Starting phenix.real_space_refine (version: 1.21rc1) on Wed Aug 9 18:18:39 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q66_13853/08_2023/7q66_13853.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q66_13853/08_2023/7q66_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_13853/08_2023/7q66_13853.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q66_13853/08_2023/7q66_13853.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q66_13853/08_2023/7q66_13853.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q66_13853/08_2023/7q66_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-1.21rc1-5044/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: 2.43, per 1000 atoms: 0.51 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: 2.00 Conformation dependent library (CDL) restraints added in 684.0 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: 0.70 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: 1.43 Time building geometry restraints manager: 2.15 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: 0.810 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: 0.000 Extract box with map and model: 3.560 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 17.600 Find NCS groups from input model: 0.380 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:12.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.110 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 0.549 Fit side-chains outliers start: 33 outliers final: 6 residues processed: 269 average time/residue: 0.4677 time to fit residues: 137.1034 Evaluate side-chains 181 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 175 time to evaluate : 0.535 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 1 average time/residue: 0.0976 time to fit residues: 0.8140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 23 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 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 H 105 GLN ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 112 ASN J 105 GLN ** K 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 112 ASN ** M 106 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** P 105 GLN ** 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: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 4884 Z= 0.237 Angle : 0.692 9.623 6611 Z= 0.327 Chirality : 0.045 0.217 770 Planarity : 0.003 0.018 880 Dihedral : 5.292 12.302 660 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 19.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer Outliers : 17.59 % 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 (0.15), residues: 638 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.20 (0.12), residues: 638 *********************** 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 298 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 209 time to evaluate : 0.561 Fit side-chains outliers start: 89 outliers final: 49 residues processed: 250 average time/residue: 0.3329 time to fit residues: 93.6913 Evaluate side-chains 223 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 174 time to evaluate : 0.524 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 28 residues processed: 22 average time/residue: 0.0835 time to fit residues: 3.3193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 41 optimal weight: 9.9990 chunk 34 optimal weight: 0.9980 chunk 13 optimal weight: 7.9990 chunk 50 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- 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 89 ASN B 105 GLN C 112 ASN 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** H 89 ASN ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 112 ASN L 89 ASN ** M 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 112 ASN N 89 ASN N 105 GLN ** O 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 89 ASN ** Q 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 89 ASN R 105 GLN ** S 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 105 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 4884 Z= 0.353 Angle : 0.708 9.604 6611 Z= 0.324 Chirality : 0.045 0.244 770 Planarity : 0.003 0.017 880 Dihedral : 4.887 12.130 660 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer Outliers : 15.02 % 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: -4.25 (0.14), residues: 638 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.23 (0.11), residues: 638 *********************** 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 268 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 192 time to evaluate : 0.545 Fit side-chains outliers start: 76 outliers final: 48 residues processed: 222 average time/residue: 0.3066 time to fit residues: 77.5828 Evaluate side-chains 224 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 176 time to evaluate : 0.536 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 23 residues processed: 28 average time/residue: 0.0821 time to fit residues: 4.0414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 49 optimal weight: 0.9990 chunk 37 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 23 optimal weight: 10.0000 chunk 33 optimal weight: 0.7980 chunk 50 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 chunk 26 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 ASN E 112 ASN ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 112 ASN J 89 ASN ** K 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 112 ASN ** 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 105 GLN ** 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: 0.8112 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 4884 Z= 0.211 Angle : 0.633 9.546 6611 Z= 0.283 Chirality : 0.041 0.210 770 Planarity : 0.002 0.014 880 Dihedral : 4.580 11.777 660 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer Outliers : 12.65 % 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: -4.28 (0.14), residues: 638 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.26 (0.11), residues: 638 *********************** 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 246 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 182 time to evaluate : 0.553 Fit side-chains outliers start: 64 outliers final: 43 residues processed: 211 average time/residue: 0.3336 time to fit residues: 79.3037 Evaluate side-chains 210 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 167 time to evaluate : 0.489 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 22 residues processed: 24 average time/residue: 0.0848 time to fit residues: 3.5929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 44 optimal weight: 9.9990 chunk 30 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 21 optimal weight: 8.9990 chunk 45 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 chunk 17 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN B 89 ASN ** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 ASN F 105 GLN ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 112 ASN L 105 GLN M 106 ASN M 112 ASN N 105 GLN N 107 ASN ** O 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 89 ASN ** 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: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.069 4884 Z= 0.692 Angle : 0.817 10.615 6611 Z= 0.382 Chirality : 0.053 0.318 770 Planarity : 0.003 0.017 880 Dihedral : 5.154 15.531 660 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer Outliers : 14.82 % 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: -4.05 (0.14), residues: 638 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.08 (0.11), residues: 638 *********************** 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 245 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 170 time to evaluate : 0.510 Fit side-chains outliers start: 75 outliers final: 52 residues processed: 214 average time/residue: 0.3431 time to fit residues: 82.5275 Evaluate side-chains 213 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 161 time to evaluate : 0.489 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 29 residues processed: 24 average time/residue: 0.0762 time to fit residues: 3.3564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 47 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 44 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 GLN D 105 GLN ** E 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 GLN G 106 ASN ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 112 ASN J 105 GLN ** K 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 112 ASN M 112 ASN N 105 GLN ** O 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 89 ASN ** Q 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 105 GLN ** S 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 112 ASN U 106 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 4884 Z= 0.214 Angle : 0.650 9.044 6611 Z= 0.294 Chirality : 0.042 0.236 770 Planarity : 0.002 0.015 880 Dihedral : 4.629 13.575 660 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer Outliers : 11.07 % 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: -4.21 (0.14), residues: 638 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.20 (0.11), residues: 638 *********************** 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 230 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 174 time to evaluate : 0.485 Fit side-chains outliers start: 56 outliers final: 42 residues processed: 209 average time/residue: 0.3392 time to fit residues: 80.0757 Evaluate side-chains 203 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 161 time to evaluate : 0.537 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 27 residues processed: 17 average time/residue: 0.0922 time to fit residues: 2.8749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 5 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 38 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 21 optimal weight: 8.9990 chunk 31 optimal weight: 4.