Starting phenix.real_space_refine on Tue Mar 3 14:09:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zrr_11383/03_2026/6zrr_11383.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zrr_11383/03_2026/6zrr_11383.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6zrr_11383/03_2026/6zrr_11383.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zrr_11383/03_2026/6zrr_11383.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6zrr_11383/03_2026/6zrr_11383.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zrr_11383/03_2026/6zrr_11383.map" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians C 1908 2.51 5 N 540 2.21 5 O 612 1.98 5 H 2862 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5922 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 329 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "B" Number of atoms: 329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 329 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "C" Number of atoms: 329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 329 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "D" Number of atoms: 329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 329 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "E" Number of atoms: 329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 329 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "F" Number of atoms: 329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 329 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "G" Number of atoms: 329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 329 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "H" Number of atoms: 329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 329 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "I" Number of atoms: 329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 329 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "J" Number of atoms: 329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 329 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "K" Number of atoms: 329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 329 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "L" Number of atoms: 329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 329 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "M" Number of atoms: 329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 329 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "N" Number of atoms: 329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 329 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "O" Number of atoms: 329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 329 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "P" Number of atoms: 329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 329 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "Q" Number of atoms: 329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 329 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "R" Number of atoms: 329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 329 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Time building chain proxies: 1.20, per 1000 atoms: 0.20 Number of scatterers: 5922 At special positions: 0 Unit cell: (61.77, 87.33, 44.73, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) O 612 8.00 N 540 7.00 C 1908 6.00 H 2862 1.00 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.54 Conformation dependent library (CDL) restraints added in 255.2 milliseconds 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 720 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 39.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing sheet with id=1, first strand: chain 'A' and resid 15 through 18 removed outlier: 8.132A pdb=" N PHE D 15 " --> pdb=" O LEU A 16 " (cutoff:3.500A) removed outlier: 10.524A pdb=" N HIS A 18 " --> pdb=" O PHE D 15 " (cutoff:3.500A) removed outlier: 9.506A pdb=" N VAL D 17 " --> pdb=" O HIS A 18 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N PHE G 15 " --> pdb=" O LEU D 16 " (cutoff:3.500A) removed outlier: 10.557A pdb=" N HIS D 18 " --> pdb=" O PHE G 15 " (cutoff:3.500A) removed outlier: 9.522A pdb=" N VAL G 17 " --> pdb=" O HIS D 18 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N PHE J 15 " --> pdb=" O LEU G 16 " (cutoff:3.500A) removed outlier: 10.564A pdb=" N HIS G 18 " --> pdb=" O PHE J 15 " (cutoff:3.500A) removed outlier: 9.528A pdb=" N VAL J 17 " --> pdb=" O HIS G 18 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N PHE M 15 " --> pdb=" O LEU J 16 " (cutoff:3.500A) removed outlier: 10.495A pdb=" N HIS J 18 " --> pdb=" O PHE M 15 " (cutoff:3.500A) removed outlier: 9.444A pdb=" N VAL M 17 " --> pdb=" O HIS J 18 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N PHE P 15 " --> pdb=" O LEU M 16 " (cutoff:3.500A) removed outlier: 10.549A pdb=" N HIS M 18 " --> pdb=" O PHE P 15 " (cutoff:3.500A) removed outlier: 9.532A pdb=" N VAL P 17 " --> pdb=" O HIS M 18 " (cutoff:3.500A) No H-bonds generated for sheet with id=1 Processing sheet with id=2, first strand: chain 'A' and resid 21 through 23 removed outlier: 6.662A pdb=" N ASN D 21 " --> pdb=" O ASN A 21 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N PHE A 23 " --> pdb=" O ASN D 21 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N PHE D 23 " --> pdb=" O PHE A 23 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ASN G 21 " --> pdb=" O ASN D 21 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N PHE D 23 " --> pdb=" O ASN G 21 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N PHE G 23 " --> pdb=" O PHE D 23 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ASN J 21 " --> pdb=" O ASN G 21 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N PHE G 23 " --> pdb=" O ASN J 21 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N PHE J 23 " --> pdb=" O PHE G 23 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ASN M 21 " --> pdb=" O ASN J 21 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N PHE