Starting phenix.real_space_refine on Thu Jul 24 09:32:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zrr_11383/07_2025/6zrr_11383.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zrr_11383/07_2025/6zrr_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6zrr_11383/07_2025/6zrr_11383.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zrr_11383/07_2025/6zrr_11383.map" model { file = "/net/cci-nas-00/data/ceres_data/6zrr_11383/07_2025/6zrr_11383.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zrr_11383/07_2025/6zrr_11383.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 3.95, per 1000 atoms: 0.67 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: 1.63 Conformation dependent library (CDL) restraints added in 375.5 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: 0.69 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: 0.27 Time building geometry restraints manager: 1.83 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: 18.540 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: 0.100 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 16.240 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.290 ------------------------------------------------------------------------------- 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 : 28.46 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.56 (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 HIS 0.013 0.007 HIS O 18 PHE 0.019 0.005 PHE I 15 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 : 0.466 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: 0.1482 time to fit residues: 18.8172 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 : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 14 optimal weight: 0.3980 chunk 28 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 35 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 = 0.5106 r_free = 0.5106 target = 0.267249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.5712 r_free = 0.5712 target = 0.196928 restraints weight = 15608.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.5756 r_free = 0.5756 target = 0.199628 restraints weight = 7955.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.5779 r_free = 0.5779 target = 0.201233 restraints weight = 4612.265| |-----------------------------------------------------------------------------| r_work (final): 0.5088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6808 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3114 Z= 0.134 Angle : 0.622 4.141 4230 Z= 0.325 Chirality : 0.046 0.135 486 Planarity : 0.002 0.012 558 Dihedral : 13.657 72.339 522 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 0.00 % Allowed : 15.43 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.60 (0.29), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.50 (0.22), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS P 18 PHE 0.008 0.002 PHE J 15 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 3114) covalent geometry : angle 0.62219 ( 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 66 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.452 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: B 27 LEU cc_start: 0.8205 (tp) cc_final: 0.7980 (mp) REVERT: C 35 ASN cc_start: 0.8890 (m-40) cc_final: 0.8676 (m-40) REVERT: L 35 ASN cc_start: 0.8947 (m-40) cc_final: 0.8556 (m-40) REVERT: O 35 ASN cc_start: 0.8797 (m-40) cc_final: 0.8561 (m110) REVERT: R 35 ASN cc_start: 0.7783 (m-40) cc_final: 0.7312 (p0) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.1370 time to fit residues: 13.1821 Evaluate side-chains 41 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 5 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 10 optimal weight: 0.2980 chunk 21 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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** N 31 ASN P 31 ASN ** Q 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5008 r_free = 0.5008 target = 0.247234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.5541 r_free = 0.5541 target = 0.174464 restraints weight = 15897.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.5570 r_free = 0.5570 target = 0.177065 restraints weight = 9081.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.5600 r_free = 0.5600 target = 0.178740 restraints weight = 5803.632| |-----------------------------------------------------------------------------| r_work (final): 0.4986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.4440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 3114 Z= 0.133 Angle : 0.591 4.567 4230 Z= 0.310 Chirality : 0.046 0.132 486 Planarity : 0.002 0.010 558 Dihedral : 11.764 76.446 522 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 0.93 % Allowed : 17.59 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.65 (0.29), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.54 (0.22), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS P 18 PHE 0.022 0.001 PHE E 23 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 3114) covalent geometry : angle 0.59101 ( 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 48 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.424 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: C 35 ASN cc_start: 0.8838 (m-40) cc_final: 0.8413 (m-40) REVERT: I 35 ASN cc_start: 0.8917 (m-40) cc_final: 0.8646 (m-40) REVERT: O 35 ASN cc_start: 0.8939 (m-40) cc_final: 0.8627 (m110) REVERT: R 35 ASN cc_start: 0.8076 (m-40) cc_final: 0.7595 (p0) outliers start: 3 outliers final: 0 residues processed: 48 average time/residue: 0.1276 time to fit residues: 9.2091 Evaluate side-chains 36 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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** D 35 ASN ** H 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4754 r_free = 0.4754 target = 0.120410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.102450 restraints weight = 17465.