Starting phenix.real_space_refine on Wed Mar 5 23:11:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8az7_15756/03_2025/8az7_15756.cif Found real_map, /net/cci-nas-00/data/ceres_data/8az7_15756/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8az7_15756/03_2025/8az7_15756.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8az7_15756/03_2025/8az7_15756.map" model { file = "/net/cci-nas-00/data/ceres_data/8az7_15756/03_2025/8az7_15756.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8az7_15756/03_2025/8az7_15756.cif" } resolution = 2.9 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: 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 2.87, per 1000 atoms: 0.72 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: 0.96 Conformation dependent library (CDL) restraints added in 427.4 milliseconds 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: 0.73 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: 0.99 Time building geometry restraints manager: 1.08 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: 0.04 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: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.720 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.500 ------------------------------------------------------------------------------- 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 : 0.003 0.013 4050 Z= 0.176 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 (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: -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 HIS 0.005 0.001 HIS S 18 PHE 0.013 0.002 PHE L 15 TYR 0.003 0.001 TYR Q 37 ARG 0.001 0.000 ARG A 11 *********************** 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 : 0.401 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: 0.6822 time to fit residues: 62.6355 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 : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 8.9990 chunk 30 optimal weight: 0.3980 chunk 16 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 20 optimal weight: 20.0000 chunk 31 optimal weight: 5.9990 chunk 12 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 36 optimal weight: 0.6980 chunk 11 optimal weight: 7.9990 overall best weight: 4.0186 ------------------------------------------------------------------------------- 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** A 21 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.133548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.086918 restraints weight = 5272.781| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.47 r_work: 0.3126 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 4050 Z= 0.320 Angle : 0.564 4.464 5490 Z= 0.325 Chirality : 0.044 0.138 640 Planarity : 0.003 0.020 720 Dihedral : 4.835 11.915 550 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 2.73 % Allowed : 5.23 % Favored : 92.05 % 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: -3.55 (0.24), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.70 (0.19), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS Q 18 PHE 0.011 0.002 PHE E 15 TYR 0.006 0.001 TYR E 37 ARG 0.003 0.001 ARG F 11 *********************** 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 99 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.445 Fit side-chains REVERT: A 10 GLN cc_start: 0.8059 (mt0) cc_final: 0.7816 (mp10) REVERT: A 12 LEU cc_start: 0.8880 (mt) cc_final: 0.8634 (tp) REVERT: E 10 GLN cc_start: 0.7473 (mt0) cc_final: 0.7166 (mp10) REVERT: H 31 ASN cc_start: 0.7998 (t0) cc_final: 0.7724 (t0) REVERT: O 31 ASN cc_start: 0.8197 (t0) cc_final: 0.7915 (t0) REVERT: R 11 ARG cc_start: 0.8746 (mtp180) cc_final: 0.8536 (mtp85) outliers start: 12 outliers final: 3 residues processed: 87 average time/residue: 0.6531 time to fit residues: 60.2945 Evaluate side-chains 89 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 86 time to evaluate : 0.445 ------------------------------------------------------------------------------- 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 32 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 35 optimal weight: 0.0670 chunk 18 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 chunk 15 optimal weight: 20.0000 chunk 33 optimal weight: 4.9990 overall best weight: 5.4126 ------------------------------------------------------------------------------- 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** F 21 ASN ** 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 ** 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 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 21 ASN N 18 HIS ** O 