J 23 " --> pdb=" O ASN M 21 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N PHE M 23 " --> pdb=" O PHE J 23 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ASN P 21 " --> pdb=" O ASN M 21 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N PHE M 23 " --> pdb=" O ASN P 21 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N PHE P 23 " --> pdb=" O PHE M 23 " (cutoff:3.500A) No H-bonds generated for sheet with id=2 Processing sheet with id=3, first strand: chain 'B' and resid 15 through 18 removed outlier: 8.251A pdb=" N PHE E 15 " --> pdb=" O LEU B 16 " (cutoff:3.500A) removed outlier: 10.651A pdb=" N HIS B 18 " --> pdb=" O PHE E 15 " (cutoff:3.500A) removed outlier: 9.578A pdb=" N VAL E 17 " --> pdb=" O HIS B 18 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N PHE H 15 " --> pdb=" O LEU E 16 " (cutoff:3.500A) removed outlier: 10.727A pdb=" N HIS E 18 " --> pdb=" O PHE H 15 " (cutoff:3.500A) removed outlier: 9.645A pdb=" N VAL H 17 " --> pdb=" O HIS E 18 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N PHE K 15 " --> pdb=" O LEU H 16 " (cutoff:3.500A) removed outlier: 10.732A pdb=" N HIS H 18 " --> pdb=" O PHE K 15 " (cutoff:3.500A) removed outlier: 9.641A pdb=" N VAL K 17 " --> pdb=" O HIS H 18 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N PHE N 15 " --> pdb=" O LEU K 16 " (cutoff:3.500A) removed outlier: 10.712A pdb=" N HIS K 18 " --> pdb=" O PHE N 15 " (cutoff:3.500A) removed outlier: 9.623A pdb=" N VAL N 17 " --> pdb=" O HIS K 18 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N PHE Q 15 " --> pdb=" O LEU N 16 " (cutoff:3.500A) removed outlier: 10.660A pdb=" N HIS N 18 " --> pdb=" O PHE Q 15 " (cutoff:3.500A) removed outlier: 9.587A pdb=" N VAL Q 17 " --> pdb=" O HIS N 18 " (cutoff:3.500A) No H-bonds generated for sheet with id=3 Processing sheet with id=4, first strand: chain 'B' and resid 21 through 23 removed outlier: 6.645A pdb=" N ASN E 21 " --> pdb=" O ASN B 21 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N PHE B 23 " --> pdb=" O ASN E 21 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N PHE E 23 " --> pdb=" O PHE B 23 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ASN H 21 " --> pdb=" O ASN E 21 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N PHE E 23 " --> pdb=" O ASN H 21 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N PHE H 23 " --> pdb=" O PHE E 23 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ASN K 21 " --> pdb=" O ASN H 21 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N PHE H 23 " --> pdb=" O ASN K 21 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N PHE K 23 " --> pdb=" O PHE H 23 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ASN N 21 " --> pdb=" O ASN K 21 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N PHE K 23 " --> pdb=" O ASN N 21 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N PHE N 23 " --> pdb=" O PHE K 23 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASN Q 21 " --> pdb=" O ASN N 21 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N PHE N 23 " --> pdb=" O ASN Q 21 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N PHE Q 23 " --> pdb=" O PHE N 23 " (cutoff:3.500A) No H-bonds generated for sheet with id=4 Processing sheet with id=5, first strand: chain 'B' and resid 28 through 31 removed outlier: 7.136A pdb=" N SER E 28 " --> pdb=" O SER B 29 " (cutoff:3.500A) removed outlier: 9.795A pdb=" N ASN B 31 " --> pdb=" O SER E 28 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N THR E 30 " --> pdb=" O ASN B 31 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N SER H 28 " --> pdb=" O SER E 29 " (cutoff:3.500A) removed outlier: 9.883A pdb=" N ASN E 31 " --> pdb=" O SER H 28 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N THR H 30 " --> pdb=" O ASN E 31 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N SER K 28 " --> pdb=" O SER H 29 " (cutoff:3.500A) removed outlier: 9.844A pdb=" N ASN H 31 " --> pdb=" O SER K 28 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N THR K 30 " --> pdb=" O ASN H 31 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N SER N 28 " --> pdb=" O SER K 29 " (cutoff:3.500A) removed outlier: 9.831A pdb=" N ASN K 31 " --> pdb=" O SER N 28 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N THR N 30 " --> pdb=" O ASN K 31 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N SER Q 28 " --> pdb=" O SER N 29 " (cutoff:3.500A) removed outlier: 9.804A pdb=" N ASN N 31 " --> pdb=" O SER Q 28 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N THR Q 30 " --> pdb=" O ASN N 31 " (cutoff:3.500A) No H-bonds generated for sheet with id=5 Processing sheet with id=6, first strand: chain 'C' and resid 25 through 29 removed outlier: 11.279A pdb=" N ALA F 25 " --> pdb=" O LEU C 27 " (cutoff:3.500A) removed outlier: 11.835A pdb=" N SER C 29 " --> pdb=" O ALA F 25 " (cutoff:3.500A) removed outlier: 11.461A pdb=" N LEU F 27 " --> pdb=" O SER C 29 " (cutoff:3.500A) removed outlier: 11.405A pdb=" N ALA I 25 " --> pdb=" O LEU F 27 " (cutoff:3.500A) removed outlier: 11.929A pdb=" N SER F 29 " --> pdb=" O ALA I 25 " (cutoff:3.500A) removed outlier: 11.545A pdb=" N LEU I 27 " --> pdb=" O SER F 29 " (cutoff:3.500A) removed outlier: 11.418A pdb=" N ALA L 25 " --> pdb=" O LEU I 27 " (cutoff:3.500A) removed outlier: 11.970A pdb=" N SER I 29 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 11.573A pdb=" N LEU L 27 " --> pdb=" O SER I 29 " (cutoff:3.500A) removed outlier: 11.407A pdb=" N ALA O 25 " --> pdb=" O LEU L 27 " (cutoff:3.500A) removed outlier: 11.951A pdb=" N SER L 29 " --> pdb=" O ALA O 25 " (cutoff:3.500A) removed outlier: 11.555A pdb=" N LEU O 27 " --> pdb=" O SER L 29 " (cutoff:3.500A) removed outlier: 11.302A pdb=" N ALA R 25 " --> pdb=" O LEU O 27 " (cutoff:3.500A) removed outlier: 11.848A pdb=" N SER O 29 " --> pdb=" O ALA R 25 " (cutoff:3.500A) removed outlier: 11.476A pdb=" N LEU R 27 " --> pdb=" O SER O 29 " (cutoff:3.500A) No H-bonds generated for sheet with id=6 Processing sheet with id=7, first