Starting phenix.real_space_refine on Fri Aug 22 14:20:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8az7_15756/08_2025/8az7_15756.cif Found real_map, /net/cci-nas-00/data/ceres_data/8az7_15756/08_2025/8az7_15756.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8az7_15756/08_2025/8az7_15756.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8az7_15756/08_2025/8az7_15756.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8az7_15756/08_2025/8az7_15756.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8az7_15756/08_2025/8az7_15756.map" } resolution = 2.9 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: 3 Type Number sf(0) Gaussians C 2470 2.51 5 N 740 2.21 5 O 800 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4010 Number of models: 1 Model: "" Number of chains: 40 Chain: "A" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 217 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 217 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 182 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 182 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 217 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 217 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 182 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 182 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 217 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 217 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 182 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 182 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 217 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 217 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 182 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 182 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 217 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 217 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 182 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 182 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.06, per 1000 atoms: 0.26 Number of scatterers: 4010 At special positions: 0 Unit cell: (70.2, 89.1, 48.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 800 8.00 N 740 7.00 C 2470 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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=20, symmetry=0 Number of additional bonds: simple=20, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.28 Conformation dependent library (CDL) restraints added in 166.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 960 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 14 sheets defined 0.0% alpha, 50.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 22 removed outlier: 7.026A pdb=" N ASN A 21 " --> pdb=" O GLY E 20 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ASN E 22 " --> pdb=" O ASN A 21 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ASN E 21 " --> pdb=" O GLY I 20 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ASN I 22 " --> pdb=" O ASN E 21 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ASN I 21 " --> pdb=" O GLY M 20 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ASN M 22 " --> pdb=" O ASN I 21 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ASN M 21 " --> pdb=" O GLY Q 20 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ASN Q 22 " --> pdb=" O ASN M 21 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.616A pdb=" N SER A 29 " --> pdb=" O THR E 30 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N VAL E 32 " --> pdb=" O SER A 29 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ASN A 31 " --> pdb=" O VAL E 32 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N SER E 29 " --> pdb=" O THR I 30 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N VAL I 32 " --> pdb=" O SER E 29 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ASN E 31 " --> pdb=" O VAL I 32 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N SER I 29 " --> pdb=" O THR M 30 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N VAL M 32 " --> pdb=" O SER I 29 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ASN I 31 " --> pdb=" O VAL M 32 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 10 through 22 removed outlier: 7.003A pdb=" N ASN B 21 " --> pdb=" O GLY F 20 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ASN F 22 " --> pdb=" O ASN B 21 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ASN F 21 " --> pdb=" O GLY J 20 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ASN J 22 " --> pdb=" O ASN F 21 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ASN J 21 " --> pdb=" O GLY N 20 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ASN N 22 " --> pdb=" O ASN J 21 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ASN N 21 " --> pdb=" O GLY R 20 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ASN R 22 " --> pdb=" O ASN N 21 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 25 through 26 Processing sheet with id=AA6, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.584A pdb=" N SER J 29 " --> pdb=" O THR N 30 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N VAL N 32 " --> pdb=" O SER J 29 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ASN J 31 " --> pdb=" O VAL N 32 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 14 through 16 removed outlier: 6.529A pdb=" N ASN C 14 " --> pdb=" O PHE G 15 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ASN G 14 " --> pdb=" O PHE K 15 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ASN K 14 " --> pdb=" O