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.106921 restraints weight = 8790.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.109864 restraints weight = 5354.468| |-----------------------------------------------------------------------------| r_work (final): 0.4615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.5490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3114 Z= 0.153 Angle : 0.592 4.476 4230 Z= 0.321 Chirality : 0.046 0.132 486 Planarity : 0.003 0.010 558 Dihedral : 10.761 63.382 522 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 18.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 1.23 % Allowed : 19.44 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.63 (0.32), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.52 (0.24), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.003 HIS N 18 PHE 0.017 0.002 PHE E 23 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 3114) covalent geometry : angle 0.59200 ( 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: 4 poor density : 33 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 35 ASN cc_start: 0.8895 (m-40) cc_final: 0.8417 (m110) REVERT: E 16 LEU cc_start: 0.7198 (OUTLIER) cc_final: 0.6947 (pt) REVERT: I 35 ASN cc_start: 0.8924 (m-40) cc_final: 0.8637 (m-40) REVERT: L 35 ASN cc_start: 0.9015 (m-40) cc_final: 0.8693 (m-40) REVERT: O 35 ASN cc_start: 0.8963 (m-40) cc_final: 0.8759 (m110) REVERT: R 35 ASN cc_start: 0.8611 (m-40) cc_final: 0.7975 (p0) outliers start: 4 outliers final: 1 residues processed: 37 average time/residue: 0.1258 time to fit residues: 7.4394 Evaluate side-chains 30 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 28 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain K residue 16 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 22 optimal weight: 0.0770 chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 32 optimal weight: 0.2980 chunk 18 optimal weight: 0.5980 overall best weight: 0.4538 ------------------------------------------------------------------------------- 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** ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4970 r_free = 0.4970 target = 0.241943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.5447 r_free = 0.5447 target = 0.163839 restraints weight = 16028.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.5481 r_free = 0.5481 target = 0.166936 restraints weight = 9192.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.5529 r_free = 0.5529 target = 0.169088 restraints weight = 5907.723| |-----------------------------------------------------------------------------| r_work (final): 0.4934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 moved from start: 0.5756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 3114 Z= 0.094 Angle : 0.487 3.706 4230 Z= 0.266 Chirality : 0.045 0.131 486 Planarity : 0.002 0.008 558 Dihedral : 10.155 66.607 522 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % Rotamer: Outliers : 1.23 % Allowed : 19.75 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.51 (0.34), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.43 (0.26), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.003 HIS N 18 PHE 0.012 0.001 PHE E 23 Details of bonding type rmsd covalent geometry : bond 0.00202 ( 3114) covalent geometry : angle 0.48719 ( 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 36 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.452 Fit side-chains revert: symmetry clash REVERT: C 35 ASN cc_start: 0.8612 (m-40) cc_final: 0.8263 (m-40) REVERT: I 35 ASN cc_start: 0.8920 (m-40) cc_final: 0.8548 (m-40) REVERT: L 35 ASN cc_start: 0.9001 (m-40) cc_final: 0.8663 (m-40) REVERT: O 35 ASN cc_start: 0.8963 (m-40) cc_final: 0.8718 (m110) REVERT: R 35 ASN cc_start: 0.8469 (m-40) cc_final: 0.7720 (p0) outliers start: 4 outliers final: 1 residues processed: 35 average time/residue: 0.1228 time to fit residues: 6.8718 Evaluate side-chains 28 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 27 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 22 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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** ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN ** P 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4883 r_free = 0.4883 target = 0.228509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.5305 r_free = 0.5305 target = 0.152243 restraints weight = 16450.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.5345 r_free = 0.5345 target = 0.155194 restraints weight = 9966.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.5384 r_free = 0.5384 target = 0.157187 restraints weight = 6672.018| |-----------------------------------------------------------------------------| r_work (final): 0.4752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.6175 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= 0.137 Angle : 0.548 4.666 4230 Z= 0.298 Chirality : 0.046 0.129 486 Planarity : 0.002 0.009 558 Dihedral : 10.190 61.793 522 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.61 % Favored : 86.39 % Rotamer: Outliers : 0.62 % Allowed : 21.60 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.51 (0.35), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.43 (0.26), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.003 HIS N 18 PHE 0.018 0.002 PHE P 23 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 3114) covalent geometry : angle 0.54827 ( 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: 2 poor density : 28 time to evaluate : 0.465 Fit side-chains revert: symmetry clash REVERT: C 35 ASN cc_start: 0.8605 (m-40) cc_final: 0.8204 (m110) REVERT: F 35 ASN cc_start: 0.8943 (m-40) cc_final: 0.8565 (m110) REVERT: I 35 ASN cc_start: 0.8972 (m-40) cc_final: 0.8480 (m-40) REVERT: L 35 ASN cc_start: 0.8973 (m-40) cc_final: 0.8732 (m110) REVERT: O 35 ASN cc_start: 0.8907 (m-40) cc_final: 0.8645 (m110) REVERT: R 35 ASN cc_start: 0.8572 (m-40) cc_final: 0.7849 (p0) outliers start: 2 outliers final: 1 residues processed: 30 average time/residue: 0.1277 time to fit residues: 6.1177 Evaluate side-chains 26 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 25 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 16 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 26 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 32 optimal weight: 0.0980 chunk 5 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 11 optimal weight: 0.0970 chunk 34 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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** ** 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 31 ASN ** P 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4894 r_free = 0.4894 target = 0.238300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.5337 r_free = 0.5337 target = 0.158065 restraints weight = 16206.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.5367 r_free = 0.5367 target = 0.160689 restraints weight = 9791.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.5422 r_free = 0.5422 target = 0.162810 restraints weight = 6657.062| |-----------------------------------------------------------------------------| r_work (final): 0.4666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.6390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 3114 Z= 0.107 Angle : 0.501 3.785 4230 Z= 0.275 Chirality : 0.046 0.146 486 Planarity : 0.002 0.009 558 Dihedral : 9.937 63.323 522 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.39 % Favored : 88.61 % Rotamer: Outliers : 0.62 % Allowed : 22.84 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.49 (0.35), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.41 (0.27), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.003 HIS N 18 PHE 0.011 0.001 PHE P 23 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 3114) covalent geometry : angle 0.50055 ( 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 29 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 27 time to evaluate : 0.466 Fit side-chains REVERT: C 35 ASN cc_start: 0.8588 (m-40) cc_final: 0.8160 (m110) REVERT: E 16 LEU cc_start: 0.6982 (OUTLIER) cc_final: 0.6706 (pt) REVERT: F 35 ASN cc_start: 0.8954 (m-40) cc_final: 0.8554 (m110) REVERT: I 35 ASN cc_start: 0.9015 (m-40) cc_final: 0.8450 (m-40) REVERT: L 35 ASN cc_start: 0.8963 (m-40) cc_final: 0.8726 (m110) REVERT: O 35 ASN cc_start: 0.8901 (m-40) cc_final: 0.8583 (m110) REVERT: R 35 ASN cc_start: 0.8576 (m-40) cc_final: 0.7825 (p0) outliers start: 2 outliers final: 0 residues processed: 29 average time/residue: 0.1327 time to fit residues: 6.2191 Evaluate side-chains 27 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 26 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 16 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 26 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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** ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4854 r_free = 0.4854 target = 0.227752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.5281 r_free = 0.5281 target = 0.154490 restraints weight = 16486.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.5320 r_free = 0.5320 target = 0.156317 restraints weight = 11054.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.5345 r_free = 0.5345 target = 0.157585 restraints weight = 8042.802| |-----------------------------------------------------------------------------| r_work (final): 0.4597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.6693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 3114 Z= 0.129 Angle : 0.538 4.772 4230 Z= 0.293 Chirality : 0.046 0.133 486 Planarity : 0.002 0.008 558 Dihedral : 9.917 62.178 522 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 20.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.72 % Favored : 85.28 % Rotamer: Outliers : 1.23 % Allowed : 23.46 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.52 (0.36), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.44 (0.27), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.003 HIS B 18 PHE 0.010 0.002 PHE E 23 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 3114) covalent geometry : angle 0.53829 ( 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 28 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.483 Fit side-chains revert: symmetry clash REVERT: C 35 ASN cc_start: 0.8637 (m-40) cc_final: 0.8218 (m110) REVERT: E 16 LEU cc_start: 0.6749 (OUTLIER) cc_final: 0.6448 (pt) REVERT: F 35 ASN cc_start: 0.8974 (m-40) cc_final: 0.8574 (m110) REVERT: I 35 ASN cc_start: 0.9041 (m-40) cc_final: 0.8396 (m-40) REVERT: L 35 ASN cc_start: 0.8982 (m-40) cc_final: 0.8736 (m110) REVERT: O 35 ASN cc_start: 0.8962 (m-40) cc_final: 0.8636 (m110) REVERT: R 35 ASN cc_start: 0.8663 (m-40) cc_final: 0.7887 (p0) outliers start: 4 outliers final: 2 residues processed: 28 average time/residue: 0.1274 time to fit residues: 5.8505 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 : 0.439 ------------------------------------------------------------------------------- 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 27 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 HIS ** 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 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 = 0.4873 r_free = 0.4873 target = 0.231250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.5273 r_free = 0.5273 target = 0.152034 restraints weight = 16754.