Starting phenix.real_space_refine on Sun Mar 10 20:27:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q66_13853/03_2024/7q66_13853.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q66_13853/03_2024/7q66_13853.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q66_13853/03_2024/7q66_13853.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q66_13853/03_2024/7q66_13853.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q66_13853/03_2024/7q66_13853.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q66_13853/03_2024/7q66_13853.pdb" } resolution = 2.79 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= 0.009 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: 3 Type Number sf(0) Gaussians C 2959 2.51 5 N 814 2.21 5 O 1034 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 4807 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 262 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "B" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 175 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "C" Number of atoms: 262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 262 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "D" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 175 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "E" Number of atoms: 262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 262 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "F" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 175 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "G" Number of atoms: 262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 262 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "H" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 175 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "I" Number of atoms: 262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 262 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "J" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 175 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "K" Number of atoms: 262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 262 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "L" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 175 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "M" Number of atoms: 262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 262 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "N" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 175 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "O" Number of atoms: 262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 262 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "P" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 175 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "Q" Number of atoms: 262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 262 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "R" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 175 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "S" Number of atoms: 262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 262 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "T" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 175 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "U" Number of atoms: 262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 262 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "V" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 175 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Time building chain proxies: 2.91, per 1000 atoms: 0.61 Number of scatterers: 4807 At special positions: 0 Unit cell: (66.15, 61.95, 72.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 1034 8.00 N 814 7.00 C 2959 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: 1.98 Conformation dependent library (CDL) restraints added in 951.2 milliseconds 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1166 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 7 sheets defined 0.0% alpha, 53.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 88 through 92 removed outlier: 6.095A pdb=" N ALA A 88 " --> pdb=" O ASN C 89 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N LEU C 91 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 8.956A pdb=" N THR A 90 " --> pdb=" O LEU C 91 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ALA C 88 " --> pdb=" O ASN E 89 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N LEU E 91 " --> pdb=" O ALA C 88 " (cutoff:3.500A) removed outlier: 8.956A pdb=" N THR C 90 " --> pdb=" O LEU E 91 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ALA E 88 " --> pdb=" O ASN G 89 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N LEU G 91 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 8.956A pdb=" N THR E 90 " --> pdb=" O LEU G 91 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ALA G 88 " --> pdb=" O ASN I 89 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N LEU I 91 " --> pdb=" O ALA G 88 " (cutoff:3.500A) removed outlier: 8.956A pdb=" N THR G 90 " --> pdb=" O LEU I 91 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ALA I 88 " --> pdb=" O ASN K 89 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N LEU K 91 " --> pdb=" O ALA I 88 " (cutoff:3.500A) removed outlier: 8.955A pdb=" N THR I 90 " --> pdb=" O LEU K 91 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ALA K 88 " --> pdb=" O ASN M 89 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N LEU M 91 " --> pdb=" O ALA K 88 " (cutoff:3.500A) removed outlier: 8.955A pdb=" N THR K 90 " --> pdb=" O LEU M 91 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ALA M 88 " --> pdb=" O ASN O 89 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N LEU O 91 " --> pdb=" O ALA M 88 " (cutoff:3.500A) removed outlier: 8.956A pdb=" N THR M 90 " --> pdb=" O LEU O 91 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ALA O 88 " --> pdb=" O ASN Q 89 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N LEU Q 91 " --> pdb=" O ALA O 88 " (cutoff:3.500A) removed outlier: 8.956A pdb=" N THR O 90 " --> pdb=" O LEU Q 91 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ALA Q 88 " --> pdb=" O ASN S 89 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N LEU S 91 " --> pdb=" O ALA Q 88 " (cutoff:3.500A) removed outlier: 8.956A pdb=" N THR Q 90 " --> pdb=" O LEU S 91 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ALA S 88 " --> pdb=" O ASN U 89 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N LEU U 91 " --> pdb=" O ALA S 88 " (cutoff:3.500A) removed outlier: 8.956A pdb=" N THR S 90 " --> pdb=" O LEU U 91 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 95 through 96 removed outlier: 6.382A pdb=" N ALA A 95 " --> pdb=" O SER C 96 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ALA C 95 " --> pdb=" O SER E 96 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ALA E 95 " --> pdb=" O SER G 96 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ALA G 95 " --> pdb=" O SER I 96 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ALA I 95 " --> pdb=" O SER K 96 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ALA K 95 " --> pdb=" O SER M 96 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ALA M 95 " --> pdb=" O SER O 96 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ALA O 95 " --> pdb=" O SER Q 96 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ALA Q 95 " --> pdb=" O SER S 96 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ALA S 95 " --> pdb=" O SER U 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 100 through 101 Processing sheet with id=AA4, first strand: chain 'A' and resid 105 through 112 removed outlier: 6.882A pdb=" N ASN A 106 " --> pdb=" O ASN C 107 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N