90e-01 1.26e+00 9.52e+00 angle pdb=" N VAL J 41 " pdb=" CA VAL J 41 " pdb=" C VAL J 41 " ideal model delta sigma weight residual 112.96 110.57 2.39 1.00e+00 1.00e+00 5.69e+00 angle pdb=" CB MET B 81 " pdb=" CG MET B 81 " pdb=" SD MET B 81 " ideal model delta sigma weight residual 112.70 119.59 -6.89 3.00e+00 1.11e-01 5.28e+00 angle pdb=" CA LEU N 8 " pdb=" CB LEU N 8 " pdb=" CG LEU N 8 " ideal model delta sigma weight residual 116.30 108.42 7.88 3.50e+00 8.16e-02 5.07e+00 ... (remaining 17383 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.45: 6827 16.45 - 32.90: 393 32.90 - 49.35: 55 49.35 - 65.81: 7 65.81 - 82.26: 12 Dihedral angle restraints: 7294 sinusoidal: 2226 harmonic: 5068 Sorted by residual: dihedral pdb=" CA ASN F 89 " pdb=" CB ASN F 89 " pdb=" CG ASN F 89 " pdb=" OD1 ASN F 89 " ideal model delta sinusoidal sigma weight residual 120.00 -173.49 -66.51 2 2.00e+01 2.50e-03 1.01e+01 dihedral pdb=" CG ARG B 105 " pdb=" CD ARG B 105 " pdb=" NE ARG B 105 " pdb=" CZ ARG B 105 " ideal model delta sinusoidal sigma weight residual 90.00 50.99 39.01 2 1.50e+01 4.44e-03 8.45e+00 dihedral pdb=" CA PHE J 29 " pdb=" CB PHE J 29 " pdb=" CG PHE J 29 " pdb=" CD1 PHE J 29 " ideal model delta sinusoidal sigma weight residual 90.00 35.07 54.93 2 2.00e+01 2.50e-03 8.04e+00 ... (remaining 7291 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1852 0.037 - 0.075: 428 0.075 - 0.112: 215 0.112 - 0.149: 71 0.149 - 0.187: 10 Chirality restraints: 2576 Sorted by residual: chirality pdb=" CG LEU G 57 " pdb=" CB LEU G 57 " pdb=" CD1 LEU G 57 " pdb=" CD2 LEU G 57 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.71e-01 chirality pdb=" CB VAL G 55 " pdb=" CA VAL G 55 " pdb=" CG1 VAL G 55 " pdb=" CG2 VAL G 55 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.60e-01 chirality pdb=" CB ILE N 17 " pdb=" CA ILE N 17 " pdb=" CG1 ILE N 17 " pdb=" CG2 ILE N 17 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.58e-01 ... (remaining 2573 not shown) Planarity restraints: 2058 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET N 81 " 0.006 2.00e-02 2.50e+03 1.17e-02 1.36e+00 pdb=" C MET N 81 " -0.020 2.00e-02 2.50e+03 pdb=" O MET N 81 " 0.008 2.00e-02 2.50e+03 pdb=" N THR N 82 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN M 72 " -0.006 2.00e-02 2.50e+03 1.15e-02 1.32e+00 pdb=" C ASN M 72 " 0.020 2.00e-02 2.50e+03 pdb=" O ASN M 72 " -0.007 2.00e-02 2.50e+03 pdb=" N GLY M 73 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 29 " 0.009 2.00e-02 2.50e+03 8.39e-03 1.23e+00 pdb=" CG PHE B 29 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 PHE B 29 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE B 29 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE B 29 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 29 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 29 " 0.000 2.00e-02 2.50e+03 ... (remaining 2055 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 139 2.64 - 3.20: 12025 3.20 - 3.77: 18557 3.77 - 4.33: 24216 4.33 - 4.90: 42452 Nonbonded interactions: 97389 Sorted by model distance: nonbonded pdb=" O VAL E 108 " pdb=" OG SER K 119 " model vdw 2.069 2.440 nonbonded pdb=" O ILE G 100 " pdb=" OG1 THR G 103 " model vdw 2.168 2.440 nonbonded pdb=" OD1 ASN A 72 " pdb=" N GLY A 73 " model vdw 2.197 2.520 nonbonded pdb=" OD1 ASN H 74 " pdb=" OG SER H 99 " model vdw 2.220 2.440 nonbonded pdb=" NE2 GLN H 40 " pdb=" O GLY H 42 " model vdw 2.235 2.520 ... (remaining 97384 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } 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 group one per residue 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: 2.340 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: 11.890 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 32.720 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 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 : 0.003 0.042 12684 Z= 0.192 Angle : 0.555 7.883 17388 Z= 0.311 Chirality : 0.045 0.187 2576 Planarity : 0.002 0.030 2058 Dihedral : 11.080 82.258 4074 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.14 % Allowed : 0.35 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.20), residues: 1820 helix: 2.72 (0.22), residues: 574 sheet: 0.03 (0.19), residues: 742 loop : -0.94 (0.23), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.019 0.001 PHE B 29 TYR 0.007 0.001 TYR L 91 ARG 0.007 0.001 ARG B 105 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 209 time to evaluate : 1.