strand: chain 'C' and resid 15 through 18 removed outlier: 9.352A pdb=" N PHE F 15 " --> pdb=" O LEU C 16 " (cutoff:3.500A) removed outlier: 10.817A pdb=" N HIS C 18 " --> pdb=" O PHE F 15 " (cutoff:3.500A) removed outlier: 9.152A pdb=" N VAL F 17 " --> pdb=" O HIS C 18 " (cutoff:3.500A) removed outlier: 9.278A pdb=" N PHE I 15 " --> pdb=" O LEU F 16 " (cutoff:3.500A) removed outlier: 10.722A pdb=" N HIS F 18 " --> pdb=" O PHE I 15 " (cutoff:3.500A) removed outlier: 9.086A pdb=" N VAL I 17 " --> pdb=" O HIS F 18 " (cutoff:3.500A) removed outlier: 9.176A pdb=" N PHE L 15 " --> pdb=" O LEU I 16 " (cutoff:3.500A) removed outlier: 10.614A pdb=" N HIS I 18 " --> pdb=" O PHE L 15 " (cutoff:3.500A) removed outlier: 8.975A pdb=" N VAL L 17 " --> pdb=" O HIS I 18 " (cutoff:3.500A) removed outlier: 9.203A pdb=" N PHE O 15 " --> pdb=" O LEU L 16 " (cutoff:3.500A) removed outlier: 10.648A pdb=" N HIS L 18 " --> pdb=" O PHE O 15 " (cutoff:3.500A) removed outlier: 9.009A pdb=" N VAL O 17 " --> pdb=" O HIS L 18 " (cutoff:3.500A) removed outlier: 9.370A pdb=" N PHE R 15 " --> pdb=" O LEU O 16 " (cutoff:3.500A) removed outlier: 10.822A pdb=" N HIS O 18 " --> pdb=" O PHE R 15 " (cutoff:3.500A) removed outlier: 9.164A pdb=" N VAL R 17 " --> pdb=" O HIS O 18 " (cutoff:3.500A) No H-bonds generated for sheet with id=7 Processing sheet with id=8, first strand: chain 'B' and resid 34 through 36 removed outlier: 6.733A pdb=" N SER E 34 " --> pdb=" O SER B 34 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N THR B 36 " --> pdb=" O SER E 34 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N THR E 36 " --> pdb=" O THR B 36 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N SER H 34 " --> pdb=" O SER E 34 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N THR E 36 " --> pdb=" O SER H 34 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N THR H 36 " --> pdb=" O THR E 36 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N SER K 34 " --> pdb=" O SER H 34 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N THR H 36 " --> pdb=" O SER K 34 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N THR K 36 " --> pdb=" O THR H 36 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N SER N 34 " --> pdb=" O SER K 34 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N THR K 36 " --> pdb=" O SER N 34 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N THR N 36 " --> pdb=" O THR K 36 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER Q 34 " --> pdb=" O SER N 34 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N THR N 36 " --> pdb=" O SER Q 34 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N THR Q 36 " --> pdb=" O THR N 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=8 Processing sheet with id=9, first strand: chain 'A' and resid 28 through 31 removed outlier: 7.290A pdb=" N SER D 28 " --> pdb=" O SER A 29 " (cutoff:3.500A) removed outlier: 9.859A pdb=" N ASN A 31 " --> pdb=" O SER D 28 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N THR D 30 " --> pdb=" O ASN A 31 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N SER G 28 " --> pdb=" O SER D 29 " (cutoff:3.500A) removed outlier: 9.882A pdb=" N ASN D 31 " --> pdb=" O SER G 28 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N THR G 30 " --> pdb=" O ASN D 31 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N SER J 28 " --> pdb=" O SER G 29 " (cutoff:3.500A) removed outlier: 9.929A pdb=" N ASN G 31 " --> pdb=" O SER J 28 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N THR J 30 " --> pdb=" O ASN G 31 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N SER M 28 " --> pdb=" O SER J 29 " (cutoff:3.500A) removed outlier: 9.868A pdb=" N ASN J 31 " --> pdb=" O SER M 28 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N THR M 30 " --> pdb=" O ASN J 31 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N SER P 28 " --> pdb=" O SER M 29 " (cutoff:3.500A) removed outlier: 9.880A pdb=" N ASN M 31 " --> pdb=" O SER P 28 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N THR P 30 " --> pdb=" O ASN M 31 " (cutoff:3.500A) No H-bonds generated for sheet with id=9 Processing sheet with id=10, first strand: chain 'A' and resid 34 through 36 removed outlier: 6.911A pdb=" N SER D 34 " --> pdb=" O SER A 34 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N THR A 36 " --> pdb=" O SER D 34 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N THR D 36 " --> pdb=" O THR A 36 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N SER G 34 " --> pdb=" O SER D 34 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N THR D 36 " --> pdb=" O SER G 34 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N THR G 36 " --> pdb=" O THR D 36 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N SER J 34 " --> pdb=" O SER G 34 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N THR G 36 " --> pdb=" O SER J 34 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N THR J 36 " --> pdb=" O THR G 36 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N SER M 34 " --> pdb=" O SER J 34 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N THR J 36 " --> pdb=" O SER M 34 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N THR M 36 " --> pdb=" O THR J 36 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N SER P 34 " --> pdb=" O SER M 34 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N THR M 36 " --> pdb=" O SER P 34 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N THR P 36 " --> pdb=" O THR M 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=10 No hydrogen bonds 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: 0.08 Time building geometry restraints manager: 0.