PHE O 15 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ASN O 14 " --> pdb=" O PHE S 15 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 21 through 27 removed outlier: 6.343A pdb=" N ASN C 22 " --> pdb=" O PHE G 23 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N ALA G 25 " --> pdb=" O ASN C 22 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N GLY C 24 " --> pdb=" O ALA G 25 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N LEU G 27 " --> pdb=" O GLY C 24 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ILE C 26 " --> pdb=" O LEU G 27 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ASN G 22 " --> pdb=" O PHE K 23 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N ALA K 25 " --> pdb=" O ASN G 22 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLY G 24 " --> pdb=" O ALA K 25 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N LEU K 27 " --> pdb=" O GLY G 24 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ILE G 26 " --> pdb=" O LEU K 27 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ASN K 22 " --> pdb=" O PHE O 23 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N ALA O 25 " --> pdb=" O ASN K 22 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N GLY K 24 " --> pdb=" O ALA O 25 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N LEU O 27 " --> pdb=" O GLY K 24 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE K 26 " --> pdb=" O LEU O 27 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ASN O 22 " --> pdb=" O PHE S 23 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N ALA S 25 " --> pdb=" O ASN O 22 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N GLY O 24 " --> pdb=" O ALA S 25 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N LEU S 27 " --> pdb=" O GLY O 24 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ILE O 26 " --> pdb=" O LEU S 27 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 30 through 32 removed outlier: 6.951A pdb=" N VAL G 32 " --> pdb=" O ASN C 31 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N VAL K 32 " --> pdb=" O ASN G 31 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL O 32 " --> pdb=" O ASN K 31 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL S 32 " --> pdb=" O ASN O 31 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 35 through 36 removed outlier: 6.965A pdb=" N ASN C 35 " --> pdb=" O THR G 36 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ASN G 35 " --> pdb=" O THR K 36 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ASN K 35 " --> pdb=" O THR O 36 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ASN O 35 " --> pdb=" O THR S 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 14 through 16 removed outlier: 6.530A pdb=" N ASN D 14 " --> pdb=" O PHE H 15 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ASN H 14 " --> pdb=" O PHE L 15 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ASN L 14 " --> pdb=" O PHE P 15 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ASN P 14 " --> pdb=" O PHE T 15 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'D' and resid 21 through 27 removed outlier: 6.353A pdb=" N ASN D 22 " --> pdb=" O PHE H 23 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N ALA H 25 " --> pdb=" O ASN D 22 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLY D 24 " --> pdb=" O ALA H 25 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N LEU H 27 " --> pdb=" O GLY D 24 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE D 26 " --> pdb=" O LEU H 27 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ASN H 22 " --> pdb=" O PHE L 23 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N ALA L 25 " --> pdb=" O ASN H 22 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLY H 24 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N LEU L 27 " --> pdb=" O GLY H 24 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE H 26 " --> pdb=" O LEU L 27 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ASN L 22 " --> pdb=" O PHE P 23 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N ALA P 25 " --> pdb=" O ASN L 22 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N GLY L 24 " --> pdb=" O ALA P 25 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N LEU P 27 " --> pdb=" O GLY L 24 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE L 26 " --> pdb=" O LEU P 27 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ASN P 22 " --> pdb=" O PHE T 23 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N ALA T 25 " --> pdb=" O ASN P 22 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLY P 24 " --> pdb=" O ALA T 25 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N LEU T 27 " --> pdb=" O GLY P 24 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE P 26 " --> pdb=" O LEU T 27 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'D' and resid 30 through 32 removed outlier: 6.934A pdb=" N VAL H 32 " --> pdb=" O ASN D 31 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL L 32 " --> pdb=" O ASN H 31 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL P 32 " --> pdb=" O ASN L 31 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL T 32 " --> pdb=" O ASN P 31 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 35 through 36 removed outlier: 6.964A pdb=" N ASN D 35 " --> pdb=" O THR H 36 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ASN H 35 " --> pdb=" O THR L 36 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ASN L 35 " --> pdb=" O THR P 36 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ASN P 35 " --> pdb=" O THR T 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 108 hydrogen bonds defined for protein. 