PHE C 109 " --> pdb=" O ASN A 106 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ALA A 108 " --> pdb=" O PHE C 109 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLN C 111 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ALA A 110 " --> pdb=" O GLN C 111 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ASN C 106 " --> pdb=" O ASN E 107 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N PHE E 109 " --> pdb=" O ASN C 106 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ALA C 108 " --> pdb=" O PHE E 109 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLN E 111 " --> pdb=" O ALA C 108 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ALA C 110 " --> pdb=" O GLN E 111 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ASN E 106 " --> pdb=" O ASN G 107 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N PHE G 109 " --> pdb=" O ASN E 106 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ALA E 108 " --> pdb=" O PHE G 109 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLN G 111 " --> pdb=" O ALA E 108 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ALA E 110 " --> pdb=" O GLN G 111 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ASN G 106 " --> pdb=" O ASN I 107 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N PHE I 109 " --> pdb=" O ASN G 106 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ALA G 108 " --> pdb=" O PHE I 109 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N GLN I 111 " --> pdb=" O ALA G 108 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ALA G 110 " --> pdb=" O GLN I 111 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ASN I 106 " --> pdb=" O ASN K 107 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N PHE K 109 " --> pdb=" O ASN I 106 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ALA I 108 " --> pdb=" O PHE K 109 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLN K 111 " --> pdb=" O ALA I 108 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ALA I 110 " --> pdb=" O GLN K 111 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ASN K 106 " --> pdb=" O ASN M 107 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N PHE M 109 " --> pdb=" O ASN K 106 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ALA K 108 " --> pdb=" O PHE M 109 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLN M 111 " --> pdb=" O ALA K 108 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ALA K 110 " --> pdb=" O GLN M 111 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ASN M 106 " --> pdb=" O ASN O 107 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N PHE O 109 " --> pdb=" O ASN M 106 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ALA M 108 " --> pdb=" O PHE O 109 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLN O 111 " --> pdb=" O ALA M 108 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ALA M 110 " --> pdb=" O GLN O 111 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ASN O 106 " --> pdb=" O ASN Q 107 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N PHE Q 109 " --> pdb=" O ASN O 106 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ALA O 108 " --> pdb=" O PHE Q 109 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLN Q 111 " --> pdb=" O ALA O 108 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ALA O 110 " --> pdb=" O GLN Q 111 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ASN Q 106 " --> pdb=" O ASN S 107 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N PHE S 109 " --> pdb=" O ASN Q 106 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ALA Q 108 " --> pdb=" O PHE S 109 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLN S 111 " --> pdb=" O ALA Q 108 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ALA Q 110 " --> pdb=" O GLN S 111 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ASN S 106 " --> pdb=" O ASN U 107 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N PHE U 109 " --> pdb=" O ASN S 106 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ALA S 108 " --> pdb=" O PHE U 109 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLN U 111 " --> pdb=" O ALA S 108 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ALA S 110 " --> pdb=" O GLN U 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 115 through 120 removed outlier: 6.517A pdb=" N THR A 115 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N GLY C 118 " --> pdb=" O THR A 115 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N PHE A 117 " --> pdb=" O GLY C 118 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N PHE C 120 " --> pdb=" O PHE A 117 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ASN A 119 " --> pdb=" O PHE C 120 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N THR C 115 " --> pdb=" O GLY E 116 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N GLY E 118 " --> pdb=" O THR C 115 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N PHE C 117 " --> pdb=" O GLY E 118 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N PHE E 120 " --> pdb=" O PHE C 117 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ASN C 119 " --> pdb=" O PHE E 120 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N THR E 115 " --> pdb=" O GLY G 116 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N GLY G 118 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N PHE E 117 " --> pdb=" O GLY G 118 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N PHE G 120 " --> pdb=" O PHE E 117 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ASN E 119 " --> pdb=" O PHE G 120 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N THR G 115 " --> pdb=" O GLY I 116 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N GLY I 118 " --> pdb=" O THR G 115 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N PHE G 117 " --> pdb=" O GLY I 118 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N PHE I 120 " --> pdb=" O PHE G 117 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ASN G 119 " --> pdb=" O PHE I 120 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N THR I 115 " --> pdb=" O GLY K 116 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N GLY K 118 " --> pdb=" O THR I 115 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N PHE I 117 " --> pdb=" O GLY K 118 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N PHE K 120 " --> pdb=" O PHE I 117 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ASN I 119 " --> pdb=" O PHE K 120 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N THR K 115 " --> pdb=" O GLY M 116 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N GLY M 118 " --> pdb=" O THR K 115 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N PHE K 117 " --> pdb=" O GLY M 118 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N PHE M 120 " --> pdb=" O PHE K 117 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ASN K 119 " --> pdb=" O PHE M 120 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N THR M 115 " --> pdb=" O GLY O 116 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N GLY O 118 " --> pdb=" O THR M 115 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N PHE M 117 " --> pdb=" O GLY O 118 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N PHE O 120 " --> pdb=" O PHE M 117 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ASN M 119 " --> pdb=" O PHE O 120 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N THR O 115 " --> pdb=" O GLY Q 116 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N GLY Q 118 " --> pdb=" O THR O 115 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N PHE O 117 " --> pdb=" O GLY Q 118 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N PHE Q 120 " --> pdb=" O PHE O 117 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ASN O 119 " --> pdb=" O PHE Q 120 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N THR Q 115 " --> pdb=" O GLY S 116 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N GLY S 118 " --> pdb=" O THR Q 115 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N PHE Q 117 " --> pdb=" O GLY S 118 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N PHE S 120 " --> pdb=" O PHE Q 117 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ASN Q 119 " --> pdb=" O PHE S 120 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N THR S 115 " --> pdb=" O GLY U 116 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N GLY U 118 " --> pdb=" O THR S 115 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N PHE S 117 " --> pdb=" O GLY U 118 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N PHE U 120 " --> pdb=" O PHE S 117 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ASN S 119 " --> pdb=" O PHE U 120 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 87 through 92 Processing sheet with id=AA7, first strand: chain 'B' and resid 98 through 108 160 hydrogen bonds defined for protein. 