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 31 ASN Q 21 ASN R 18 HIS T 31 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.131445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.084407 restraints weight = 5247.952| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.72 r_work: 0.3056 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.029 4050 Z= 0.420 Angle : 0.634 7.602 5490 Z= 0.353 Chirality : 0.046 0.144 640 Planarity : 0.003 0.018 720 Dihedral : 5.145 12.991 550 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 2.27 % Allowed : 9.09 % 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 (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: -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 HIS 0.006 0.002 HIS N 18 PHE 0.010 0.002 PHE E 15 TYR 0.008 0.001 TYR S 37 ARG 0.004 0.001 ARG F 11 *********************** 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 101 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.456 Fit side-chains REVERT: A 10 GLN cc_start: 0.8156 (mt0) cc_final: 0.7403 (mp10) REVERT: A 11 ARG cc_start: 0.7891 (mtp180) cc_final: 0.6825 (mmm160) REVERT: A 12 LEU cc_start: 0.8869 (mt) cc_final: 0.8655 (tp) REVERT: E 10 GLN cc_start: 0.7460 (mt0) cc_final: 0.7179 (mp10) REVERT: E 12 LEU cc_start: 0.8751 (mp) cc_final: 0.8286 (tm) REVERT: H 31 ASN cc_start: 0.8086 (t0) cc_final: 0.7837 (t0) REVERT: H 34 SER cc_start: 0.8509 (t) cc_final: 0.8277 (t) REVERT: I 11 ARG cc_start: 0.8318 (mtp85) cc_final: 0.8072 (mtp85) REVERT: I 12 LEU cc_start: 0.8792 (mp) cc_final: 0.8201 (tm) REVERT: N 12 LEU cc_start: 0.8687 (mp) cc_final: 0.8205 (tm) REVERT: R 11 ARG cc_start: 0.8556 (mtp180) cc_final: 0.8339 (mtp85) outliers start: 10 outliers final: 4 residues processed: 92 average time/residue: 0.6602 time to fit residues: 64.3302 Evaluate side-chains 95 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 91 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 35 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 29 optimal weight: 8.9990 chunk 26 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 31 optimal weight: 20.0000 chunk 8 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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** ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 35 ASN ** L 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 14 ASN ** M 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 Q 14 ASN Q 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 = 0.3977 r_free = 0.3977 target = 0.132713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.085760 restraints weight = 5274.792| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.46 r_work: 0.3131 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 4050 Z= 0.229 Angle : 0.570 6.987 5490 Z= 0.302 Chirality : 0.043 0.140 640 Planarity : 0.002 0.023 720 Dihedral : 4.745 12.794 550 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 1.14 % Allowed : 10.45 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.64 (0.25), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.77 (0.19), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 18 PHE 0.007 0.001 PHE K 15 TYR 0.009 0.001 TYR S 37 ARG 0.004 0.001 ARG M 11 *********************** 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: 5 poor density : 88 time to evaluate : 0.451 Fit side-chains REVERT: A 10 GLN cc_start: 0.8112 (mt0) cc_final: 0.7479 (mp10) REVERT: A 11 ARG cc_start: 0.7746 (mtp180) cc_final: 0.6731 (mmm160) REVERT: B 12 LEU cc_start: 0.8688 (mp) cc_final: 0.8349 (tp) REVERT: E 10 GLN cc_start: 0.7490 (mt0) cc_final: 0.7290 (mp10) REVERT: E 12 LEU cc_start: 0.8713 (mp) cc_final: 0.8256 (tm) REVERT: H 31 ASN cc_start: 0.8150 (t0) cc_final: 0.7853 (t0) REVERT: I 12 LEU cc_start: 0.8714 (mp) cc_final: 0.8160 (tm) REVERT: O 31 ASN cc_start: 0.8229 (t0) cc_final: 0.8009 (t0) outliers start: 5 outliers final: 5 residues processed: 88 average time/residue: 0.6920 time to fit residues: 64.2596 Evaluate side-chains 93 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 88 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 ASN 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 T residue 35 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 29 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 36 optimal weight: 0.2980 chunk 32 optimal weight: 7.9990 chunk 13 optimal weight: 20.0000 chunk 30 optimal weight: 5.9990 chunk 31 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 overall best weight: 6.2588 ------------------------------------------------------------------------------- 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 