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 105 ARG cc_start: 0.7874 (tpp80) cc_final: 0.7435 (tpt170) REVERT: C 110 SER cc_start: 0.9240 (m) cc_final: 0.8748 (t) REVERT: F 125 THR cc_start: 0.9457 (t) cc_final: 0.9181 (m) REVERT: G 120 ASN cc_start: 0.6126 (t0) cc_final: 0.5478 (m-40) REVERT: M 89 ASN cc_start: 0.8807 (m110) cc_final: 0.7671 (m-40) REVERT: H 59 ASN cc_start: 0.6534 (OUTLIER) cc_final: 0.6328 (m-40) REVERT: N 17 ILE cc_start: 0.7996 (mm) cc_final: 0.7795 (mm) outliers start: 2 outliers final: 0 residues processed: 210 average time/residue: 0.1891 time to fit residues: 61.8553 Evaluate side-chains 158 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 157 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 59 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 0.9990 chunk 137 optimal weight: 0.0770 chunk 76 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 chunk 142 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 overall best weight: 1.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN K 89 ASN M 65 GLN ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12684 Z= 0.263 Angle : 0.555 9.088 17388 Z= 0.298 Chirality : 0.046 0.197 2576 Planarity : 0.002 0.021 2058 Dihedral : 4.058 18.235 1878 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.57 % Allowed : 7.63 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.19), residues: 1820 helix: 2.76 (0.22), residues: 574 sheet: -0.14 (0.19), residues: 700 loop : -0.96 (0.23), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.002 PHE G 32 TYR 0.022 0.002 TYR M 91 ARG 0.005 0.001 ARG B 105 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 164 time to evaluate : 1.401 Fit side-chains revert: symmetry clash REVERT: B 105 ARG cc_start: 0.7876 (tpp80) cc_final: 0.7515 (tpt170) REVERT: I 8 LEU cc_start: 0.9173 (tp) cc_final: 0.8947 (tp) REVERT: F 125 THR cc_start: 0.9616 (t) cc_final: 0.9339 (m) REVERT: H 32 PHE cc_start: 0.7665 (m-80) cc_final: 0.7454 (t80) outliers start: 37 outliers final: 25 residues processed: 185 average time/residue: 0.1945 time to fit residues: 55.5709 Evaluate side-chains 168 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 143 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 132 SER Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain K residue 43 THR Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 89 ASN Chi-restraints excluded: chain L residue 89 ASN Chi-restraints excluded: chain G residue 91 TYR Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain N residue 37 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 137 optimal weight: 0.9980 chunk 112 optimal weight: 5.9990 chunk 45 optimal weight: 0.0980 chunk 165 optimal weight: 2.9990 chunk 178 optimal weight: 8.9990 chunk 147 optimal weight: 0.1980 chunk 164 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN C 59 ASN I 40 GLN ** G 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12684 Z= 0.151 Angle : 0.497 9.034 17388 Z= 0.262 Chirality : 0.045 0.215 2576 Planarity : 0.002 0.016 2058 Dihedral : 3.844 15.756 1876 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.87 % Allowed : 11.65 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.20), residues: 1820 helix: 2.93 (0.22), residues: 574 sheet: -0.15 (0.19), residues: 700 loop : -0.97 (0.22), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.001 PHE G 32 TYR 0.007 0.001 TYR D 91 ARG 0.003 0.000 ARG B 105 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 170 time to evaluate : 1.373 Fit side-chains revert: symmetry clash REVERT: A 110 SER cc_start: 0.9377 (m) cc_final: 0.8930 (t) REVERT: B 105 ARG cc_start: 0.7881 (tpp80) cc_final: 0.7415 (tpt170) REVERT: B 117 ILE cc_start: 0.8818 (mm) cc_final: 0.8572 (mt) REVERT: J 105 ARG cc_start: 0.8323 (mtp85) cc_final: 0.8049 (tpp80) REVERT: E 105 ARG cc_start: 0.8186 (mtm-85) cc_final: 0.7742 (mtm-85) REVERT: F 125 THR cc_start: 0.9607 (t) cc_final: 0.9330 (m) REVERT: G 81 MET cc_start: 0.7012 (tpp) cc_final: 0.6478 (mtt) outliers start: 27 outliers final: 21 residues processed: 186 average time/residue: 0.2056 time to fit residues: 58.8661 Evaluate side-chains 176 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 155 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 