324 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.53 Time building geometry restraints manager: 0.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 650 1.29 - 1.36: 720 1.36 - 1.42: 500 1.42 - 1.49: 600 1.49 - 1.55: 1580 Bond restraints: 4050 Sorted by residual: bond pdb=" N GLY C 20 " pdb=" CA GLY C 20 " ideal model delta sigma weight residual 1.442 1.455 -0.013 7.70e-03 1.69e+04 2.73e+00 bond pdb=" N GLY K 20 " pdb=" CA GLY K 20 " ideal model delta sigma weight residual 1.442 1.454 -0.013 7.70e-03 1.69e+04 2.69e+00 bond pdb=" N GLY H 20 " pdb=" CA GLY H 20 " ideal model delta sigma weight residual 1.442 1.454 -0.012 7.70e-03 1.69e+04 2.59e+00 bond pdb=" N GLY G 20 " pdb=" CA GLY G 20 " ideal model delta sigma weight residual 1.442 1.454 -0.012 7.70e-03 1.69e+04 2.49e+00 bond pdb=" N GLY L 20 " pdb=" CA GLY L 20 " ideal model delta sigma weight residual 1.442 1.454 -0.012 7.70e-03 1.69e+04 2.44e+00 ... (remaining 4045 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.69: 4831 0.69 - 1.38: 486 1.38 - 2.06: 129 2.06 - 2.75: 26 2.75 - 3.44: 18 Bond angle restraints: 5490 Sorted by residual: angle pdb=" C SER T 19 " pdb=" N GLY T 20 " pdb=" CA GLY T 20 " ideal model delta sigma weight residual 122.69 119.55 3.14 1.04e+00 9.25e-01 9.13e+00 angle pdb=" C SER S 19 " pdb=" N GLY S 20 " pdb=" CA GLY S 20 " ideal model delta sigma weight residual 122.69 119.55 3.14 1.04e+00 9.25e-01 9.12e+00 angle pdb=" C SER P 19 " pdb=" N GLY P 20 " pdb=" CA GLY P 20 " ideal model delta sigma weight residual 122.69 119.57 3.12 1.04e+00 9.25e-01 9.01e+00 angle pdb=" C SER O 19 " pdb=" N GLY O 20 " pdb=" CA GLY O 20 " ideal model delta sigma weight residual 122.69 119.59 3.10 1.04e+00 9.25e-01 8.89e+00 angle pdb=" N SER T 19 " pdb=" CA SER T 19 " pdb=" C SER T 19 " ideal model delta sigma weight residual 110.61 113.76 -3.15 1.25e+00 6.40e-01 6.34e+00 ... (remaining 5485 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.85: 2071 10.85 - 21.69: 139 21.69 - 32.54: 30 32.54 - 43.38: 0 43.38 - 54.23: 10 Dihedral angle restraints: 2250 sinusoidal: 750 harmonic: 1500 Sorted by residual: dihedral pdb=" CA PHE S 23 " pdb=" CB PHE S 23 " pdb=" CG PHE S 23 " pdb=" CD1 PHE S 23 " ideal model delta sinusoidal sigma weight residual -20.00 34.23 -54.23 2 2.00e+01 2.50e-03 7.90e+00 dihedral pdb=" CA PHE T 23 " pdb=" CB PHE T 23 " pdb=" CG PHE T 23 " pdb=" CD1 PHE T 23 " ideal model delta sinusoidal sigma weight residual -20.00 34.18 -54.18 2 2.00e+01 2.50e-03 7.89e+00 dihedral pdb=" CA PHE O 23 " pdb=" CB PHE O 23 " pdb=" CG PHE O 23 " pdb=" CD1 PHE O 23 " ideal model delta sinusoidal sigma weight residual -20.00 34.03 -54.03 2 2.00e+01 2.50e-03 7.86e+00 ... (remaining 2247 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 421 0.028 - 0.055: 148 0.055 - 0.083: 12 0.083 - 0.111: 29 0.111 - 0.138: 30 Chirality restraints: 640 Sorted by residual: chirality pdb=" CA ILE G 26 " pdb=" N ILE G 26 " pdb=" C ILE G 26 " pdb=" CB ILE G 26 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.79e-01 chirality pdb=" CA ILE H 26 " pdb=" N ILE H 26 " pdb=" C ILE H 26 " pdb=" CB ILE H 26 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.65e-01 chirality pdb=" CA ILE K 26 " pdb=" N ILE K 26 " pdb=" C ILE K 26 " pdb=" CB ILE K 26 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.61e-01 ... (remaining 637 not shown) Planarity restraints: 720 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE H 15 " -0.003 2.00e-02 2.50e+03 6.32e-03 6.99e-01 pdb=" CG PHE H 15 " 0.013 2.00e-02 2.50e+03 pdb=" CD1 PHE H 15 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE H 15 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE H 15 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE H 15 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE H 15 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE K 15 " -0.003 2.00e-02 2.50e+03 6.31e-03 6.96e-01 pdb=" CG PHE K 15 " 0.013 2.00e-02 2.50e+03 pdb=" CD1 PHE K 15 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE K 15 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE K 15 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE K 15 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE K 15 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE L 15 " -0.003 2.00e-02 2.50e+03 6.23e-03 6.78e-01 pdb=" CG PHE L 15 " 0.013 2.00e-02 2.50e+03 pdb=" CD1 PHE L 15 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE L 15 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE L 15 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE L 15 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE L 15 " -0.000 2.00e-02 2.50e+03 ... (remaining 717 not shown) Histogram of nonbonded interaction distances: 2.66 - 3.11: 2783 3.11 - 3.56: 4227 3.56 - 4.01: 6109 4.01 - 4.45: 7397 4.45 - 4.90: 12586 Nonbonded interactions: 33102 Sorted by model distance: nonbonded pdb=" O ASN I 22 " pdb=" N PHE M 23 " model vdw 2.665 3.120 nonbonded pdb=" O SER P 19 " pdb=" CB SER P 19 " model vdw 2.667 2.752 nonbonded pdb=" O SER S 19 " pdb=" CB SER S 19 " model vdw 2.667 2.752 nonbonded pdb=" O SER T 19 " pdb=" CB SER T 19 " model vdw 2.667 2.752 nonbonded pdb=" O SER O 19 " pdb=" CB SER O 19 " model vdw 2.667 2.752 ... (remaining 33097 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'E' selection = chain 'F' selection = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'N' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'G' selection = chain 'H' selection = chain 'K' selection = chain 'L' selection = chain 'O' selection = chain 'P' selection = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.630 Find NCS groups from input model: 0.040 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:6.