480 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: 1.26 Time building geometry restraints manager: 2.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.27: 803 1.27 - 1.34: 803 1.34 - 1.41: 594 1.41 - 1.47: 979 1.47 - 1.54: 1705 Bond restraints: 4884 Sorted by residual: bond pdb=" CB THR A 90 " pdb=" CG2 THR A 90 " ideal model delta sigma weight residual 1.521 1.354 0.167 3.30e-02 9.18e+02 2.57e+01 bond pdb=" CB THR C 90 " pdb=" CG2 THR C 90 " ideal model delta sigma weight residual 1.521 1.354 0.167 3.30e-02 9.18e+02 2.56e+01 bond pdb=" CB THR K 90 " pdb=" CG2 THR K 90 " ideal model delta sigma weight residual 1.521 1.354 0.167 3.30e-02 9.18e+02 2.56e+01 bond pdb=" CB THR O 90 " pdb=" CG2 THR O 90 " ideal model delta sigma weight residual 1.521 1.354 0.167 3.30e-02 9.18e+02 2.56e+01 bond pdb=" CB THR M 90 " pdb=" CG2 THR M 90 " ideal model delta sigma weight residual 1.521 1.354 0.167 3.30e-02 9.18e+02 2.56e+01 ... (remaining 4879 not shown) Histogram of bond angle deviations from ideal: 102.44 - 107.94: 312 107.94 - 113.43: 2266 113.43 - 118.93: 1127 118.93 - 124.43: 2840 124.43 - 129.92: 66 Bond angle restraints: 6611 Sorted by residual: angle pdb=" N LYS A 113 " pdb=" CA LYS A 113 " pdb=" C LYS A 113 " ideal model delta sigma weight residual 111.53 119.09 -7.56 2.18e+00 2.10e-01 1.20e+01 angle pdb=" N LYS G 113 " pdb=" CA LYS G 113 " pdb=" C LYS G 113 " ideal model delta sigma weight residual 111.53 119.08 -7.55 2.18e+00 2.10e-01 1.20e+01 angle pdb=" N LYS U 113 " pdb=" CA LYS U 113 " pdb=" C LYS U 113 " ideal model delta sigma weight residual 111.53 119.08 -7.55 2.18e+00 2.10e-01 1.20e+01 angle pdb=" N LYS K 113 " pdb=" CA LYS K 113 " pdb=" C LYS K 113 " ideal model delta sigma weight residual 111.53 119.08 -7.55 2.18e+00 2.10e-01 1.20e+01 angle pdb=" N LYS O 113 " pdb=" CA LYS O 113 " pdb=" C LYS O 113 " ideal model delta sigma weight residual 111.53 119.07 -7.54 2.18e+00 2.10e-01 1.20e+01 ... (remaining 6606 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.71: 2376 12.71 - 25.42: 209 25.42 - 38.13: 66 38.13 - 50.84: 11 50.84 - 63.55: 11 Dihedral angle restraints: 2673 sinusoidal: 847 harmonic: 1826 Sorted by residual: dihedral pdb=" C LYS K 113 " pdb=" N LYS K 113 " pdb=" CA LYS K 113 " pdb=" CB LYS K 113 " ideal model delta harmonic sigma weight residual -122.60 -131.58 8.98 0 2.50e+00 1.60e-01 1.29e+01 dihedral pdb=" C LYS M 113 " pdb=" N LYS M 113 " pdb=" CA LYS M 113 " pdb=" CB LYS M 113 " ideal model delta harmonic sigma weight residual -122.60 -131.54 8.94 0 2.50e+00 1.60e-01 1.28e+01 dihedral pdb=" C LYS I 113 " pdb=" N LYS I 113 " pdb=" CA LYS I 113 " pdb=" CB LYS I 113 " ideal model delta harmonic sigma weight residual -122.60 -131.54 8.94 0 2.50e+00 1.60e-01 1.28e+01 ... (remaining 2670 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 638 0.096 - 0.191: 66 0.191 - 0.287: 33 0.287 - 0.383: 11 0.383 - 0.478: 22 Chirality restraints: 770 Sorted by residual: chirality pdb=" CG LEU B 101 " pdb=" CB LEU B 101 " pdb=" CD1 LEU B 101 " pdb=" CD2 LEU B 101 " both_signs ideal model delta sigma weight residual False -2.59 -2.11 -0.48 2.00e-01 2.50e+01 5.72e+00 chirality pdb=" CG LEU T 101 " pdb=" CB LEU T 101 " pdb=" CD1 LEU T 101 " pdb=" CD2 LEU T 101 " both_signs ideal model delta sigma weight residual False -2.59 -2.11 -0.48 2.00e-01 2.50e+01 5.71e+00 chirality pdb=" CG LEU F 101 " pdb=" CB LEU F 101 " pdb=" CD1 LEU F 101 " pdb=" CD2 LEU F 101 " both_signs ideal model delta sigma weight residual False -2.59 -2.11 -0.48 2.00e-01 2.50e+01 5.71e+00 ... (remaining 767 not shown) Planarity restraints: 880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA Q 110 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.90e+00 pdb=" C ALA Q 110 " -0.042 2.00e-02 2.50e+03 pdb=" O ALA Q 110 " 0.016 2.00e-02 2.50e+03 pdb=" N GLN Q 111 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA U 110 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.90e+00 pdb=" C ALA U 110 " -0.042 2.00e-02 2.50e+03 pdb=" O ALA U 110 " 0.016 2.00e-02 2.50e+03 pdb=" N GLN U 111 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA S 110 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.90e+00 pdb=" C ALA S 110 " -0.042 2.00e-02 2.50e+03 pdb=" O ALA S 110 " 0.016 2.00e-02 2.50e+03 pdb=" N GLN S 111 " 0.014 2.00e-02 2.50e+03 ... (remaining 877 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1632 2.80 - 3.33: 4132 3.33 - 3.85: 9177 3.85 - 4.38: 11100 4.38 - 4.90: 21252 Nonbonded interactions: 47293 Sorted by model distance: nonbonded pdb=" ND2 ASN A 106 " pdb=" OG SER B 103 " model vdw 2.277 2.520 nonbonded pdb=" ND2 ASN G 106 " pdb=" OG SER H 103 " model vdw 2.277 2.520 nonbonded pdb=" ND2 ASN S 106 " pdb=" OG SER T 103 " model vdw 2.278 2.520 nonbonded pdb=" ND2 ASN O 106 " pdb=" OG SER P 103 " model vdw 2.278 2.520 nonbonded pdb=" ND2 ASN U 106 " pdb=" OG SER V 103 " model vdw 2.278 2.520 ... (remaining 47288 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 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.720 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: 3.370 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 18.200 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 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 : 0.021 0.167 4884 Z= 1.342 Angle : 1.424 9.452 6611 Z= 0.782 Chirality : 0.115 0.478 770 Planarity : 0.007 0.024 880 Dihedral : 12.578 63.547 1507 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 6.52 % Allowed : 4.35 % Favored : 89.13 % 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: -4.18 (0.15), residues: 638 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.18 (0.11), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.034 0.006 PHE S 109 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 258 time to evaluate : 0.546 Fit side-chains REVERT: H 105 GLN cc_start: 0.8627 (tt0) cc_final: 0.8409 (tt0) REVERT: K 107 ASN cc_start: 0.8585 (OUTLIER) cc_final: 0.8224 (p0) REVERT: M 105 GLN cc_start: 0.8601 (tm130) cc_final: 0.8332 (tm-30) REVERT: O 107 ASN cc_start: 0.8586 (OUTLIER) cc_final: 0.8261 (p0) REVERT: P 105 GLN cc_start: 0.8903 (tt0) cc_final: 0.8616 (tt0) REVERT: R 87 THR cc_start: 0.8477 (p) cc_final: 0.8115 (t) REVERT: S 105 GLN cc_start: 0.8773 (tm130) cc_final: 0.8525 (tm130) outliers start: 33 outliers final: 6 residues processed: 269 average time/residue: 0.4828 time to fit residues: 141.1491 Evaluate side-chains 184 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 176 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain K residue 107 ASN Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain M residue 101 LEU Chi-restraints excluded: chain N residue 101 LEU Chi-restraints excluded: chain O residue 107 ASN Chi-restraints excluded: chain P residue 101 LEU Chi-restraints excluded: chain R residue 101 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 46 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 107 ASN B 105 GLN ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 GLN ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 ASN F 105 GLN ** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 ASN ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 112 ASN ** K 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 112 ASN ** M 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 105 GLN ** O 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 112 ASN U 106 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4884 Z= 0.246 Angle : 0.693 9.541 6611 Z= 0.324 Chirality : 0.045 0.216 770 Planarity : 0.003 0.018 880 Dihedral : 6.432 47.445 676 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 19.