89 ASN Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 89 ASN Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 91 TYR Chi-restraints excluded: chain M residue 28 LEU Chi-restraints excluded: chain M residue 29 PHE Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 37 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 163 optimal weight: 10.0000 chunk 124 optimal weight: 3.9990 chunk 85 optimal weight: 0.4980 chunk 18 optimal weight: 6.9990 chunk 79 optimal weight: 0.8980 chunk 111 optimal weight: 4.9990 chunk 166 optimal weight: 0.9990 chunk 175 optimal weight: 9.9990 chunk 86 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN ** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 ASN ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 12684 Z= 0.323 Angle : 0.565 10.404 17388 Z= 0.298 Chirality : 0.046 0.170 2576 Planarity : 0.002 0.021 2058 Dihedral : 4.052 18.816 1876 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.68 % Allowed : 12.97 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.19), residues: 1820 helix: 2.95 (0.22), residues: 532 sheet: -0.34 (0.19), residues: 700 loop : -0.97 (0.22), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.002 PHE G 29 TYR 0.008 0.001 TYR L 91 ARG 0.002 0.000 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 153 time to evaluate : 1.373 Fit side-chains revert: symmetry clash REVERT: A 110 SER cc_start: 0.9443 (m) cc_final: 0.9047 (t) REVERT: B 105 ARG cc_start: 0.7868 (tpp80) cc_final: 0.7486 (tpt170) REVERT: B 117 ILE cc_start: 0.8959 (mm) cc_final: 0.8723 (mt) REVERT: J 105 ARG cc_start: 0.8344 (mtp85) cc_final: 0.8137 (tpp80) REVERT: E 105 ARG cc_start: 0.8293 (mtm-85) cc_final: 0.8046 (mtm-85) REVERT: F 125 THR cc_start: 0.9642 (t) cc_final: 0.9382 (m) outliers start: 53 outliers final: 37 residues processed: 188 average time/residue: 0.2133 time to fit residues: 61.8640 Evaluate side-chains 181 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 144 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 19 LEU Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 132 SER Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 89 ASN Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 89 ASN Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 91 TYR Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain M residue 29 PHE Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 64 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 146 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 2 optimal weight: 0.5980 chunk 130 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 150 optimal weight: 0.0020 chunk 121 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 157 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12684 Z= 0.160 Angle : 0.494 8.572 17388 Z= 0.262 Chirality : 0.045 0.202 2576 Planarity : 0.002 0.016 2058 Dihedral : 3.823 16.357 1876 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.91 % Allowed : 14.98 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.20), residues: 1820 helix: 2.82 (0.22), residues: 574 sheet: -0.27 (0.19), residues: 700 loop : -1.07 (0.22), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.015 0.001 PHE C 29 TYR 0.006 0.001 TYR A 91 ARG 0.004 0.000 ARG D 105 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 167 time to evaluate : 1.360 Fit side-chains revert: symmetry clash REVERT: A 37 THR cc_start: 0.8178 (OUTLIER) cc_final: 0.7962 (p) REVERT: A 89 ASN cc_start: 0.9109 (m-40) cc_final: 0.8791 (m110) REVERT: A 110 SER cc_start: 0.9393 (m) cc_final: 0.8972 (t) REVERT: B 105 ARG cc_start: 0.7827 (tpp80) cc_final: 0.7433 (tpt170) REVERT: B 117 ILE cc_start: 0.8931 (mm) cc_final: 0.8689 (mt) REVERT: J 105 ARG cc_start: 0.8348 (mtp85) cc_final: 0.8118 (tpp80) REVERT: F 125 THR cc_start: 0.9614 (t) cc_final: 0.9383 (m) REVERT: G 81 MET cc_start: 0.6566 (tpt) cc_final: 0.5871 (mpp) REVERT: N 120 ASN cc_start: 0.8440 (p0) cc_final: 0.8189 (p0) outliers start: 42 outliers final: 27 residues processed: 197 average time/residue: 0.2028 time to fit residues: 61.2445 Evaluate side-chains 178 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 150 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 19 LEU Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain J residue 132 SER Chi-restraints excluded: chain E residue 35 