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 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 : 0.008 0.103 4070 Z= 0.729 Angle : 0.508 3.439 5490 Z= 0.343 Chirality : 0.042 0.138 640 Planarity : 0.001 0.006 720 Dihedral : 8.791 54.230 1290 Min Nonbonded Distance : 2.665 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % 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 aren not related in a simple way. whole: -3.51 (0.23), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.67 (0.17), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 11 TYR 0.003 0.001 TYR Q 37 PHE 0.013 0.002 PHE L 15 HIS 0.005 0.001 HIS S 18 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 4050) covalent geometry : angle 0.50779 ( 5490) hydrogen bonds : bond 0.16975 ( 108) hydrogen bonds : angle 6.67305 ( 324) Misc. bond : bond 0.10200 ( 20) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.164 Fit side-chains REVERT: A 11 ARG cc_start: 0.7483 (mtp180) cc_final: 0.7256 (mmm160) REVERT: D 31 ASN cc_start: 0.8426 (t0) cc_final: 0.8222 (t0) REVERT: P 31 ASN cc_start: 0.8366 (t0) cc_final: 0.8155 (t0) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.3668 time to fit residues: 33.5241 Evaluate side-chains 78 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 chunk 19 optimal weight: 7.9990 chunk 30 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 chunk 37 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 21 ASN C 14 ASN ** C 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 14 ASN ** D 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 21 ASN ** F 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 14 ASN ** G 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 14 ASN ** H 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 ASN ** I 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 21 ASN K 14 ASN ** K 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 14 ASN ** L 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 ASN ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 14 ASN ** O 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 31 ASN P 14 ASN ** P 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 18 HIS Q 21 ASN ** R 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 21 ASN S 14 ASN ** S 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 14 ASN ** T 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.133479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.086811 restraints weight = 5282.737| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.47 r_work: 0.3118 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 4070 Z= 0.218 Angle : 0.572 4.484 5490 Z= 0.329 Chirality : 0.044 0.138 640 Planarity : 0.003 0.022 720 Dihedral : 4.870 12.036 550 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 2.95 % Allowed : 5.23 % Favored : 91.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.56 (0.24), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.70 (0.18), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F 11 TYR 0.007 0.001 TYR E 37 PHE 0.011 0.002 PHE F 15 HIS 0.005 0.002 HIS Q 18 Details of bonding type rmsd covalent geometry : bond 0.00500 ( 4050) covalent geometry : angle 0.57167 ( 5490) hydrogen bonds : bond 0.04725 ( 108) hydrogen bonds : angle 4.96390 ( 324) Misc. bond : bond 0.00119 ( 20) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.159 Fit side-chains REVERT: A 10 GLN cc_start: 0.8061 (mt0) cc_final: 0.7417 (mp10) REVERT: A 11 ARG cc_start: 0.7972 (mtp180) cc_final: 0.6827 (mmm160) REVERT: A 12 LEU cc_start: 0.8875 (mt) cc_final: 0.8635 (tp) REVERT: E 10 GLN cc_start: 0.7470 (mt0) cc_final: 0.7160 (mp10) REVERT: H 31 ASN cc_start: 0.8011 (t0) cc_final: 0.7732 (t0) REVERT: N 11 ARG cc_start: 0.8465 (mtp180) cc_final: 0.8254 (mtp85) REVERT: O 31 ASN cc_start: 0.8210 (t0) cc_final: 0.7950 (t0) REVERT: R 11 ARG cc_start: 0.8740 (mtp180) cc_final: 0.8528 (mtp85) outliers start: 13 outliers final: 3 residues processed: 89 average time/residue: 0.3295 time to fit residues: 30.8839 Evaluate side-chains 90 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 87 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain L residue 35 ASN Chi-restraints excluded: chain T residue 35 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 12 optimal weight: 30.0000 chunk 24 optimal weight: 8.9990 chunk 38 optimal weight: 0.9980 chunk 21 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 chunk 31 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 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** ** F 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 18 HIS ** K 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 18 HIS N 18 HIS ** O 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 31 ASN R 18 HIS T 31 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.131260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.085949 restraints weight = 5327.724| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.57 r_work: 0.3033 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.031 4070 Z= 0.289 Angle : 0.657 7.366 5490 Z= 0.363 Chirality : 0.046 0.145 640 Planarity : 0.003 0.011 720 Dihedral : 5.216 13.069 550 