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 0.96: 913 0.96 - 1.11: 1949 1.11 - 1.25: 486 1.25 - 1.40: 918 1.40 - 1.54: 1710 Bond restraints: 5976 Sorted by residual: bond pdb=" N TYC H 37 " pdb=" H TYC H 37 " ideal model delta sigma weight residual 0.860 1.033 -0.173 2.00e-02 2.50e+03 7.52e+01 bond pdb=" N TYC E 37 " pdb=" H TYC E 37 " ideal model delta sigma weight residual 0.860 1.033 -0.173 2.00e-02 2.50e+03 7.47e+01 bond pdb=" N TYC K 37 " pdb=" H TYC K 37 " ideal model delta sigma weight residual 0.860 1.033 -0.173 2.00e-02 2.50e+03 7.46e+01 bond pdb=" N TYC Q 37 " pdb=" H TYC Q 37 " ideal model delta sigma weight residual 0.860 1.032 -0.172 2.00e-02 2.50e+03 7.41e+01 bond pdb=" N TYC N 37 " pdb=" H TYC N 37 " ideal model delta sigma weight residual 0.860 1.031 -0.171 2.00e-02 2.50e+03 7.34e+01 ... (remaining 5971 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 10099 2.30 - 4.60: 334 4.60 - 6.90: 67 6.90 - 9.20: 6 9.20 - 11.50: 24 Bond angle restraints: 10530 Sorted by residual: angle pdb=" CG LEU F 16 " pdb=" CB LEU F 16 " pdb=" HB2 LEU F 16 " ideal model delta sigma weight residual 108.00 96.96 11.04 3.00e+00 1.11e-01 1.36e+01 angle pdb=" CG LEU C 16 " pdb=" CB LEU C 16 " pdb=" HB2 LEU C 16 " ideal model delta sigma weight residual 108.00 96.96 11.04 3.00e+00 1.11e-01 1.35e+01 angle pdb=" CG LEU I 16 " pdb=" CB LEU I 16 " pdb=" HB2 LEU I 16 " ideal model delta sigma weight residual 108.00 97.00 11.00 3.00e+00 1.11e-01 1.35e+01 angle pdb=" CG LEU R 16 " pdb=" CB LEU R 16 " pdb=" HB2 LEU R 16 " ideal model delta sigma weight residual 108.00 97.15 10.85 3.00e+00 1.11e-01 1.31e+01 angle pdb=" CG LEU L 16 " pdb=" CB LEU L 16 " pdb=" HB2 LEU L 16 " ideal model delta sigma weight residual 108.00 97.18 10.82 3.00e+00 1.11e-01 1.30e+01 ... (remaining 10525 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 2465 17.83 - 35.66: 251 35.66 - 53.50: 91 53.50 - 71.33: 79 71.33 - 89.16: 12 Dihedral angle restraints: 2898 sinusoidal: 1548 harmonic: 1350 Sorted by residual: dihedral pdb=" CA SER D 19 " pdb=" C SER D 19 " pdb=" N GLY D 20 " pdb=" CA GLY D 20 " ideal model delta harmonic sigma weight residual 180.00 154.63 25.37 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" CA SER H 19 " pdb=" C SER H 19 " pdb=" N GLY H 20 " pdb=" CA GLY H 20 " ideal model delta harmonic sigma weight residual 180.00 154.64 25.36 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" CA SER B 19 " pdb=" C SER B 19 " pdb=" N GLY B 20 " pdb=" CA GLY B 20 " ideal model delta harmonic sigma weight residual 180.00 154.65 25.35 0 5.00e+00 4.00e-02 2.57e+01 ... (remaining 2895 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 176 0.029 - 0.057: 145 0.057 - 0.086: 116 0.086 - 0.114: 30 0.114 - 0.142: 19 Chirality restraints: 486 Sorted by residual: chirality pdb=" CB ILE O 26 " pdb=" CA ILE O 26 " pdb=" CG1 ILE O 26 " pdb=" CG2 ILE O 26 " both_signs ideal model delta sigma weight residual False 2.64 2.79 -0.14 2.00e-01 2.50e+01 5.06e-01 chirality pdb=" CB ILE L 26 " pdb=" CA ILE L 26 " pdb=" CG1 ILE L 26 " pdb=" CG2 ILE L 26 " both_signs ideal model delta sigma weight residual False 2.64 2.79 -0.14 2.00e-01 2.50e+01 4.93e-01 chirality pdb=" CB ILE I 26 " pdb=" CA ILE I 26 " pdb=" CG1 ILE I 26 " pdb=" CG2 ILE I 26 " both_signs ideal model delta sigma weight residual False 2.64 2.78 -0.14 2.00e-01 2.50e+01 4.91e-01 ... (remaining 483 not shown) Planarity restraints: 954 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE I 15 " 0.005 2.00e-02 2.50e+03 7.28e-03 1.59e+00 pdb=" CG PHE I 15 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE I 15 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE I 15 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE I 15 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE I 15 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE I 15 " 0.000 2.00e-02 2.50e+03 pdb=" HD1 PHE I 15 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE I 15 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE I 15 " 0.000 2.00e-02 2.50e+03 pdb=" HE2 PHE I 15 " 0.004 2.00e-02 2.50e+03 pdb=" HZ PHE I 15 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 15 " 0.005 2.00e-02 2.50e+03 7.24e-03 1.57e+00 pdb=" CG PHE C 15 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 PHE C 15 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE C 15 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE C 15 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE C 15 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE C 15 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 PHE C 15 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE C 15 " 0.002 2.00e-02 2.50e+03 pdb=" HE1 PHE C 15 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE C 15 " 0.004 2.00e-02 2.50e+03 pdb=" HZ PHE C 15 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE O 15 " 0.005 2.00e-02 2.50e+03 7.21e-03 1.56e+00 pdb=" CG PHE O 15 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE O 15 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE O 15 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE O 15 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE O 15 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE O 15 " 0.000 2.00e-02 2.50e+03 pdb=" HD1 PHE O 15 " -0.000 2.00e-02 2.50e+03 pdb=" HD2 PHE O 15 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE O 15 " -0.000 2.00e-02 2.50e+03 pdb=" HE2 PHE O 15 " 0.004 2.00e-02 2.50e+03 pdb=" HZ PHE O 15 " -0.002 2.00e-02 2.50e+03 ... (remaining 951 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.25: 981 2.25 - 2.81: 12864 2.81 - 3.38: 14206 3.38 - 3.94: 20445 3.94 - 4.50: 28700 Nonbonded interactions: 77196 Sorted by model distance: nonbonded pdb=" HG SER A 28 " pdb=" OH TYC C 37 " model vdw 1.691 2.450 nonbonded pdb=" HG SER D 28 " pdb=" OH TYC F 37 " model vdw 1.708 2.450 nonbonded pdb=" HG SER G 28 " pdb=" OH TYC I 37 " model vdw 1.708 2.450 nonbonded pdb=" HG SER M 28 " pdb=" OH TYC O 37 " model vdw 1.710 2.450 nonbonded pdb=" HG SER J 28 " pdb=" OH TYC L 37 " model vdw 1.722 2.450 ... (remaining 77191 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.080 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: 0.030 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.970 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 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:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6820 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 : 0.010 0.059 3114 Z= 0.446 Angle : 1.269 11.503 4230 Z= 0.570 Chirality : 0.057 0.142 486 Planarity : 0.004 0.011 558 Dihedral : 14.911 64.942 1026 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 28.