GLN Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 89 ASN Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 89 ASN Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 91 TYR Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain M residue 28 LEU Chi-restraints excluded: chain M residue 29 PHE Chi-restraints excluded: chain M residue 32 PHE Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain N residue 37 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 59 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 34 optimal weight: 0.0980 chunk 103 optimal weight: 3.9990 chunk 43 optimal weight: 0.0270 chunk 176 optimal weight: 7.9990 chunk 146 optimal weight: 10.0000 chunk 81 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 overall best weight: 0.9642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 ASN ** I 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12684 Z= 0.195 Angle : 0.494 7.481 17388 Z= 0.262 Chirality : 0.045 0.172 2576 Planarity : 0.002 0.020 2058 Dihedral : 3.777 15.709 1876 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.19 % Allowed : 15.74 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.20), residues: 1820 helix: 3.11 (0.22), residues: 532 sheet: -0.29 (0.19), residues: 700 loop : -0.96 (0.22), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.015 0.001 PHE C 29 TYR 0.007 0.001 TYR G 91 ARG 0.004 0.001 ARG E 105 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 156 time to evaluate : 1.468 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 SER cc_start: 0.9435 (m) cc_final: 0.9005 (t) REVERT: B 105 ARG cc_start: 0.7856 (tpp80) cc_final: 0.7448 (tpt170) REVERT: B 117 ILE cc_start: 0.9023 (mm) cc_final: 0.8790 (mt) REVERT: J 105 ARG cc_start: 0.8332 (mtp85) cc_final: 0.8111 (tpp80) REVERT: F 125 THR cc_start: 0.9590 (t) cc_final: 0.9278 (p) REVERT: M 84 ILE cc_start: 0.6641 (tt) cc_final: 0.6312 (pt) REVERT: H 40 GLN cc_start: 0.8558 (tm-30) cc_final: 0.8226 (tm-30) REVERT: N 120 ASN cc_start: 0.8464 (p0) cc_final: 0.8231 (p0) outliers start: 46 outliers final: 33 residues processed: 187 average time/residue: 0.2016 time to fit residues: 58.5398 Evaluate side-chains 183 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 150 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 19 LEU Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain J residue 132 SER Chi-restraints excluded: chain E residue 35 GLN Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 89 ASN Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain L residue 29 PHE Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain L residue 89 ASN Chi-restraints excluded: chain G residue 91 TYR Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain M residue 32 PHE Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain N residue 37 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 169 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 128 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 175 optimal weight: 6.9990 chunk 109 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 chunk 80 optimal weight: 0.5980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 12684 Z= 0.362 Angle : 0.575 9.444 17388 Z= 0.306 Chirality : 0.047 0.212 2576 Planarity : 0.002 0.025 2058 Dihedral : 4.084 19.893 1876 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.74 % Allowed : 16.50 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.19), residues: 1820 helix: 2.81 (0.22), residues: 532 sheet: -0.39 (0.20), residues: 658 loop : -1.12 (0.21), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.002 PHE G 32 TYR 0.009 0.002 TYR L 91 ARG 0.004 0.001 ARG D 105 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 139 time to evaluate : 1.400 Fit side-chains revert: symmetry clash REVERT: A 110 SER cc_start: 0.9493 (m) cc_final: 0.9115 (t) REVERT: B 105 ARG cc_start: 0.7866 (tpp80) cc_final: 0.7481 (tpt170) REVERT: B 117 ILE cc_start: 0.9075 (mm) cc_final: 0.8828 (mt) REVERT: J 105 ARG cc_start: 0.8343 (mtp85) cc_final: 0.8078 (tpp80) REVERT: F 125 THR cc_start: 0.9613 (t) cc_final: 0.9349 (m) REVERT: N 120 ASN cc_start: 0.8519 (p0) cc_final: 0.8298 (p0) outliers start: 54 outliers final: 42 residues processed: 184 average time/residue: 0.2024 time to fit residues: 57.6150 Evaluate side-chains 178 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 136 