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 2.05 % Allowed : 9.32 % Favored : 88.64 % 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 aren not related in a simple way. whole: -3.62 (0.24), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.75 (0.19), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG M 11 TYR 0.009 0.001 TYR S 37 PHE 0.011 0.002 PHE E 15 HIS 0.006 0.002 HIS N 18 Details of bonding type rmsd covalent geometry : bond 0.00663 ( 4050) covalent geometry : angle 0.65664 ( 5490) hydrogen bonds : bond 0.05088 ( 108) hydrogen bonds : angle 5.00223 ( 324) Misc. bond : bond 0.00176 ( 20) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 0.096 Fit side-chains REVERT: A 10 GLN cc_start: 0.8154 (mt0) cc_final: 0.7406 (mp10) REVERT: A 11 ARG cc_start: 0.7923 (mtp180) cc_final: 0.6877 (mmm160) REVERT: E 10 GLN cc_start: 0.7487 (mt0) cc_final: 0.7200 (mp10) REVERT: E 12 LEU cc_start: 0.8774 (mp) cc_final: 0.8301 (tm) REVERT: H 31 ASN cc_start: 0.8110 (t0) cc_final: 0.7862 (t0) REVERT: H 34 SER cc_start: 0.8535 (t) cc_final: 0.8292 (t) REVERT: I 12 LEU cc_start: 0.8783 (mp) cc_final: 0.8207 (tm) REVERT: M 11 ARG cc_start: 0.8432 (mtp85) cc_final: 0.8182 (mtp85) REVERT: N 11 ARG cc_start: 0.8347 (mtp180) cc_final: 0.8102 (mtp85) REVERT: N 12 LEU cc_start: 0.8687 (mp) cc_final: 0.8211 (tm) REVERT: R 11 ARG cc_start: 0.8553 (mtp180) cc_final: 0.8339 (mtp85) outliers start: 9 outliers final: 5 residues processed: 93 average time/residue: 0.3191 time to fit residues: 31.2251 Evaluate side-chains 97 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 92 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 35 ASN Chi-restraints excluded: chain L residue 21 ASN Chi-restraints excluded: chain L residue 35 ASN Chi-restraints excluded: chain S residue 21 ASN Chi-restraints excluded: chain T residue 35 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 16 optimal weight: 2.9990 chunk 14 optimal weight: 20.0000 chunk 19 optimal weight: 2.9990 chunk 21 optimal weight: 20.0000 chunk 33 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 31 optimal weight: 20.0000 chunk 7 optimal weight: 10.0000 chunk 4 optimal weight: 20.0000 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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** ** C 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** ** F 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 31 ASN ** P 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 31 ASN T 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.133126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.086137 restraints weight = 5408.188| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.48 r_work: 0.3134 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 4070 Z= 0.133 Angle : 0.555 6.611 5490 Z= 0.297 Chirality : 0.043 0.139 640 Planarity : 0.002 0.018 720 Dihedral : 4.727 12.831 550 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 1.36 % Allowed : 10.91 % Favored : 87.73 % 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 aren not related in a simple way. whole: -3.62 (0.25), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.75 (0.19), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 11 TYR 0.009 0.001 TYR S 37 PHE 0.008 0.001 PHE K 15 HIS 0.003 0.001 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 4050) covalent geometry : angle 0.55524 ( 5490) hydrogen bonds : bond 0.03483 ( 108) hydrogen bonds : angle 4.60386 ( 324) Misc. bond : bond 0.00074 ( 20) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 87 time to evaluate : 0.160 Fit side-chains REVERT: A 10 GLN cc_start: 0.8150 (mt0) cc_final: 0.7468 (mp10) REVERT: A 11 ARG cc_start: 0.7754 (mtp180) cc_final: 0.6769 (mmm160) REVERT: E 10 GLN cc_start: 0.7449 (mt0) cc_final: 0.7245 (mp10) REVERT: E 12 LEU cc_start: 0.8733 (mp) cc_final: 0.8242 (tm) REVERT: G 34 SER cc_start: 0.8611 (m) cc_final: 0.8396 (t) REVERT: H 31 ASN cc_start: 0.8150 (t0) cc_final: 0.7809 (t0) REVERT: I 11 ARG cc_start: 0.8276 (mtp85) cc_final: 0.8060 (mtp85) REVERT: I 12 LEU cc_start: 0.8695 (mp) cc_final: 0.8151 (tm) REVERT: N 11 ARG cc_start: 0.8218 (mtp180) cc_final: 0.7882 (mtp85) REVERT: O 31 ASN cc_start: 0.8204 (t0) cc_final: 0.7980 (t0) outliers start: 6 outliers final: 4 residues processed: 87 average time/residue: 0.3456 time to fit residues: 31.6205 Evaluate side-chains 91 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 87 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain L residue 35 ASN Chi-restraints excluded: chain Q residue 11 ARG Chi-restraints excluded: chain T residue 35 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 8 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 26 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 31 optimal weight: 20.0000 chunk 21 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 30 optimal weight: 10.0000 chunk 6 optimal weight: 30.0000 chunk 0 optimal weight: 0.8980 chunk 1 optimal weight: 6.