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.56 (0.31), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.47 (0.24), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.019 0.005 PHE I 15 HIS 0.013 0.007 HIS O 18 Details of bonding type rmsd covalent geometry : bond 0.01048 ( 3114) covalent geometry : angle 1.26863 ( 4230) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 31 ASN cc_start: 0.8142 (t0) cc_final: 0.7936 (m-40) REVERT: O 35 ASN cc_start: 0.8849 (m-40) cc_final: 0.8623 (m110) REVERT: R 35 ASN cc_start: 0.8141 (m-40) cc_final: 0.7713 (p0) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.0542 time to fit residues: 7.0756 Evaluate side-chains 39 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 24 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 0.2980 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.1980 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN ** D 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 35 ASN P 31 ASN P 35 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5119 r_free = 0.5119 target = 0.270144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.5728 r_free = 0.5728 target = 0.200046 restraints weight = 15762.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.5780 r_free = 0.5780 target = 0.202829 restraints weight = 7941.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.5799 r_free = 0.5799 target = 0.204367 restraints weight = 4523.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.5816 r_free = 0.5816 target = 0.205384 restraints weight = 2903.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.5828 r_free = 0.5828 target = 0.206069 restraints weight = 1966.166| |-----------------------------------------------------------------------------| r_work (final): 0.5111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6751 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3114 Z= 0.127 Angle : 0.603 3.718 4230 Z= 0.317 Chirality : 0.046 0.136 486 Planarity : 0.002 0.012 558 Dihedral : 13.750 73.049 522 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 0.00 % Allowed : 14.51 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.59 (0.29), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.49 (0.22), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.002 PHE J 15 HIS 0.005 0.002 HIS P 18 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 3114) covalent geometry : angle 0.60311 ( 4230) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 26 ILE cc_start: 0.7728 (pt) cc_final: 0.7335 (pt) REVERT: C 35 ASN cc_start: 0.8864 (m-40) cc_final: 0.8648 (m-40) REVERT: L 35 ASN cc_start: 0.8928 (m-40) cc_final: 0.8553 (m-40) REVERT: R 35 ASN cc_start: 0.7780 (m-40) cc_final: 0.7313 (p0) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.0502 time to fit residues: 5.4526 Evaluate side-chains 39 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 1 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 0 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4986 r_free = 0.4986 target = 0.244205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.5486 r_free = 0.5486 target = 0.167396 restraints weight = 15816.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.5540 r_free = 0.5540 target = 0.170850 restraints weight = 8649.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.5565 r_free = 0.5565 target = 0.172910 restraints weight = 5353.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.5588 r_free = 0.5588 target = 0.174337 restraints weight = 3659.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.5602 r_free = 0.5602 target = 0.175260 restraints weight = 2660.250| |-----------------------------------------------------------------------------| r_work (final): 0.4968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.4765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3114 Z= 0.143 Angle : 0.627 5.115 4230 Z= 0.325 Chirality : 0.047 0.140 486 Planarity : 0.002 0.012 558 Dihedral : 11.567 76.530 522 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 0.62 % Allowed : 18.83 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.61 (0.29), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.51 (0.22), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.027 0.002 PHE E 23 HIS 0.007 0.002 HIS Q 18 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 3114) covalent geometry : angle 0.62685 ( 4230) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 43 time to evaluate : 0.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 35 ASN cc_start: 0.8816 (m-40) cc_final: 0.8383 (m-40) REVERT: I 35 ASN cc_start: 0.8898 (m-40) cc_final: 0.8643 (m-40) REVERT: N 34 SER cc_start: 0.7351 (OUTLIER) cc_final: 0.7067 (m) REVERT: O 35 ASN cc_start: 0.8982 (m-40) cc_final: 0.8666 (m110) REVERT: R 35 ASN cc_start: 0.8359 (m-40) cc_final: 0.7678 (p0) outliers start: 2 outliers final: 0 residues processed: 45 average time/residue: 0.0495 time to fit residues: 3.4858 Evaluate side-chains 35 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 34 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 34 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 4 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 20 optimal weight: 0.4980 chunk 24 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.115006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.097375 restraints weight = 18446.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.101267 restraints weight = 9823.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.103791 restraints weight = 6229.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.105638 restraints weight = 4460.