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 132 SER Chi-restraints excluded: chain E residue 35 GLN Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 89 ASN Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain L residue 29 PHE Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain L residue 89 ASN Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 91 TYR Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain M residue 32 PHE Chi-restraints excluded: chain M residue 72 ASN Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain N residue 37 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 108 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 137 optimal weight: 0.0030 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 40 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12684 Z= 0.171 Angle : 0.500 8.278 17388 Z= 0.262 Chirality : 0.044 0.170 2576 Planarity : 0.002 0.018 2058 Dihedral : 3.811 17.575 1876 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.05 % Allowed : 17.89 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.20), residues: 1820 helix: 3.06 (0.23), residues: 532 sheet: -0.42 (0.19), residues: 700 loop : -0.98 (0.22), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.001 PHE G 32 TYR 0.006 0.001 TYR G 91 ARG 0.004 0.001 ARG D 105 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 153 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 SER cc_start: 0.9478 (m) cc_final: 0.9044 (t) REVERT: B 105 ARG cc_start: 0.7872 (tpp80) cc_final: 0.7351 (tpt170) REVERT: B 117 ILE cc_start: 0.9004 (mm) cc_final: 0.8780 (mt) REVERT: J 105 ARG cc_start: 0.8336 (mtp85) cc_final: 0.8054 (tpp80) REVERT: F 125 THR cc_start: 0.9620 (t) cc_final: 0.9395 (m) REVERT: L 32 PHE cc_start: 0.6995 (m-80) cc_final: 0.6787 (m-80) REVERT: H 91 TYR cc_start: 0.8044 (m-80) cc_final: 0.7799 (m-80) REVERT: N 120 ASN cc_start: 0.8477 (p0) cc_final: 0.8190 (p0) outliers start: 44 outliers final: 38 residues processed: 187 average time/residue: 0.1988 time to fit residues: 57.4076 Evaluate side-chains 180 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 142 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 19 LEU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 132 SER Chi-restraints excluded: chain E residue 35 GLN Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 89 ASN Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain L residue 29 PHE Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain L residue 89 ASN Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 91 TYR Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain M residue 32 PHE Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain N residue 37 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 159 optimal weight: 7.9990 chunk 168 optimal weight: 2.9990 chunk 153 optimal weight: 20.0000 chunk 163 optimal weight: 9.9990 chunk 98 optimal weight: 7.9990 chunk 71 optimal weight: 0.5980 chunk 128 optimal weight: 0.9980 chunk 50 optimal weight: 0.0270 chunk 147 optimal weight: 9.9990 chunk 154 optimal weight: 0.5980 chunk 162 optimal weight: 7.9990 overall best weight: 1.0440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12684 Z= 0.206 Angle : 0.503 7.875 17388 Z= 0.267 Chirality : 0.044 0.172 2576 Planarity : 0.002 0.019 2058 Dihedral : 3.771 16.809 1876 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.19 % Allowed : 17.89 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.20), residues: 1820 helix: 3.04 (0.22), residues: 532 sheet: -0.44 (0.19), residues: 700 loop : -1.01 (0.22), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.001 PHE G 32 TYR 0.006 0.001 TYR L 91 ARG 0.006 0.001 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 149 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 SER cc_start: 0.9459 (m) cc_final: 0.9086 (t) REVERT: B 105 ARG cc_start: 0.7863 (tpp80) cc_final: 0.7344 (tpt170) REVERT: B 117 ILE cc_start: 0.8960 (mm) cc_final: 0.8749 (mt) REVERT: J 105 ARG cc_start: 0.8344 (mtp85) cc_final: 0.8068 (tpp80) REVERT: F 125 THR cc_start: 0.9574 (t) cc_final: 0.9299 (m) REVERT: L 32 PHE cc_start: 0.6982 (m-80) cc_final: 0.6763 (m-80) REVERT: L 81 MET cc_start: 0.7341 (ttm) cc_final: 0.6940 (mtp) outliers start: 46 outliers final: 43 residues processed: 182 average time/residue: 0.1999 time to fit residues: 56.1622 Evaluate side-chains 191 