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 17.79 % Allowed : 16.01 % Favored : 66.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.22 (0.15), residues: 638 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.21 (0.12), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.002 PHE G 102 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 204 time to evaluate : 0.551 Fit side-chains REVERT: A 99 THR cc_start: 0.9024 (OUTLIER) cc_final: 0.8692 (p) REVERT: C 106 ASN cc_start: 0.8442 (OUTLIER) cc_final: 0.7980 (p0) REVERT: C 112 ASN cc_start: 0.8460 (t0) cc_final: 0.8081 (t0) REVERT: E 112 ASN cc_start: 0.8817 (t0) cc_final: 0.8539 (t0) REVERT: K 107 ASN cc_start: 0.8187 (OUTLIER) cc_final: 0.7894 (p0) REVERT: M 106 ASN cc_start: 0.8753 (OUTLIER) cc_final: 0.7878 (p0) REVERT: M 107 ASN cc_start: 0.8647 (OUTLIER) cc_final: 0.8286 (p0) REVERT: N 89 ASN cc_start: 0.8728 (m-40) cc_final: 0.8401 (m110) REVERT: P 105 GLN cc_start: 0.8749 (tt0) cc_final: 0.8494 (tt0) REVERT: R 91 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7817 (tt) REVERT: R 96 SER cc_start: 0.9183 (p) cc_final: 0.8958 (p) REVERT: S 100 SER cc_start: 0.9009 (OUTLIER) cc_final: 0.8719 (m) REVERT: S 105 GLN cc_start: 0.8763 (tm130) cc_final: 0.8494 (tm-30) REVERT: S 107 ASN cc_start: 0.8530 (OUTLIER) cc_final: 0.8248 (p0) REVERT: T 91 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8367 (mm) outliers start: 90 outliers final: 51 residues processed: 247 average time/residue: 0.3265 time to fit residues: 90.8129 Evaluate side-chains 230 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 170 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 106 ASN Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 104 SER Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 106 ASN Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain I residue 106 ASN Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain J residue 96 SER Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 106 ASN Chi-restraints excluded: chain K residue 107 ASN Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain M residue 106 ASN Chi-restraints excluded: chain M residue 107 ASN Chi-restraints excluded: chain N residue 101 LEU Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 99 THR Chi-restraints excluded: chain O residue 106 ASN Chi-restraints excluded: chain P residue 96 SER Chi-restraints excluded: chain P residue 101 LEU Chi-restraints excluded: chain Q residue 94 THR Chi-restraints excluded: chain Q residue 99 THR Chi-restraints excluded: chain Q residue 100 SER Chi-restraints excluded: chain Q residue 106 ASN Chi-restraints excluded: chain Q residue 107 ASN Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain S residue 94 THR Chi-restraints excluded: chain S residue 100 SER Chi-restraints excluded: chain S residue 106 ASN Chi-restraints excluded: chain S residue 107 ASN Chi-restraints excluded: chain T residue 91 LEU Chi-restraints excluded: chain T residue 96 SER Chi-restraints excluded: chain T residue 101 LEU Chi-restraints excluded: chain U residue 106 ASN Chi-restraints excluded: chain V residue 91 LEU Chi-restraints excluded: chain V residue 100 SER Chi-restraints excluded: chain V residue 101 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 27 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 41 optimal weight: 8.9990 chunk 34 optimal weight: 6.9990 chunk 13 optimal weight: 7.9990 chunk 50 optimal weight: 0.0570 chunk 54 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 49 optimal weight: 0.8980 chunk 17 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 overall best weight: 2.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 ASN B 105 GLN D 89 ASN ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 89 ASN ** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 ASN H 89 ASN H 105 GLN ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 105 GLN K 112 ASN L 89 ASN ** M 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 112 ASN ** O 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 89 ASN ** Q 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 89 ASN ** S 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 106 ASN V 105 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 4884 Z= 0.414 Angle : 0.734 9.564 6611 Z= 0.335 Chirality : 0.047 0.249 770 Planarity : 0.003 0.015 880 Dihedral : 5.942 57.027 672 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 16.60 % Allowed : 22.13 % Favored : 61.26 % 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: -4.21 (0.14), residues: 638 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.20 (0.11), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.002 PHE U 109 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 187 time to evaluate : 0.531 Fit side-chains REVERT: C 106 ASN cc_start: 0.8468 (OUTLIER) cc_final: 0.7959 (p0) REVERT: D 106 ASN cc_start: 0.8048 (OUTLIER) cc_final: 0.7806 (m-40) REVERT: M 106 ASN cc_start: 0.8908 (OUTLIER) cc_final: 0.8124 (p0) REVERT: M 107 ASN cc_start: 0.8441 (OUTLIER) cc_final: 0.7810 (p0) REVERT: N 89 ASN cc_start: 0.8695 (m-40) cc_final: 0.8474 (m110) REVERT: N 106 ASN cc_start: 0.8319 (OUTLIER) cc_final: 0.7903 (m110) REVERT: P 91 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7871 (tt) REVERT: P 105 GLN cc_start: 0.8770 (tt0) cc_final: 0.8487 (tt0) REVERT: R 91 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7909 (tt) REVERT: R 106 ASN cc_start: 0.8319 (OUTLIER) cc_final: 0.7855 (m110) REVERT: S 105 GLN cc_start: 0.8810 (tm130) cc_final: 0.8576 (tm-30) REVERT: S 107 ASN cc_start: 0.8543 (OUTLIER) cc_final: 0.8316 (p0) outliers start: 84 outliers final: 54 residues processed: 223 average time/residue: 0.3284 time to fit residues: 82.9295 Evaluate side-chains 232 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 169 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 106 ASN Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 107 ASN Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 106 ASN Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain I residue 100 SER Chi-restraints excluded: chain I residue 106 ASN Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain J residue 96 SER Chi-restraints excluded: chain J residue 106 ASN Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 106 ASN Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain M residue 96 SER Chi-restraints excluded: chain M residue 106 ASN Chi-restraints excluded: chain M residue 107 ASN Chi-restraints excluded: chain N residue 91 LEU Chi-restraints excluded: chain N residue 101 LEU Chi-restraints excluded: chain N residue 106 ASN Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 99 THR Chi-restraints excluded: chain O residue 106 ASN Chi-restraints