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** J 18 HIS ** K 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 14 ASN M 18 HIS ** O 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 14 ASN S 14 ASN T 31 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.130500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.082565 restraints weight = 6069.392| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.59 r_work: 0.3071 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.3845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.034 4050 Z= 0.479 Angle : 0.672 6.670 5490 Z= 0.369 Chirality : 0.047 0.149 640 Planarity : 0.003 0.026 720 Dihedral : 5.255 13.224 550 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 2.05 % Allowed : 12.50 % Favored : 85.45 % 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: -3.71 (0.24), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.82 (0.19), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS B 18 PHE 0.011 0.002 PHE E 15 TYR 0.011 0.001 TYR S 37 ARG 0.007 0.001 ARG M 11 *********************** 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 101 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.408 Fit side-chains REVERT: A 10 GLN cc_start: 0.8256 (mt0) cc_final: 0.7436 (mp10) REVERT: A 11 ARG cc_start: 0.7851 (mtp180) cc_final: 0.6794 (mmm160) REVERT: B 12 LEU cc_start: 0.8768 (mp) cc_final: 0.8356 (tp) REVERT: E 10 GLN cc_start: 0.7570 (mt0) cc_final: 0.7290 (mp10) REVERT: H 31 ASN cc_start: 0.8158 (t0) cc_final: 0.7930 (t0) REVERT: H 34 SER cc_start: 0.8586 (t) cc_final: 0.8323 (t) REVERT: I 12 LEU cc_start: 0.8768 (mp) cc_final: 0.8202 (tm) REVERT: T 31 ASN cc_start: 0.8277 (t0) cc_final: 0.7998 (t160) outliers start: 9 outliers final: 5 residues processed: 92 average time/residue: 0.6633 time to fit residues: 64.6599 Evaluate side-chains 98 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 93 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU 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 T residue 35 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 0.5980 chunk 12 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 36 optimal weight: 20.0000 chunk 11 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 38 optimal weight: 20.0000 chunk 28 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- 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** ** 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 = 0.3982 r_free = 0.3982 target = 0.133210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.084964 restraints weight = 6500.369| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.71 r_work: 0.3110 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4050 Z= 0.189 Angle : 0.604 8.446 5490 Z= 0.306 Chirality : 0.043 0.139 640 Planarity : 0.002 0.029 720 Dihedral : 4.683 12.748 550 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.14 % Allowed : 13.86 % 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 (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: -3.72 (0.24), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.82 (0.19), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 18 PHE 0.008 0.001 PHE F 15 TYR 0.010 0.001 TYR S 37 ARG 0.008 0.001 ARG M 11 *********************** 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 93 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 88 time to evaluate : 0.450 Fit side-chains REVERT: A 10 GLN cc_start: 0.8172 (mt0) cc_final: 0.7483 (mp10) REVERT: A 11 ARG cc_start: 0.7726 (mtp180) cc_final: 0.6741 (mmm160) REVERT: B 12 LEU cc_start: 0.8726 (mp) cc_final: 0.8336 (tp) REVERT: E 10 GLN cc_start: 0.7561 (mt0) cc_final: 0.7230 (mp10) REVERT: E 12 LEU cc_start: 0.8725 (mp) cc_final: 0.8247 (tm) REVERT: F 12 LEU cc_start: 0.8749 (mp) cc_final: 0.8317 (tm) REVERT: H 31 ASN cc_start: 0.8112 (t0) cc_final: 0.7789 (t0) REVERT: I 12 LEU cc_start: 0.8775 (mp) cc_final: 0.8148 (tm) REVERT: J 12 LEU cc_start: 0.8546 (tp) cc_final: 0.8327 (mp) REVERT: O 31 ASN cc_start: 0.8184 (t0) cc_final: 0.7957 (t0) REVERT: T 31 ASN cc_start: 0.8251 (t0) cc_final: 0.7972 (t160) outliers start: 5 outliers final: 2 residues processed: 88 average time/residue: 0.6698 time to fit residues: 62.4572 Evaluate side-chains 89 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 87 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 0 optimal weight: 10.0000 chunk 31 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 chunk 11 optimal weight: 8.9990 chunk 3 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 14 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 12 optimal weight: 30.0000 chunk 1 optimal weight: 0.