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.106918 restraints weight = 3400.677| |-----------------------------------------------------------------------------| r_work (final): 0.4554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.5840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 3114 Z= 0.228 Angle : 0.710 6.590 4230 Z= 0.387 Chirality : 0.049 0.145 486 Planarity : 0.004 0.015 558 Dihedral : 11.330 65.132 522 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 29.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.83 % Favored : 84.17 % Rotamer: Outliers : 1.85 % Allowed : 22.22 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.84 (0.31), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.68 (0.24), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.028 0.003 PHE K 23 HIS 0.010 0.004 HIS P 18 Details of bonding type rmsd covalent geometry : bond 0.00508 ( 3114) covalent geometry : angle 0.70978 ( 4230) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.165 Fit side-chains revert: symmetry clash REVERT: C 35 ASN cc_start: 0.8959 (m-40) cc_final: 0.8534 (m110) REVERT: E 16 LEU cc_start: 0.7201 (OUTLIER) cc_final: 0.6875 (pt) REVERT: I 35 ASN cc_start: 0.8983 (m-40) cc_final: 0.8599 (m-40) REVERT: K 16 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.7245 (pt) REVERT: L 35 ASN cc_start: 0.9120 (m-40) cc_final: 0.8896 (m110) REVERT: O 35 ASN cc_start: 0.9052 (m-40) cc_final: 0.8777 (m110) REVERT: R 35 ASN cc_start: 0.8785 (m-40) cc_final: 0.8024 (p0) outliers start: 6 outliers final: 2 residues processed: 37 average time/residue: 0.0414 time to fit residues: 2.5039 Evaluate side-chains 31 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 27 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain I residue 22 ASN Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 23 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 32 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN ** P 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4781 r_free = 0.4781 target = 0.122763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.103946 restraints weight = 18512.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.108180 restraints weight = 10036.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4612 r_free = 0.4612 target = 0.111163 restraints weight = 6457.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.113154 restraints weight = 4536.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4656 r_free = 0.4656 target = 0.114432 restraints weight = 3432.346| |-----------------------------------------------------------------------------| r_work (final): 0.4666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.6187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3114 Z= 0.160 Angle : 0.594 5.156 4230 Z= 0.326 Chirality : 0.047 0.158 486 Planarity : 0.003 0.011 558 Dihedral : 10.477 65.304 522 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 25.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.28 % Favored : 84.72 % Rotamer: Outliers : 1.85 % Allowed : 24.38 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.86 (0.33), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.70 (0.25), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.014 0.002 PHE E 23 HIS 0.011 0.003 HIS K 18 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 3114) covalent geometry : angle 0.59382 ( 4230) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 29 time to evaluate : 0.160 Fit side-chains revert: symmetry clash REVERT: C 35 ASN cc_start: 0.8854 (m-40) cc_final: 0.8395 (m110) REVERT: I 35 ASN cc_start: 0.8981 (m-40) cc_final: 0.8552 (m-40) REVERT: K 16 LEU cc_start: 0.7492 (OUTLIER) cc_final: 0.7240 (pt) REVERT: L 35 ASN cc_start: 0.9040 (m-40) cc_final: 0.8765 (m110) REVERT: O 35 ASN cc_start: 0.9035 (m-40) cc_final: 0.8735 (m110) REVERT: R 35 ASN cc_start: 0.8630 (m-40) cc_final: 0.7910 (p0) outliers start: 6 outliers final: 1 residues processed: 33 average time/residue: 0.0502 time to fit residues: 2.7777 Evaluate side-chains 28 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 21 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 10 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4769 r_free = 0.4769 target = 0.120931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.102294 restraints weight = 18264.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.106414 restraints weight = 9897.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.109240 restraints weight = 6419.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.111284 restraints weight = 4592.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.112687 restraints weight = 3461.703| |-----------------------------------------------------------------------------| r_work (final): 0.4661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.6493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 3114 Z= 0.160 Angle : 0.599 5.340 4230 Z= 0.327 Chirality : 0.047 0.155 486 Planarity : 0.003 0.011 558 Dihedral : 10.432 64.389 522 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 25.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.39 % Favored : 83.61 % Rotamer: Outliers : 1.23 % Allowed : 24.07 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.85 (0.34), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.69 (0.26), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.024 0.002 PHE K 23 HIS 0.010 0.003 HIS N 18 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 3114) covalent geometry : angle 0.59909 ( 4230) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.108 Fit side-chains REVERT: C 35 ASN cc_start: 0.8894 (m-40) cc_final: 0.8453 (m110) REVERT: E 16 LEU cc_start: 0.7168 (OUTLIER) cc_final: 0.6801 (pt) REVERT: F 35 ASN cc_start: 0.9024 (m-40) cc_final: 0.8666 (m-40) REVERT: I 35 ASN cc_start: 0.8992 (m-40) cc_final: 0.8577 (m-40) REVERT: K 16 LEU cc_start: 0.7455 (OUTLIER) cc_final: 0.7197 (pt) REVERT: L 35 ASN cc_start: 0.9021 (m-40) cc_final: 0.8769 (m110) REVERT: O 35 ASN cc_start: 0.9062 (m-40) cc_final: 0.8739 (m110) REVERT: R 35 ASN cc_start: 0.8719 (m-40) cc_final: 0.7918 (p0) outliers start: 4 outliers final: 1 residues processed: 29 average time/residue: 0.0440 time to fit residues: 2.1101 Evaluate side-chains 27 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 21 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 29 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4690 r_free = 0.4690 target = 0.116301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.099287 restraints weight = 18419.