excluded: chain P residue 91 LEU Chi-restraints excluded: chain P residue 101 LEU Chi-restraints excluded: chain Q residue 94 THR Chi-restraints excluded: chain Q residue 99 THR Chi-restraints excluded: chain Q residue 100 SER Chi-restraints excluded: chain Q residue 103 SER Chi-restraints excluded: chain Q residue 106 ASN Chi-restraints excluded: chain Q residue 107 ASN Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain R residue 106 ASN Chi-restraints excluded: chain S residue 94 THR Chi-restraints excluded: chain S residue 99 THR Chi-restraints excluded: chain S residue 106 ASN Chi-restraints excluded: chain S residue 107 ASN Chi-restraints excluded: chain T residue 101 LEU Chi-restraints excluded: chain U residue 96 SER Chi-restraints excluded: chain U residue 99 THR Chi-restraints excluded: chain V residue 91 LEU Chi-restraints excluded: chain V residue 100 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 49 optimal weight: 5.9990 chunk 37 optimal weight: 0.1980 chunk 25 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 23 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 50 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 14 optimal weight: 8.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 89 ASN ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 ASN G 112 ASN ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 89 ASN K 112 ASN ** M 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 112 ASN ** O 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 89 ASN ** Q 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 105 GLN ** S 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 112 ASN T 105 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 4884 Z= 0.454 Angle : 0.742 10.219 6611 Z= 0.336 Chirality : 0.047 0.271 770 Planarity : 0.003 0.018 880 Dihedral : 5.512 23.536 670 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 16.60 % Allowed : 21.74 % Favored : 61.66 % 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: -4.08 (0.14), residues: 638 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.10 (0.11), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.018 0.002 PHE Q 109 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 185 time to evaluate : 0.581 Fit side-chains REVERT: C 106 ASN cc_start: 0.8475 (OUTLIER) cc_final: 0.7822 (p0) REVERT: D 106 ASN cc_start: 0.8046 (OUTLIER) cc_final: 0.7829 (m-40) REVERT: M 106 ASN cc_start: 0.9006 (OUTLIER) cc_final: 0.8220 (p0) REVERT: M 107 ASN cc_start: 0.8573 (OUTLIER) cc_final: 0.8180 (p0) REVERT: N 106 ASN cc_start: 0.8266 (OUTLIER) cc_final: 0.7936 (m110) REVERT: P 91 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7877 (tt) REVERT: R 91 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7888 (tt) REVERT: R 106 ASN cc_start: 0.8281 (OUTLIER) cc_final: 0.7857 (m110) REVERT: S 105 GLN cc_start: 0.8871 (tm130) cc_final: 0.8639 (tm130) REVERT: T 105 GLN cc_start: 0.8852 (tt0) cc_final: 0.8614 (tt0) outliers start: 84 outliers final: 64 residues processed: 221 average time/residue: 0.3125 time to fit residues: 78.3370 Evaluate side-chains 245 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 173 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 106 ASN Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 107 ASN Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 106 ASN Chi-restraints excluded: chain G residue 107 ASN Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain I residue 100 SER Chi-restraints excluded: chain I residue 106 ASN Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain J residue 96 SER Chi-restraints excluded: chain J residue 106 ASN Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 106 ASN Chi-restraints excluded: chain L residue 87 THR Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain M residue 96 SER Chi-restraints excluded: chain M residue 99 THR Chi-restraints excluded: chain M residue 106 ASN Chi-restraints excluded: chain M residue 107 ASN Chi-restraints excluded: chain N residue 91 LEU Chi-restraints excluded: chain N residue 101 LEU Chi-restraints excluded: chain N residue 106 ASN Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 99 THR Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain O residue 106 ASN Chi-restraints excluded: chain P residue 91 LEU Chi-restraints excluded: chain P residue 96 SER Chi-restraints excluded: chain P residue 101 LEU Chi-restraints excluded: chain Q residue 94 THR Chi-restraints excluded: chain Q residue 96 SER Chi-restraints excluded: chain Q residue 99 THR Chi-restraints excluded: chain Q residue 100 SER Chi-restraints excluded: chain Q residue 103 SER Chi-restraints excluded: chain Q residue 106 ASN Chi-restraints excluded: chain Q residue 107 ASN Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain R residue 106 ASN Chi-restraints excluded: chain S residue 94 THR Chi-restraints excluded: chain S residue 99 THR Chi-restraints excluded: chain S residue 104 SER Chi-restraints excluded: chain S residue 106 ASN Chi-restraints excluded: chain T residue 96 SER Chi-restraints excluded: chain T residue 101 LEU Chi-restraints excluded: chain U residue 96 SER Chi-restraints excluded: chain U residue 99 THR Chi-restraints excluded: chain V residue 91 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 44 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 21 optimal weight: 8.9990 chunk 45 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 13 optimal weight: 9.9990 chunk 17 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 ASN ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 ASN G 112 ASN ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 112 ASN ** M 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 112 ASN N 89 ASN ** O 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 89 ASN P 105 GLN ** Q 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 112 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 4884 Z= 0.293 Angle : 0.687 10.268 6611 Z= 0.302 Chirality : 0.043 0.239 770 Planarity : 0.002 0.016 880 Dihedral : 5.332 25.608 670 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 15.61 % Allowed : 22.33 % Favored : 62.06 % 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: -4.11 (0.14), residues: 638 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.13 (0.11), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.001 PHE Q 109 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 186 time to evaluate : 0.582 Fit side-chains REVERT: C 106 ASN cc_start: 0.8499 (OUTLIER) cc_final: 0.7925 (p0) REVERT: D 106 ASN cc_start: 0.8004 (OUTLIER) cc_final: 0.7785 (m-40) REVERT: I 94 THR cc_start: 0.8699 (t) cc_final: 0.8483 (m) REVERT: M 99 THR cc_start: 0.9380 (OUTLIER) cc_final: 0.9141 (p) REVERT: M 101 LEU cc_start: 0.9055 (tt) cc_final: 0.8838 (tm) REVERT: M 106 ASN cc_start: 0.9008 (OUTLIER) cc_final: 0.8340 (p0) REVERT: N 106 ASN cc_start: 0.8279 (OUTLIER) cc_final: 0.7881 (m110) REVERT: P 91 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7893 (tt) REVERT: P 105 GLN cc_start: 0.8820 (tt0) cc_final: 0.8483 (tt0) REVERT: R 91 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7933 (tt) REVERT: R 106 ASN cc_start: 0.8228 (OUTLIER) cc_final: 0.7842 (m110) REVERT: S 105 GLN cc_start: 0.8876 (tm130) cc_final: 0.8664 (tm130) REVERT: T 91 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8045 (tt) outliers start: 79 outliers final: 54 residues processed: 215 average time/residue: 0.3538 time to fit residues: 85.2639 Evaluate side-chains 238 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 175 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 106 ASN Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 106 ASN Chi-restraints excluded: chain E residue 107 