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 148 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 19 LEU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 132 SER Chi-restraints excluded: chain E residue 35 GLN Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 89 ASN Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain L residue 29 PHE Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain L residue 89 ASN Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 91 TYR Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain M residue 32 PHE Chi-restraints excluded: chain M residue 72 ASN Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain N residue 37 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 107 optimal weight: 0.6980 chunk 172 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 120 optimal weight: 0.8980 chunk 181 optimal weight: 1.9990 chunk 166 optimal weight: 0.9990 chunk 144 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 111 optimal weight: 0.0770 chunk 88 optimal weight: 10.0000 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 40 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12684 Z= 0.163 Angle : 0.478 7.535 17388 Z= 0.254 Chirality : 0.044 0.157 2576 Planarity : 0.002 0.024 2058 Dihedral : 3.661 16.501 1876 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.98 % Allowed : 18.45 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.20), residues: 1820 helix: 3.13 (0.23), residues: 532 sheet: -0.41 (0.20), residues: 700 loop : -0.99 (0.22), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.017 0.001 PHE C 29 TYR 0.005 0.001 TYR G 91 ARG 0.006 0.001 ARG A 105 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 154 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 SER cc_start: 0.9437 (m) cc_final: 0.9062 (t) REVERT: B 105 ARG cc_start: 0.7879 (tpp80) cc_final: 0.7371 (tpt170) REVERT: J 105 ARG cc_start: 0.8331 (mtp85) cc_final: 0.8060 (tpp80) REVERT: F 125 THR cc_start: 0.9553 (t) cc_final: 0.9300 (p) REVERT: L 81 MET cc_start: 0.7343 (ttm) cc_final: 0.6939 (mtp) REVERT: H 91 TYR cc_start: 0.8050 (m-80) cc_final: 0.7787 (m-80) REVERT: N 28 LEU cc_start: 0.8830 (tt) cc_final: 0.8445 (tt) outliers start: 43 outliers final: 37 residues processed: 185 average time/residue: 0.1935 time to fit residues: 55.3559 Evaluate side-chains 182 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 145 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 19 LEU Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 132 SER Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain F residue 89 ASN Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain L residue 29 PHE Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain L residue 89 ASN Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 91 TYR Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain M residue 32 PHE Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain N residue 37 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 114 optimal weight: 0.2980 chunk 153 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 133 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 144 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 chunk 148 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 26 optimal weight: 0.0980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 65 GLN H 40 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.133694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.110009 restraints weight = 21798.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.110802 restraints weight = 16367.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.111291 restraints weight = 13581.441| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12684 Z= 0.179 Angle : 0.503 10.555 17388 Z= 0.263 Chirality : 0.044 0.171 2576 Planarity : 0.002 0.025 2058 Dihedral : 3.638 16.461 1876 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.77 % Allowed : 19.07 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.20), residues: 1820 helix: 3.14 (0.23), residues: 532 sheet: -0.39 (0.20), residues: 700 loop : -0.99 (0.22), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.014 0.001 PHE C 29 TYR 0.006 0.001 TYR L 91 ARG 0.006 0.001 ARG A 105 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2262.57 seconds wall clock time: 42 minutes 44.44 seconds (2564.44 seconds total)