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 GLN ** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 GLN ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 GLN G 106 ASN ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 105 GLN ** K 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 105 GLN ** O 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 89 ASN ** 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: 0.8224 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.061 4884 Z= 0.556 Angle : 0.772 10.331 6611 Z= 0.355 Chirality : 0.050 0.288 770 Planarity : 0.003 0.018 880 Dihedral : 4.965 17.122 660 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer Outliers : 11.86 % 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: -4.07 (0.15), residues: 638 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.09 (0.11), residues: 638 *********************** 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 216 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 156 time to evaluate : 0.534 Fit side-chains outliers start: 60 outliers final: 43 residues processed: 192 average time/residue: 0.3408 time to fit residues: 73.7265 Evaluate side-chains 200 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 157 time to evaluate : 0.549 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 26 residues processed: 18 average time/residue: 0.0741 time to fit residues: 2.6846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 15 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 33 optimal weight: 8.9990 chunk 36 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 50 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 GLN ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 GLN ** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 105 GLN ** K 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 112 ASN M 112 ASN ** O 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 89 ASN ** Q 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 105 GLN ** S 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 112 ASN U 106 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 4884 Z= 0.233 Angle : 0.679 9.590 6611 Z= 0.299 Chirality : 0.044 0.288 770 Planarity : 0.002 0.014 880 Dihedral : 4.598 13.322 660 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer Outliers : 9.29 % 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: -4.19 (0.15), residues: 638 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.18 (0.11), residues: 638 *********************** 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 220 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 173 time to evaluate : 0.495 Fit side-chains outliers start: 47 outliers final: 34 residues processed: 201 average time/residue: 0.3543 time to fit residues: 79.5945 Evaluate side-chains 194 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 160 time to evaluate : 0.540 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 24 residues processed: 12 average time/residue: 0.0788 time to fit residues: 2.0519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 50 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 21 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 chunk 15 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 52 optimal weight: 0.0670 chunk 31 optimal weight: 7.9990 overall best weight: 1.1922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN ** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 GLN D 89 ASN ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 ASN F 105 GLN ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 105 GLN ** O 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 105 GLN R 107 ASN ** S 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 112 ASN U 106 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 4884 Z= 0.259 Angle : 0.682 9.390 6611 Z= 0.303 Chirality : 0.045 0.295 770 Planarity : 0.002 0.015 880 Dihedral : 4.566 16.840 660 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer Outliers : 8.89 % 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 (0.14), residues: 638 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.21 (0.11), residues: 638 *********************** 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 210 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 165 time to evaluate : 0.573 Fit side-chains outliers start: 45 outliers final: 36 residues processed: 194 average time/residue: 0.3655 time to fit residues: 79.4457 Evaluate side-chains 194 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 158 time to evaluate : 0.549 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 25 residues processed: 13 average time/residue: 0.0751 time to fit residues: 2.1586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 54 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 43 optimal weight: 9.9990 chunk 4 optimal weight: 7.9990 chunk 33 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 13 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN B 89 ASN B 105 GLN ** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 GLN ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 GLN ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 105 GLN J 107 ASN ** K 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 112 ASN M 112 ASN ** O 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 107 ASN ** Q 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 105 GLN ** S 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 112 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.069 4884 Z= 0.680 Angle : 0.847 10.630 6611 Z= 0.392 Chirality : 0.057 0.397 770 Planarity : 0.003 0.020 880 Dihedral : 5.090 15.272 660 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer Outliers : 8.30 % 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 (0.14), residues: 638 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.13 (0.11), residues: 638 ********************** 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 196 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 154 time to evaluate : 0.530 Fit side-chains outliers start: 42 outliers final: 33 residues processed: 184 average time/residue: 0.3664 time to fit residues: 75.5380 Evaluate side-chains 182 residues out of total 506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 149 time to evaluate : 0.480 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 23 residues processed: 11 average time/residue: 0.0721 time to fit residues: 1.8544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 40 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 8 optimal weight: 8.9990 chunk 38 optimal weight: 0.9980 chunk 2 optimal weight: 0.0050 chunk 31 optimal weight: 0.8980 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN A 112 ASN ** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 GLN ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 ASN F 105 GLN ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 105 GLN ** S 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 112 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.077356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.069523 restraints weight = 7555.086| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.59 r_work: 0.3014 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 4884 Z= 0.212 Angle : 0.685 9.851 6611 Z= 0.303 Chirality : 0.045 0.293 770 Planarity : 0.002 0.014 880 Dihedral : 4.593 14.996 660 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer Outliers : 6.72 % 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: -4.23 (0.14), residues: 638 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.22 (0.11), residues: 638 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2041.31 seconds wall clock time: 37 minutes 28.70 seconds (2248.70 seconds total)