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.5323 r_free = 0.5323 target = 0.154833 restraints weight = 10206.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.5359 r_free = 0.5359 target = 0.156706 restraints weight = 6891.086| |-----------------------------------------------------------------------------| r_work (final): 0.4704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.6831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 3114 Z= 0.123 Angle : 0.530 4.527 4230 Z= 0.290 Chirality : 0.046 0.147 486 Planarity : 0.002 0.008 558 Dihedral : 9.878 63.755 522 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 20.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.78 % Favored : 87.22 % Rotamer: Outliers : 0.93 % Allowed : 23.77 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.60 (0.36), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.50 (0.27), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.003 HIS N 18 PHE 0.010 0.002 PHE E 23 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 3114) covalent geometry : angle 0.52978 ( 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 27 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.439 Fit side-chains REVERT: C 35 ASN cc_start: 0.8655 (m-40) cc_final: 0.8226 (m110) REVERT: E 16 LEU cc_start: 0.6788 (OUTLIER) cc_final: 0.6489 (pt) REVERT: F 35 ASN cc_start: 0.8945 (m-40) cc_final: 0.8581 (m110) REVERT: I 35 ASN cc_start: 0.9046 (m-40) cc_final: 0.8454 (m-40) REVERT: L 35 ASN cc_start: 0.8965 (m-40) cc_final: 0.8741 (m110) REVERT: O 35 ASN cc_start: 0.8935 (m-40) cc_final: 0.8608 (m110) REVERT: R 35 ASN cc_start: 0.8685 (m-40) cc_final: 0.7930 (p0) outliers start: 3 outliers final: 1 residues processed: 27 average time/residue: 0.1253 time to fit residues: 5.6144 Evaluate side-chains 26 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 24 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 18 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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** ** 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** ** 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 = 0.4740 r_free = 0.4740 target = 0.116488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.099986 restraints weight = 18748.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.103666 restraints weight = 10036.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.106277 restraints weight = 6433.377| |-----------------------------------------------------------------------------| r_work (final): 0.4573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.7002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 3114 Z= 0.185 Angle : 0.626 5.809 4230 Z= 0.339 Chirality : 0.048 0.146 486 Planarity : 0.003 0.013 558 Dihedral : 10.100 61.537 522 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 26.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.33 % Favored : 76.67 % Rotamer: Outliers : 1.23 % Allowed : 23.46 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.82 (0.35), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.67 (0.27), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.003 HIS B 18 PHE 0.014 0.002 PHE N 23 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 3114) covalent geometry : angle 0.62594 ( 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 28 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.481 Fit side-chains REVERT: C 35 ASN cc_start: 0.8680 (m-40) cc_final: 0.8253 (m110) REVERT: E 16 LEU cc_start: 0.7037 (OUTLIER) cc_final: 0.6617 (pt) REVERT: F 35 ASN cc_start: 0.9017 (m-40) cc_final: 0.8646 (m110) REVERT: I 35 ASN cc_start: 0.9086 (m-40) cc_final: 0.8488 (m-40) REVERT: K 16 LEU cc_start: 0.7552 (OUTLIER) cc_final: 0.7285 (pt) REVERT: L 35 ASN cc_start: 0.9004 (m-40) cc_final: 0.8790 (m110) REVERT: O 35 ASN cc_start: 0.8995 (m-40) cc_final: 0.8651 (m110) REVERT: R 35 ASN cc_start: 0.8850 (m-40) cc_final: 0.8066 (p0) outliers start: 4 outliers final: 1 residues processed: 28 average time/residue: 0.1359 time to fit residues: 6.2014 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 : 0.367 ------------------------------------------------------------------------------- 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 34 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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** ** 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 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 = 0.4866 r_free = 0.4866 target = 0.229236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.5246 r_free = 0.5246 target = 0.149522 restraints weight = 16788.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.5302 r_free = 0.5302 target = 0.152245 restraints weight = 10237.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.5340 r_free = 0.5340 target = 0.154077 restraints weight = 7001.511| |-----------------------------------------------------------------------------| r_work (final): 0.4695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.7000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 3114 Z= 0.122 Angle : 0.533 4.250 4230 Z= 0.293 Chirality : 0.047 0.157 486 Planarity : 0.002 0.011 558 Dihedral : 9.926 64.356 522 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 21.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.44 % Favored : 85.56 % Rotamer: Outliers : 1.23 % Allowed : 23.77 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.76 (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 HIS 0.012 0.003 HIS B 18 PHE 0.010 0.002 PHE E 23 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 3114) covalent geometry : angle 0.53264 ( 4230) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3064.96 seconds wall clock time: 53 minutes 33.77 seconds (3213.77 seconds total)