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- 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** ** C 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** ** F 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 14 ASN T 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.131716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.084107 restraints weight = 5759.383| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.55 r_work: 0.3096 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.022 4070 Z= 0.213 Angle : 0.599 6.720 5490 Z= 0.326 Chirality : 0.044 0.143 640 Planarity : 0.002 0.022 720 Dihedral : 4.909 12.814 550 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 2.05 % Allowed : 11.59 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.67 (0.25), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.79 (0.19), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 11 TYR 0.011 0.001 TYR S 37 PHE 0.009 0.002 PHE E 15 HIS 0.004 0.001 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00487 ( 4050) covalent geometry : angle 0.59904 ( 5490) hydrogen bonds : bond 0.04365 ( 108) hydrogen bonds : angle 4.69355 ( 324) Misc. bond : bond 0.00126 ( 20) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.169 Fit side-chains REVERT: A 10 GLN cc_start: 0.8229 (mt0) cc_final: 0.7463 (mp10) REVERT: A 11 ARG cc_start: 0.7772 (mtp180) cc_final: 0.6775 (mmm160) REVERT: E 10 GLN cc_start: 0.7545 (mt0) cc_final: 0.7298 (mp10) REVERT: E 12 LEU cc_start: 0.8733 (mp) cc_final: 0.8227 (tm) REVERT: H 31 ASN cc_start: 0.8146 (t0) cc_final: 0.7880 (t0) REVERT: H 34 SER cc_start: 0.8552 (t) cc_final: 0.8301 (t) REVERT: I 12 LEU cc_start: 0.8703 (mp) cc_final: 0.8099 (tm) REVERT: N 11 ARG cc_start: 0.8221 (mtp180) cc_final: 0.7805 (mtp85) REVERT: T 31 ASN cc_start: 0.8255 (t0) cc_final: 0.7990 (t160) outliers start: 9 outliers final: 5 residues processed: 89 average time/residue: 0.3519 time to fit residues: 33.0335 Evaluate side-chains 91 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain G residue 35 ASN Chi-restraints excluded: chain L residue 35 ASN Chi-restraints excluded: chain T residue 35 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 5 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 3 optimal weight: 10.0000 chunk 6 optimal weight: 30.0000 chunk 9 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 39 optimal weight: 5.9990 chunk 14 optimal weight: 9.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- 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** ** C 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** ** F 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 31 ASN ** P 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 = 0.3964 r_free = 0.3964 target = 0.131570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.084266 restraints weight = 5488.440| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.50 r_work: 0.3100 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 4070 Z= 0.213 Angle : 0.624 7.269 5490 Z= 0.334 Chirality : 0.044 0.143 640 Planarity : 0.002 0.032 720 Dihedral : 4.960 13.181 550 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 2.05 % Allowed : 12.95 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.74 (0.24), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.84 (0.18), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 11 TYR 0.012 0.001 TYR S 37 PHE 0.009 0.002 PHE E 15 HIS 0.004 0.001 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00487 ( 4050) covalent geometry : angle 0.62382 ( 5490) hydrogen bonds : bond 0.04262 ( 108) hydrogen bonds : angle 4.61395 ( 324) Misc. bond : bond 0.00128 ( 20) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.159 Fit side-chains REVERT: A 10 GLN cc_start: 0.8189 (mt0) cc_final: 0.7410 (mp10) REVERT: A 11 ARG cc_start: 0.7732 (mtp180) cc_final: 0.6761 (mmm160) REVERT: E 10 GLN cc_start: 0.7588 (mt0) cc_final: 0.7288 (mp10) REVERT: F 12 LEU cc_start: 0.8736 (mp) cc_final: 0.8136 (tp) REVERT: H 31 ASN cc_start: 0.8182 (t0) cc_final: 0.7912 (t0) REVERT: I 12 LEU cc_start: 0.8766 (mp) cc_final: 0.8174 (tm) REVERT: N 11 ARG cc_start: 0.8222 (mtp180) cc_final: 0.7796 (mtp85) REVERT: O 31 ASN cc_start: 0.8211 (t0) cc_final: 0.7990 (t0) REVERT: T 31 ASN cc_start: 0.8232 (t0) cc_final: 0.7951 (t160) outliers start: 9 outliers final: 6 residues processed: 87 average time/residue: 0.3559 time to fit residues: 32.5474 Evaluate side-chains 93 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 87 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain G residue 35 ASN Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain L residue 35 ASN Chi-restraints excluded: chain T residue 35 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 6 optimal weight: 30.0000 chunk 8 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 38 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 39 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 12 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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** ** C 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** F 18 HIS ** G 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 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 = 0.3948 r_free = 0.3948 target = 0.130255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.082154 restraints weight = 6293.335| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.62 r_work: 0.3061 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.031 4070 Z= 0.291 Angle : 0.678 8.097 5490 Z= 0.367 Chirality : 0.046 0.149 640 Planarity : 0.003 0.026 720 Dihedral : 5.229 13.596 550 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 1.36 % Allowed : 13.41 % Favored : 85.23 % 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 aren not related in a simple way. whole: -3.81 (0.24), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.89 (0.18), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 11 TYR 0.012 0.001 TYR S 37 PHE 0.011 0.002 PHE E 15 HIS 0.004 0.002 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00663 ( 4050) covalent