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.103153 restraints weight = 9722.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.105675 restraints weight = 6077.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.107277 restraints weight = 4283.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.108524 restraints weight = 3282.138| |-----------------------------------------------------------------------------| r_work (final): 0.4578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.6725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 3114 Z= 0.164 Angle : 0.605 5.578 4230 Z= 0.330 Chirality : 0.048 0.155 486 Planarity : 0.003 0.011 558 Dihedral : 10.301 63.903 522 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 26.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % Rotamer: Outliers : 2.16 % Allowed : 23.15 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.92 (0.34), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.75 (0.26), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.020 0.002 PHE K 23 HIS 0.009 0.003 HIS H 18 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 3114) covalent geometry : angle 0.60525 ( 4230) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 24 time to evaluate : 0.130 Fit side-chains REVERT: C 35 ASN cc_start: 0.8861 (m-40) cc_final: 0.8375 (m110) REVERT: E 16 LEU cc_start: 0.7061 (OUTLIER) cc_final: 0.6720 (pt) REVERT: F 35 ASN cc_start: 0.9032 (m-40) cc_final: 0.8656 (m110) REVERT: I 35 ASN cc_start: 0.9045 (m-40) cc_final: 0.8540 (m-40) REVERT: K 16 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.7296 (pt) REVERT: L 35 ASN cc_start: 0.9053 (m-40) cc_final: 0.8803 (m110) REVERT: O 35 ASN cc_start: 0.9041 (m-40) cc_final: 0.8717 (m110) REVERT: R 35 ASN cc_start: 0.8680 (m-40) cc_final: 0.7917 (p0) outliers start: 7 outliers final: 2 residues processed: 30 average time/residue: 0.0436 time to fit residues: 2.1155 Evaluate side-chains 28 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 18 HIS Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 21 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 13 optimal weight: 0.2980 chunk 23 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 32 optimal weight: 0.3980 chunk 1 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4933 r_free = 0.4933 target = 0.234137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.5356 r_free = 0.5356 target = 0.153534 restraints weight = 16644.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.5400 r_free = 0.5400 target = 0.156453 restraints weight = 10006.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.5427 r_free = 0.5427 target = 0.158356 restraints weight = 6699.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.5445 r_free = 0.5445 target = 0.159618 restraints weight = 4870.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.5462 r_free = 0.5462 target = 0.160643 restraints weight = 3812.293| |-----------------------------------------------------------------------------| r_work (final): 0.4752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.6782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 3114 Z= 0.114 Angle : 0.522 4.388 4230 Z= 0.288 Chirality : 0.046 0.157 486 Planarity : 0.002 0.015 558 Dihedral : 10.071 65.109 522 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 21.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.83 % Favored : 89.17 % Rotamer: Outliers : 0.93 % Allowed : 24.38 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.76 (0.35), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.62 (0.27), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.017 0.001 PHE K 23 HIS 0.017 0.003 HIS K 18 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 3114) covalent geometry : angle 0.52160 ( 4230) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 29 time to evaluate : 0.152 Fit side-chains revert: symmetry clash REVERT: C 26 ILE cc_start: 0.7750 (pt) cc_final: 0.7550 (pt) REVERT: C 35 ASN cc_start: 0.8645 (m-40) cc_final: 0.8203 (m110) REVERT: E 16 LEU cc_start: 0.6844 (OUTLIER) cc_final: 0.6570 (pt) REVERT: F 35 ASN cc_start: 0.9000 (m-40) cc_final: 0.8621 (m110) REVERT: I 35 ASN cc_start: 0.9021 (m-40) cc_final: 0.8510 (m-40) REVERT: L 35 ASN cc_start: 0.8953 (m-40) cc_final: 0.8707 (m110) REVERT: O 35 ASN cc_start: 0.9026 (m-40) cc_final: 0.8679 (m110) REVERT: R 35 ASN cc_start: 0.8632 (m-40) cc_final: 0.7794 (p0) outliers start: 3 outliers final: 2 residues processed: 32 average time/residue: 0.0488 time to fit residues: 2.5308 Evaluate side-chains 27 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 18 HIS Chi-restraints excluded: chain K residue 16 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 14 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 8 optimal weight: 0.2980 chunk 22 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4790 r_free = 0.4790 target = 0.123508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.105683 restraints weight = 17991.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.109909 restraints weight = 9306.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4633 r_free = 0.4633 target = 0.112757 restraints weight = 5825.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.114616 restraints weight = 4042.