ASN Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 106 ASN Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain I residue 106 ASN Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 96 SER Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 106 ASN Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain M residue 96 SER Chi-restraints excluded: chain M residue 99 THR Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain M residue 106 ASN Chi-restraints excluded: chain M residue 107 ASN Chi-restraints excluded: chain N residue 91 LEU Chi-restraints excluded: chain N residue 101 LEU Chi-restraints excluded: chain N residue 106 ASN Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 99 THR Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain O residue 106 ASN Chi-restraints excluded: chain P residue 91 LEU Chi-restraints excluded: chain P residue 96 SER Chi-restraints excluded: chain P residue 101 LEU Chi-restraints excluded: chain Q residue 94 THR Chi-restraints excluded: chain Q residue 96 SER Chi-restraints excluded: chain Q residue 99 THR Chi-restraints excluded: chain Q residue 103 SER Chi-restraints excluded: chain Q residue 106 ASN Chi-restraints excluded: chain Q residue 107 ASN Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain R residue 106 ASN Chi-restraints excluded: chain S residue 94 THR Chi-restraints excluded: chain S residue 99 THR Chi-restraints excluded: chain S residue 106 ASN Chi-restraints excluded: chain T residue 87 THR Chi-restraints excluded: chain T residue 91 LEU Chi-restraints excluded: chain T residue 96 SER Chi-restraints excluded: chain T residue 101 LEU Chi-restraints excluded: chain U residue 96 SER Chi-restraints excluded: chain U residue 99 THR Chi-restraints excluded: chain V residue 91 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 47 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 chunk 24 optimal weight: 8.9990 chunk 4 optimal weight: 7.9990 chunk 17 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 GLN ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 ASN F 105 GLN G 112 ASN ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 112 ASN L 105 GLN ** M 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 112 ASN N 105 GLN ** O 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 112 ASN ** U 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 4884 Z= 0.469 Angle : 0.741 10.081 6611 Z= 0.334 Chirality : 0.047 0.280 770 Planarity : 0.003 0.017 880 Dihedral : 5.416 24.416 670 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 15.02 % Allowed : 23.12 % Favored : 61.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.06 (0.14), residues: 638 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.09 (0.11), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.017 0.002 PHE K 92 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 172 time to evaluate : 0.497 Fit side-chains REVERT: C 106 ASN cc_start: 0.8557 (OUTLIER) cc_final: 0.8009 (p0) REVERT: D 87 THR cc_start: 0.9137 (t) cc_final: 0.8867 (t) REVERT: D 106 ASN cc_start: 0.8028 (OUTLIER) cc_final: 0.7818 (m-40) REVERT: I 99 THR cc_start: 0.9030 (OUTLIER) cc_final: 0.8746 (p) REVERT: M 106 ASN cc_start: 0.9040 (OUTLIER) cc_final: 0.8402 (p0) REVERT: N 106 ASN cc_start: 0.8282 (OUTLIER) cc_final: 0.7890 (m110) REVERT: P 91 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7890 (tt) REVERT: P 105 GLN cc_start: 0.8782 (tt0) cc_final: 0.8464 (tt0) REVERT: R 91 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.7916 (tt) REVERT: R 106 ASN cc_start: 0.8247 (OUTLIER) cc_final: 0.7862 (m110) REVERT: S 107 ASN cc_start: 0.8681 (OUTLIER) cc_final: 0.7808 (p0) REVERT: T 91 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8197 (tt) outliers start: 76 outliers final: 55 residues processed: 205 average time/residue: 0.3505 time to fit residues: 80.7369 Evaluate side-chains 230 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 165 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 106 ASN Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 107 ASN Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 106 ASN Chi-restraints excluded: chain G residue 107 ASN Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain I residue 106 ASN Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain J residue 96 SER Chi-restraints excluded: chain J residue 106 ASN Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 106 ASN Chi-restraints excluded: chain L residue 87 THR Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain M residue 96 SER Chi-restraints excluded: chain M residue 106 ASN Chi-restraints excluded: chain N residue 91 LEU Chi-restraints excluded: chain N residue 101 LEU Chi-restraints excluded: chain N residue 106 ASN Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 99 THR Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain O residue 106 ASN Chi-restraints excluded: chain P residue 91 LEU Chi-restraints excluded: chain P residue 96 SER Chi-restraints excluded: chain P residue 101 LEU Chi-restraints excluded: chain Q residue 94 THR Chi-restraints excluded: chain Q residue 96 SER Chi-restraints excluded: chain Q residue 99 THR Chi-restraints excluded: chain Q residue 103 SER Chi-restraints excluded: chain Q residue 106 ASN Chi-restraints excluded: chain Q residue 107 ASN Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain R residue 106 ASN Chi-restraints excluded: chain S residue 94 THR Chi-restraints excluded: chain S residue 99 THR Chi-restraints excluded: chain S residue 106 ASN Chi-restraints excluded: chain S residue 107 ASN Chi-restraints excluded: chain T residue 87 THR Chi-restraints excluded: chain T residue 91 LEU Chi-restraints excluded: chain T residue 96 SER Chi-restraints excluded: chain T residue 101 LEU Chi-restraints excluded: chain U residue 96 SER Chi-restraints excluded: chain U residue 99 THR Chi-restraints excluded: chain V residue 91 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 5 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 ASN F 105 GLN G 112 ASN ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 112 ASN ** M 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 112 ASN N 105 GLN ** O 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 112 ASN ** U 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 4884 Z= 0.311 Angle : 0.690 10.125 6611 Z= 0.304 Chirality : 0.043 0.252 770 Planarity : 0.002 0.015 880 Dihedral : 5.307 26.222 670 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 14.43 % Allowed : 24.11 % Favored : 61.46 % 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: -4.09 (0.14), residues: 638 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.11 (0.11), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.001 PHE Q 109 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 171 time to evaluate : 0.590 Fit side-chains REVERT: C 106 ASN cc_start: 0.8639 (OUTLIER) cc_final: 0.8124 (p0) REVERT: D 87 THR cc_start: 0.9144 (t) cc_final: 0.8896 (t) REVERT: G 96 SER cc_start: 0.8629 (t) cc_final: 0.8399 (t) REVERT: I 99 THR cc_start: 0.9026 (OUTLIER) cc_final: 0.8818 (p) REVERT: K 99 THR cc_start: 0.9197 (OUTLIER) cc_final: 0.8990 (p) REVERT: M 106 ASN cc_start: 0.9059 (OUTLIER) cc_final: 0.8544 (p0) REVERT: N 106 ASN cc_start: 0.8259 (OUTLIER) cc_final: 0.7869 (m110) REVERT: P 91 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7826 (tt) REVERT: P 105 GLN cc_start: 0.8746 (tt0) cc_final: 0.8445 (tt0) REVERT: R 91 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7933 (tt) REVERT: R 106 ASN cc_start: 0.8221 (OUTLIER) cc_final: 0.7828 (m110) REVERT: T 91 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8180 (tt) outliers start: 73 outliers final: 54 residues processed: 200 average time/residue: 