geometry : angle 0.67831 ( 5490) hydrogen bonds : bond 0.04918 ( 108) hydrogen bonds : angle 4.74054 ( 324) Misc. bond : bond 0.00180 ( 20) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 0.113 Fit side-chains REVERT: A 10 GLN cc_start: 0.8189 (mt0) cc_final: 0.7346 (mp10) REVERT: A 11 ARG cc_start: 0.7784 (mtp180) cc_final: 0.6811 (mmm160) REVERT: E 10 GLN cc_start: 0.7593 (mt0) cc_final: 0.7308 (mp10) REVERT: E 12 LEU cc_start: 0.8770 (mp) cc_final: 0.8291 (tm) REVERT: F 12 LEU cc_start: 0.8739 (mp) cc_final: 0.8168 (tp) REVERT: H 31 ASN cc_start: 0.8137 (t0) cc_final: 0.7892 (t0) REVERT: N 11 ARG cc_start: 0.8226 (mtp180) cc_final: 0.7820 (mtp85) REVERT: T 31 ASN cc_start: 0.8229 (t0) cc_final: 0.7905 (t160) outliers start: 6 outliers final: 8 residues processed: 92 average time/residue: 0.3317 time to fit residues: 32.1030 Evaluate side-chains 99 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain G residue 35 ASN Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain L residue 21 ASN Chi-restraints excluded: chain L residue 35 ASN Chi-restraints excluded: chain S residue 21 ASN Chi-restraints excluded: chain T residue 35 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 15 optimal weight: 20.0000 chunk 20 optimal weight: 20.0000 chunk 28 optimal weight: 10.0000 chunk 35 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 7 optimal weight: 20.0000 chunk 34 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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** ** C 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 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 14 ASN ** O 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 14 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.134846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.087836 restraints weight = 5641.334| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.53 r_work: 0.3165 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 4070 Z= 0.096 Angle : 0.582 7.800 5490 Z= 0.295 Chirality : 0.043 0.137 640 Planarity : 0.002 0.029 720 Dihedral : 4.508 12.401 550 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.36 % Allowed : 15.23 % Favored : 83.41 % 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 aren not related in a simple way. whole: -3.75 (0.24), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.85 (0.18), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 11 TYR 0.012 0.001 TYR S 37 PHE 0.005 0.001 PHE K 15 HIS 0.003 0.001 HIS S 18 Details of bonding type rmsd covalent geometry : bond 0.00212 ( 4050) covalent geometry : angle 0.58249 ( 5490) hydrogen bonds : bond 0.02337 ( 108) hydrogen bonds : angle 4.13875 ( 324) Misc. bond : bond 0.00041 ( 20) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.182 Fit side-chains REVERT: A 10 GLN cc_start: 0.8118 (mt0) cc_final: 0.7781 (mp10) REVERT: E 10 GLN cc_start: 0.7533 (mt0) cc_final: 0.7241 (mp10) REVERT: E 12 LEU cc_start: 0.8713 (mp) cc_final: 0.8239 (tm) REVERT: F 12 LEU cc_start: 0.8735 (mp) cc_final: 0.8195 (tp) REVERT: H 31 ASN cc_start: 0.8125 (t0) cc_final: 0.7798 (t0) REVERT: I 12 LEU cc_start: 0.8692 (mp) cc_final: 0.8145 (tm) REVERT: M 11 ARG cc_start: 0.8239 (mtp85) cc_final: 0.7998 (mtp85) REVERT: N 11 ARG cc_start: 0.8189 (mtp180) cc_final: 0.7779 (mtp85) REVERT: O 31 ASN cc_start: 0.8160 (t0) cc_final: 0.7936 (t0) REVERT: T 31 ASN cc_start: 0.8232 (t0) cc_final: 0.7914 (t160) outliers start: 6 outliers final: 2 residues processed: 88 average time/residue: 0.3191 time to fit residues: 29.5858 Evaluate side-chains 88 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 86 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 35 ASN Chi-restraints excluded: chain L residue 35 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 0 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 20 optimal weight: 30.0000 chunk 32 optimal weight: 6.9990 chunk 13 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 31 optimal weight: 20.0000 chunk 28 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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** ** C 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 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 31 ASN ** P 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 = 0.3951 r_free = 0.3951 target = 0.130212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.082488 restraints weight = 6045.950| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.60 r_work: 0.3068 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 4070 Z= 0.283 Angle : 0.675 7.648 5490 Z= 0.364 Chirality : 0.045 0.146 640 Planarity : 0.003 0.044 720 Dihedral : 5.068 13.353 550 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 1.14 % Allowed : 15.23 % Favored : 83.64 % 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 aren not related in a simple way. whole: -3.80 (0.24), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.89 (0.18), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.002 ARG I 11 TYR 0.013 0.001 TYR S 37 PHE 0.010 0.002 PHE E 15 HIS 0.005 0.002 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00643 ( 4050) covalent geometry : angle 0.67508 ( 5490) hydrogen bonds : bond 0.04666 ( 108) hydrogen bonds : angle 4.65036 ( 324) Misc. bond : bond 0.00177 ( 20) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 90 time to evaluate : 0.143 Fit side-chains REVERT: A 10 GLN cc_start: 0.8152 (mt0) cc_final: 0.7392 (mp10) REVERT: A 11 ARG cc_start: 0.7750 (mtp180) cc_final: 0.6816 (mmm160) REVERT: E 10 GLN cc_start: 0.7572 (mt0) cc_final: 0.7212 (mp10) REVERT: E 12 LEU cc_start: 0.8766 (mp) cc_final: 0.8292 (tm) REVERT: F 12 LEU cc_start: 0.8744 (mp) cc_final: 0.8160 (tp) REVERT: H 31 ASN cc_start: 0.8152 (t0) cc_final: 0.7906 (t0) REVERT: I 12 LEU cc_start: 0.8748 (mp) cc_final: 0.8152 (tm) REVERT: N 11 ARG cc_start: 0.8228 (mtp180) cc_final: 0.7831 (mtp85) REVERT: O 31 ASN cc_start: 0.8247 (t0) cc_final: 0.8010 (t0) REVERT: T 31 ASN cc_start: 0.8262 (t0) cc_final: 0.7960 (t160) outliers start: 5 outliers final: 4 residues processed: 90 average time/residue: 0.3277 time to fit residues: 31.0967 Evaluate side-chains 94 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 90 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain G residue 35 ASN Chi-restraints excluded: chain L residue 35 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 17 optimal weight: 0.9980 chunk 7 optimal weight: 20.0000 chunk 23 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 36 optimal weight: 20.0000 chunk 14 optimal weight: 20.0000 chunk 27 optimal weight: 3.9990 chunk 38 optimal weight: 0.1980 chunk 37 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 overall best weight: 3.0386 ------------------------------------------------------------------------------- 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** ** C 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 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 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 = 0.3973 r_free = 0.3973 target = 0.131851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.084240 restraints weight = 5964.109| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.58 r_work: 0.3097 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.3912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4070 Z= 0.164 Angle : 0.637 8.273 5490 Z= 0.331 Chirality : 0.044 0.142 640 Planarity : 0.002 0.030 720 Dihedral : 4.830 12.878 550 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 1.14 % Allowed : 16.14 % Favored : 82.73 % 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 aren not related in a simple way. whole: -3.78 (0.24), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.87 (0.18), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 11 TYR 0.012 0.001 TYR S 37 PHE 0.008 0.001 PHE E 15 HIS 0.003 0.001 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 4050) covalent geometry : angle 0.63695 ( 5490) hydrogen bonds : bond 0.03710 ( 108) hydrogen bonds : angle 4.42826 ( 324) Misc. bond : bond 0.00096 ( 20) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 90 time to evaluate : 0.121 Fit side-chains REVERT: A 10 GLN cc_start: 0.8157 (mt0) cc_final: 0.7395 (mp10) REVERT: A 11 ARG cc_start: 0.7664 (mtp180) cc_final: 0.6782 (mmm160) REVERT: E 10 GLN cc_start: 0.7569 (mt0) cc_final: 0.7241 (mp10) REVERT: E 12 LEU cc_start: 0.8755 (mp) cc_final: 0.8259 (tm) REVERT: F 12 LEU cc_start: 0.8770 (mp) cc_final: 0.8214 (tp) REVERT: H 31 ASN cc_start: 0.8155 (t0) cc_final: 0.7854 (t0) REVERT: I 12 LEU cc_start: 0.8703 (mp) cc_final: 0.8109 (tm) REVERT: N 11 ARG cc_start: 0.8211 (mtp180) cc_final: 0.7824 (mtp85) REVERT: O 31 ASN cc_start: 0.8153 (t0) cc_final: 0.7918 (t0) REVERT: T 31 ASN cc_start: 0.8272 (t0) cc_final: 0.7947 (t160) outliers start: 5 outliers final: 5 residues processed: 90 average time/residue: 0.3350 time to fit residues: 31.7344 Evaluate side-chains 95 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 90 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain G residue 35 ASN Chi-restraints excluded: chain L residue 35 ASN Chi-restraints excluded: chain T residue 35 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 14 optimal weight: 30.0000 chunk 2 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 chunk 26 optimal weight: 9.9990 chunk 5 optimal weight: 20.0000 chunk 27 optimal weight: 6.9990 chunk 35 optimal weight: 0.3980 chunk 6 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 overall best weight: 4.6788 ------------------------------------------------------------------------------- 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** ** C 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 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 14 ASN ** H 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 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 = 0.3954 r_free = 0.3954 target = 0.130476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.082479 restraints weight = 6215.764| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.64 r_work: 0.3066 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 4070 Z= 0.239 Angle : 0.669 8.343 5490 Z= 0.355 Chirality : 0.045 0.146 640 Planarity : 0.003 0.040 720 Dihedral : 5.025 13.226 550 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 1.59 % Allowed : 15.45 % Favored : 82.95 % 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 aren not related in a simple way. whole: -3.78 (0.24), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.87 (0.18), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 11 TYR 0.013 0.001 TYR S 37 PHE 0.009 0.002 PHE E 15 HIS 0.004 0.001 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00545 ( 4050) covalent geometry : angle 0.66947 ( 5490) hydrogen bonds : bond 0.04422 ( 108) hydrogen bonds : angle 4.58735 ( 324) Misc. bond : bond 0.00148 ( 20) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1296.09 seconds wall clock time: 22 minutes 51.47 seconds (1371.47 seconds total)