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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** ** 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 = 0.3953 r_free = 0.3953 target = 0.130881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.083573 restraints weight = 5536.967| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.51 r_work: 0.3086 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.029 4050 Z= 0.373 Angle : 0.660 8.174 5490 Z= 0.348 Chirality : 0.045 0.146 640 Planarity : 0.002 0.027 720 Dihedral : 4.995 13.198 550 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 1.14 % Allowed : 14.55 % Favored : 84.32 % 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: -3.79 (0.24), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.88 (0.18), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 18 PHE 0.009 0.002 PHE E 15 TYR 0.011 0.001 TYR S 37 ARG 0.008 0.001 ARG I 11 *********************** 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 95 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 90 time to evaluate : 0.443 Fit side-chains REVERT: A 10 GLN cc_start: 0.8189 (mt0) cc_final: 0.7367 (mp10) REVERT: A 11 ARG cc_start: 0.7779 (mtp180) cc_final: 0.6809 (mmm160) REVERT: B 12 LEU cc_start: 0.8774 (mp) cc_final: 0.8365 (tp) REVERT: E 10 GLN cc_start: 0.7576 (mt0) cc_final: 0.7284 (mp10) REVERT: E 12 LEU cc_start: 0.8757 (mp) cc_final: 0.8287 (tm) REVERT: F 12 LEU cc_start: 0.8717 (mp) cc_final: 0.8283 (tm) REVERT: H 31 ASN cc_start: 0.8164 (t0) cc_final: 0.7900 (t0) REVERT: J 12 LEU cc_start: 0.8573 (tp) cc_final: 0.8362 (mp) REVERT: O 31 ASN cc_start: 0.8286 (t0) cc_final: 0.8059 (t0) REVERT: T 31 ASN cc_start: 0.8231 (t0) cc_final: 0.7852 (t160) outliers start: 5 outliers final: 6 residues processed: 90 average time/residue: 0.6667 time to fit residues: 63.6129 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 : 0.472 ------------------------------------------------------------------------------- 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 21 ASN Chi-restraints excluded: chain L residue 35 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 39 optimal weight: 8.9990 chunk 34 optimal weight: 0.8980 chunk 38 optimal weight: 8.9990 chunk 5 optimal weight: 8.9990 chunk 13 optimal weight: 8.9990 chunk 25 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 28 optimal weight: 0.0170 chunk 16 optimal weight: 2.9990 chunk 6 optimal weight: 30.0000 chunk 9 optimal weight: 1.9990 overall best weight: 1.5824 ------------------------------------------------------------------------------- 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** ** 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 = 0.3999 r_free = 0.3999 target = 0.134297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.086654 restraints weight = 5825.275| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.59 r_work: 0.3143 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 4050 Z= 0.161 Angle : 0.601 7.891 5490 Z= 0.301 Chirality : 0.043 0.138 640 Planarity : 0.002 0.033 720 Dihedral : 4.503 12.398 550 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.36 % Allowed : 14.32 % Favored : 84.32 % 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: -3.73 (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 HIS 0.002 0.001 HIS B 18 PHE 0.006 0.001 PHE M 15 TYR 0.011 0.001 TYR S 37 ARG 0.008 0.001 ARG I 11 *********************** 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 95 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.446 Fit side-chains REVERT: A 10 GLN cc_start: 0.8134 (mt0) cc_final: 0.7456 (mp10) REVERT: A 11 ARG cc_start: 0.7628 (mtp180) cc_final: 0.6721 (mmm160) REVERT: B 12 LEU cc_start: 0.8711 (mp) cc_final: 0.8339 (tp) REVERT: E 10 GLN cc_start: 0.7537 (mt0) cc_final: 0.7240 (mp10) REVERT: E 12 LEU cc_start: 0.8711 (mp) cc_final: 0.8238 (tm) REVERT: F 12 LEU cc_start: 0.8735 (mp) cc_final: 0.8288 (tm) REVERT: G 34 SER cc_start: 0.8628 (m) cc_final: 0.8402 (t) REVERT: H 31 ASN cc_start: 0.8127 (t0) cc_final: 0.7793 (t0) REVERT: I 12 LEU cc_start: 0.8697 (mp) cc_final: 0.8108 (tm) REVERT: J 12 LEU cc_start: 0.8545 (tp) cc_final: 0.8333 (mp) REVERT: O 31 ASN cc_start: 0.8151 (t0) cc_final: 0.7921 (t0) REVERT: T 31 ASN cc_start: 0.8274 (t0) cc_final: 0.7960 (t160) outliers start: 6 outliers final: 5 residues processed: 90 average time/residue: 0.6596 time to fit residues: 62.8863 Evaluate side-chains 93 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 88 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 N residue 9 THR Chi-restraints excluded: chain T residue 35 