0.3489 time to fit residues: 78.4254 Evaluate side-chains 228 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 165 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 106 ASN Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 107 ASN Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 106 ASN Chi-restraints excluded: chain G residue 107 ASN Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain I residue 106 ASN Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain J residue 96 SER Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 106 ASN Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 106 ASN Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain M residue 96 SER Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain M residue 106 ASN Chi-restraints excluded: chain N residue 91 LEU Chi-restraints excluded: chain N residue 101 LEU Chi-restraints excluded: chain N residue 106 ASN Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 99 THR Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain O residue 106 ASN Chi-restraints excluded: chain P residue 91 LEU Chi-restraints excluded: chain P residue 96 SER Chi-restraints excluded: chain P residue 101 LEU Chi-restraints excluded: chain Q residue 94 THR Chi-restraints excluded: chain Q residue 96 SER Chi-restraints excluded: chain Q residue 99 THR Chi-restraints excluded: chain Q residue 103 SER Chi-restraints excluded: chain Q residue 106 ASN Chi-restraints excluded: chain Q residue 107 ASN Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain R residue 106 ASN Chi-restraints excluded: chain S residue 99 THR Chi-restraints excluded: chain S residue 106 ASN Chi-restraints excluded: chain T residue 87 THR Chi-restraints excluded: chain T residue 90 THR Chi-restraints excluded: chain T residue 91 LEU Chi-restraints excluded: chain T residue 96 SER Chi-restraints excluded: chain T residue 101 LEU Chi-restraints excluded: chain U residue 96 SER Chi-restraints excluded: chain U residue 99 THR Chi-restraints excluded: chain V residue 91 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 15 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 chunk 36 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 48 optimal weight: 10.0000 chunk 50 optimal weight: 6.9990 chunk 46 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 ASN F 105 GLN G 112 ASN ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 112 ASN ** M 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 112 ASN N 105 GLN ** O 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 112 ASN ** U 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 4884 Z= 0.396 Angle : 0.724 9.896 6611 Z= 0.322 Chirality : 0.045 0.276 770 Planarity : 0.002 0.017 880 Dihedral : 5.380 25.939 670 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 14.23 % Allowed : 24.31 % Favored : 61.46 % 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: -4.06 (0.15), residues: 638 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.09 (0.11), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.014 0.001 PHE Q 109 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 166 time to evaluate : 0.540 Fit side-chains REVERT: C 106 ASN cc_start: 0.8661 (OUTLIER) cc_final: 0.8178 (p0) REVERT: D 87 THR cc_start: 0.9149 (t) cc_final: 0.8896 (t) REVERT: G 96 SER cc_start: 0.8633 (t) cc_final: 0.8407 (t) REVERT: K 99 THR cc_start: 0.9211 (OUTLIER) cc_final: 0.8998 (p) REVERT: N 106 ASN cc_start: 0.8269 (OUTLIER) cc_final: 0.7868 (m110) REVERT: P 91 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7868 (tt) REVERT: P 105 GLN cc_start: 0.8749 (tt0) cc_final: 0.8433 (tt0) REVERT: R 91 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.7942 (tt) REVERT: R 106 ASN cc_start: 0.8186 (OUTLIER) cc_final: 0.7822 (m110) REVERT: S 99 THR cc_start: 0.9328 (OUTLIER) cc_final: 0.9040 (p) REVERT: T 91 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8158 (tt) outliers start: 72 outliers final: 54 residues processed: 198 average time/residue: 0.3634 time to fit residues: 80.3684 Evaluate side-chains 226 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 164 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 107 ASN Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 106 ASN Chi-restraints excluded: chain G residue 107 ASN Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 106 ASN Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 96 SER Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 106 ASN Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 106 ASN Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain M residue 96 SER Chi-restraints excluded: chain M residue 106 ASN Chi-restraints excluded: chain N residue 91 LEU Chi-restraints excluded: chain N residue 101 LEU Chi-restraints excluded: chain N residue 106 ASN Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 99 THR Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain O residue 106 ASN Chi-restraints excluded: chain P residue 91 LEU Chi-restraints excluded: chain P residue 101 LEU Chi-restraints excluded: chain Q residue 94 THR Chi-restraints excluded: chain Q residue 96 SER Chi-restraints excluded: chain Q residue 99 THR Chi-restraints excluded: chain Q residue 103 SER Chi-restraints excluded: chain Q residue 106 ASN Chi-restraints excluded: chain Q residue 107 ASN Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain R residue 106 ASN Chi-restraints excluded: chain S residue 94 THR Chi-restraints excluded: chain S residue 99 THR Chi-restraints excluded: chain S residue 106 ASN Chi-restraints excluded: chain T residue 87 THR Chi-restraints excluded: chain T residue 90 THR Chi-restraints excluded: chain T residue 91 LEU Chi-restraints excluded: chain T residue 96 SER Chi-restraints excluded: chain T residue 101 LEU Chi-restraints excluded: chain U residue 96 SER Chi-restraints excluded: chain U residue 99 THR Chi-restraints excluded: chain V residue 91 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 50 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 38 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 52 optimal weight: 0.4980 chunk 31 optimal weight: 2.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 GLN ** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 ASN F 105 GLN G 112 ASN G 119 ASN ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 112 ASN N 105 GLN ** O 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 112 ASN ** U 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 4884 Z= 0.385 Angle : 0.725 9.581 6611 Z= 0.321 Chirality : 0.045 0.266 770 Planarity : 0.002 0.017 880 Dihedral : 5.376 26.227 670 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 13.24 % Allowed : 25.69 % Favored : 61.07 % 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: -4.09 (0.14), residues: 638 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.11 (0.11), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.001 PHE Q 109 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 163 time to evaluate : 0.577 Fit side-chains REVERT: C 106 ASN cc_start: 0.8662 (OUTLIER) cc_final: 0.8191 (p0) REVERT: D 87 THR cc_start: 0.9143 (t) cc_final: 0.8907 (t) REVERT: D 91 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8241 (tt) REVERT: G 96 SER cc_start: 0.8632 (t) cc_final: 0.8404 (t) REVERT: K 99 THR cc_start: 0.9249 (OUTLIER) cc_final: 0.9031 (p) REVERT: N 106 ASN cc_start: 0.8261 (OUTLIER) cc_final: 0.7870 (m110) REVERT: P 91 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7848 (tt) REVERT: P 105 GLN cc_start: 0.8700 (tt0) cc_final: 0.8421 (tt0) REVERT: R 91 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7936 (tt) REVERT: R 106 ASN cc_start: 0.8174 (OUTLIER) cc_final: 0.7803 (m110) REVERT: S 99 THR cc_start: 