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.116005 restraints weight = 3063.977| |-----------------------------------------------------------------------------| r_work (final): 0.4695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.6875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 3114 Z= 0.120 Angle : 0.530 5.029 4230 Z= 0.291 Chirality : 0.046 0.146 486 Planarity : 0.002 0.012 558 Dihedral : 9.962 65.048 522 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 21.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.89 % Favored : 86.11 % Rotamer: Outliers : 1.23 % Allowed : 25.31 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.80 (0.35), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.65 (0.27), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.017 0.001 PHE K 23 HIS 0.013 0.003 HIS K 18 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 3114) covalent geometry : angle 0.53018 ( 4230) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.148 Fit side-chains revert: symmetry clash REVERT: C 35 ASN cc_start: 0.8630 (m-40) cc_final: 0.8164 (m110) REVERT: E 16 LEU cc_start: 0.6891 (OUTLIER) cc_final: 0.6586 (pt) REVERT: F 35 ASN cc_start: 0.9012 (m-40) cc_final: 0.8629 (m110) REVERT: I 35 ASN cc_start: 0.9023 (m-40) cc_final: 0.8477 (m-40) REVERT: K 18 HIS cc_start: 0.8136 (OUTLIER) cc_final: 0.7911 (t70) REVERT: L 35 ASN cc_start: 0.8935 (m-40) cc_final: 0.8695 (m110) REVERT: O 35 ASN cc_start: 0.9041 (m-40) cc_final: 0.8681 (m110) REVERT: R 35 ASN cc_start: 0.8663 (m-40) cc_final: 0.7812 (p0) outliers start: 4 outliers final: 2 residues processed: 28 average time/residue: 0.0455 time to fit residues: 2.0461 Evaluate side-chains 28 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 18 HIS Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 18 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 7 optimal weight: 2.9990 chunk 1 optimal weight: 0.1980 chunk 33 optimal weight: 0.0770 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 overall best weight: 0.5140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN ** Q 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4948 r_free = 0.4948 target = 0.237202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.5386 r_free = 0.5386 target = 0.156368 restraints weight = 16611.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.5428 r_free = 0.5428 target = 0.159252 restraints weight = 9923.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.5457 r_free = 0.5457 target = 0.161203 restraints weight = 6626.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.5476 r_free = 0.5476 target = 0.162517 restraints weight = 4767.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.5492 r_free = 0.5492 target = 0.163525 restraints weight = 3677.499| |-----------------------------------------------------------------------------| r_work (final): 0.4784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.6941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 3114 Z= 0.100 Angle : 0.490 4.103 4230 Z= 0.272 Chirality : 0.045 0.158 486 Planarity : 0.002 0.011 558 Dihedral : 9.836 66.279 522 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 19.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.44 % Favored : 90.56 % Rotamer: Outliers : 1.23 % Allowed : 25.93 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.65 (0.35), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.54 (0.27), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.001 PHE K 23 HIS 0.012 0.003 HIS K 18 Details of bonding type rmsd covalent geometry : bond 0.00219 ( 3114) covalent geometry : angle 0.49030 ( 4230) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.127 Fit side-chains revert: symmetry clash REVERT: C 35 ASN cc_start: 0.8604 (m-40) cc_final: 0.8246 (m-40) REVERT: E 16 LEU cc_start: 0.6757 (OUTLIER) cc_final: 0.6471 (pt) REVERT: F 35 ASN cc_start: 0.8959 (m-40) cc_final: 0.8646 (m110) REVERT: I 35 ASN cc_start: 0.9019 (m-40) cc_final: 0.8472 (m-40) REVERT: L 35 ASN cc_start: 0.8916 (m-40) cc_final: 0.8674 (m110) REVERT: O 35 ASN cc_start: 0.9021 (m-40) cc_final: 0.8689 (m110) REVERT: R 35 ASN cc_start: 0.8526 (m-40) cc_final: 0.7745 (p0) outliers start: 4 outliers final: 2 residues processed: 30 average time/residue: 0.0515 time to fit residues: 2.4730 Evaluate side-chains 29 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 18 HIS Chi-restraints excluded: chain K residue 16 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 26 optimal weight: 0.2980 chunk 16 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4926 r_free = 0.4926 target = 0.233112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.5346 r_free = 0.5346 target = 0.151865 restraints weight = 16663.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.5383 r_free = 0.5383 target = 0.154667 restraints weight = 10140.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.5419 r_free = 0.5419 target = 0.156606 restraints weight = 6848.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.5435 r_free = 0.5435 target = 0.157820 restraints weight = 4990.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.5452 r_free = 0.5452 target = 0.158826 restraints weight = 3915.607| |-----------------------------------------------------------------------------| r_work (final): 0.4750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.7022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 3114 Z= 0.127 Angle : 0.529 5.088 4230 Z= 0.290 Chirality : 0.046 0.151 486 Planarity : 0.002 0.011 558 Dihedral : 9.856 65.765 522 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 20.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.72 % Favored : 85.28 % Rotamer: Outliers : 1.23 % Allowed : 25.62 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.78 (0.35), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.63 (0.27), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.018 0.002 PHE K 23 HIS 0.011 0.003 HIS K 18 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 3114) covalent geometry : angle 0.52934 ( 4230) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1410.70 seconds wall clock time: 24 minutes 43.34 seconds (1483.34 seconds total)