0.9316 (OUTLIER) cc_final: 0.9049 (p) REVERT: S 107 ASN cc_start: 0.8707 (OUTLIER) cc_final: 0.8026 (p0) REVERT: T 91 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8158 (tt) outliers start: 67 outliers final: 50 residues processed: 194 average time/residue: 0.3369 time to fit residues: 73.7101 Evaluate side-chains 223 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 163 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 107 ASN Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 106 ASN Chi-restraints excluded: chain G residue 107 ASN Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 106 ASN Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 96 SER Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 106 ASN Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 106 ASN Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain M residue 106 ASN Chi-restraints excluded: chain N residue 91 LEU Chi-restraints excluded: chain N residue 101 LEU Chi-restraints excluded: chain N residue 106 ASN Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 99 THR Chi-restraints excluded: chain O residue 106 ASN Chi-restraints excluded: chain P residue 91 LEU Chi-restraints excluded: chain P residue 96 SER Chi-restraints excluded: chain P residue 101 LEU Chi-restraints excluded: chain Q residue 94 THR Chi-restraints excluded: chain Q residue 96 SER Chi-restraints excluded: chain Q residue 99 THR Chi-restraints excluded: chain Q residue 103 SER Chi-restraints excluded: chain Q residue 106 ASN Chi-restraints excluded: chain Q residue 107 ASN Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain R residue 106 ASN Chi-restraints excluded: chain S residue 99 THR Chi-restraints excluded: chain S residue 106 ASN Chi-restraints excluded: chain S residue 107 ASN Chi-restraints excluded: chain T residue 87 THR Chi-restraints excluded: chain T residue 90 THR Chi-restraints excluded: chain T residue 91 LEU Chi-restraints excluded: chain T residue 96 SER Chi-restraints excluded: chain T residue 101 LEU Chi-restraints excluded: chain U residue 96 SER Chi-restraints excluded: chain U residue 99 THR Chi-restraints excluded: chain V residue 91 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 24 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 43 optimal weight: 10.0000 chunk 4 optimal weight: 0.7980 chunk 33 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 GLN ** G 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 105 GLN ** O 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 112 ASN ** U 106 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: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 4884 Z= 0.369 Angle : 0.727 9.991 6611 Z= 0.320 Chirality : 0.044 0.261 770 Planarity : 0.002 0.018 880 Dihedral : 5.368 27.013 670 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 12.85 % Allowed : 26.28 % Favored : 60.87 % 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: -4.10 (0.15), residues: 638 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.12 (0.11), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.001 PHE Q 109 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 162 time to evaluate : 0.568 Fit side-chains revert: symmetry clash REVERT: A 99 THR cc_start: 0.8883 (OUTLIER) cc_final: 0.8640 (p) REVERT: C 106 ASN cc_start: 0.8681 (OUTLIER) cc_final: 0.8211 (p0) REVERT: D 87 THR cc_start: 0.9151 (t) cc_final: 0.8908 (t) REVERT: D 91 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8259 (tt) REVERT: G 96 SER cc_start: 0.8654 (t) cc_final: 0.8431 (t) REVERT: K 99 THR cc_start: 0.9248 (OUTLIER) cc_final: 0.9039 (p) REVERT: N 106 ASN cc_start: 0.8266 (OUTLIER) cc_final: 0.7859 (m110) REVERT: P 91 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7846 (tt) REVERT: P 105 GLN cc_start: 0.8606 (tt0) cc_final: 0.8324 (tt0) REVERT: R 91 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.7939 (tt) REVERT: R 106 ASN cc_start: 0.8160 (OUTLIER) cc_final: 0.7805 (m110) REVERT: S 99 THR cc_start: 0.9348 (OUTLIER) cc_final: 0.9087 (p) REVERT: S 107 ASN cc_start: 0.8703 (OUTLIER) cc_final: 0.8090 (p0) REVERT: T 91 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8152 (tt) outliers start: 65 outliers final: 49 residues processed: 194 average time/residue: 0.3618 time to fit residues: 78.4300 Evaluate side-chains 219 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 159 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 107 ASN Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain G residue 106 ASN Chi-restraints excluded: chain G residue 107 ASN Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 106 ASN Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 96 SER Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 106 ASN Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 99 THR Chi-restraints excluded: chain K residue 106 ASN Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain M residue 96 SER Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain M residue 106 ASN Chi-restraints excluded: chain N residue 91 LEU Chi-restraints excluded: chain N residue 101 LEU Chi-restraints excluded: chain N residue 106 ASN Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 99 THR Chi-restraints excluded: chain O residue 106 ASN Chi-restraints excluded: chain P residue 91 LEU Chi-restraints excluded: chain P residue 96 SER Chi-restraints excluded: chain P residue 101 LEU Chi-restraints excluded: chain Q residue 94 THR Chi-restraints excluded: chain Q residue 96 SER Chi-restraints excluded: chain Q residue 99 THR Chi-restraints excluded: chain Q residue 103 SER Chi-restraints excluded: chain Q residue 106 ASN Chi-restraints excluded: chain Q residue 107 ASN Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 106 ASN Chi-restraints excluded: chain S residue 94 THR Chi-restraints excluded: chain S residue 99 THR Chi-restraints excluded: chain S residue 106 ASN Chi-restraints excluded: chain S residue 107 ASN Chi-restraints excluded: chain T residue 87 THR Chi-restraints excluded: chain T residue 90 THR Chi-restraints excluded: chain T residue 91 LEU Chi-restraints excluded: chain T residue 96 SER Chi-restraints excluded: chain T residue 101 LEU Chi-restraints excluded: chain U residue 96 SER Chi-restraints excluded: chain U residue 99 THR Chi-restraints excluded: chain V residue 91 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 40 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 chunk 43 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 chunk 8 optimal weight: 9.9990 chunk 38 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 overall best weight: 1.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 GLN ** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 ASN F 105 GLN G 112 ASN ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 105 GLN ** O 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 112 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.074366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.066324 restraints weight = 7706.921| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 1.63 r_work: 0.2930 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 4884 Z= 0.311 Angle : 0.698 10.229 6611 Z= 0.306 Chirality : 0.043 0.247 770 Planarity : 0.002 0.016 880 Dihedral : 5.153 28.077 668 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 12.85 % Allowed : 26.48 % Favored : 60.67 % 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: -4.12 (0.15), residues: 638 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.14 (0.11), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.001 PHE Q 109 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2003.26 seconds wall clock time: 37 minutes 6.40 seconds (2226.40 seconds total)