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 35 optimal weight: 8.9990 chunk 27 optimal weight: 4.9990 chunk 20 optimal weight: 30.0000 chunk 14 optimal weight: 8.9990 chunk 12 optimal weight: 6.9990 chunk 32 optimal weight: 0.0870 chunk 33 optimal weight: 2.9990 chunk 19 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 overall best weight: 3.8166 ------------------------------------------------------------------------------- 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** ** 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 = 0.3965 r_free = 0.3965 target = 0.131530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.083697 restraints weight = 5992.539| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.61 r_work: 0.3089 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 4050 Z= 0.304 Angle : 0.642 7.748 5490 Z= 0.335 Chirality : 0.044 0.143 640 Planarity : 0.002 0.034 720 Dihedral : 4.778 12.746 550 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 1.36 % Allowed : 13.86 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -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 HIS 0.004 0.001 HIS B 18 PHE 0.008 0.001 PHE E 15 TYR 0.011 0.001 TYR S 37 ARG 0.009 0.001 ARG I 11 *********************** 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 96 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 90 time to evaluate : 0.394 Fit side-chains REVERT: A 10 GLN cc_start: 0.8152 (mt0) cc_final: 0.7394 (mp10) REVERT: A 11 ARG cc_start: 0.7719 (mtp180) cc_final: 0.6798 (mmm160) REVERT: B 12 LEU cc_start: 0.8769 (mp) cc_final: 0.8377 (tp) REVERT: E 10 GLN cc_start: 0.7576 (mt0) cc_final: 0.7253 (mp10) REVERT: E 12 LEU cc_start: 0.8750 (mp) cc_final: 0.8259 (tm) REVERT: F 12 LEU cc_start: 0.8729 (mp) cc_final: 0.8311 (tm) REVERT: H 31 ASN cc_start: 0.8186 (t0) cc_final: 0.7884 (t0) REVERT: I 12 LEU cc_start: 0.8706 (mp) cc_final: 0.8119 (tm) REVERT: J 12 LEU cc_start: 0.8569 (tp) cc_final: 0.8367 (mp) REVERT: T 31 ASN cc_start: 0.8268 (t0) cc_final: 0.7853 (t160) outliers start: 6 outliers final: 6 residues processed: 91 average time/residue: 0.6758 time to fit residues: 65.1151 Evaluate side-chains 96 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 90 time to evaluate : 0.441 ------------------------------------------------------------------------------- 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 N residue 9 THR 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 39 optimal weight: 0.6980 chunk 31 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 38 optimal weight: 8.9990 chunk 4 optimal weight: 30.0000 chunk 22 optimal weight: 20.0000 chunk 6 optimal weight: 30.0000 chunk 17 optimal weight: 4.9990 chunk 15 optimal weight: 20.0000 chunk 7 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 overall best weight: 5.3388 ------------------------------------------------------------------------------- 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** ** 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 = 0.3949 r_free = 0.3949 target = 0.130375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.083168 restraints weight = 5600.521| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.51 r_work: 0.3075 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.4063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 4050 Z= 0.414 Angle : 0.700 8.307 5490 Z= 0.372 Chirality : 0.046 0.148 640 Planarity : 0.003 0.039 720 Dihedral : 5.111 13.227 550 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 1.36 % Allowed : 14.32 % Favored : 84.32 % 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: -3.79 (0.24), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.88 (0.18), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 18 PHE 0.010 0.002 PHE E 15 TYR 0.011 0.001 TYR S 37 ARG 0.009 0.001 ARG I 11 ********************** 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 98 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 0.439 Fit side-chains REVERT: A 10 GLN cc_start: 0.8181 (mt0) cc_final: 0.7348 (mp10) REVERT: A 11 ARG cc_start: 0.7746 (mtp180) cc_final: 0.6821 (mmm160) REVERT: B 12 LEU cc_start: 0.8760 (mp) cc_final: 0.8354 (tp) REVERT: E 10 GLN cc_start: 0.7572 (mt0) cc_final: 0.7228 (mp10) REVERT: E 12 LEU cc_start: 0.8762 (mp) cc_final: 0.8290 (tm) REVERT: F 12 LEU cc_start: 0.8711 (mp) cc_final: 0.8277 (tm) REVERT: H 31 ASN cc_start: 0.8162 (t0) cc_final: 0.7911 (t0) REVERT: I 12 LEU cc_start: 0.8730 (mp) cc_final: 0.8154 (tm) REVERT: J 12 LEU cc_start: 0.8583 (tp) cc_final: 0.8377 (mp) REVERT: M 11 ARG cc_start: 0.8223 (mtp180) cc_final: 0.7982 (mtp85) REVERT: T 31 ASN cc_start: 0.8278 (t0) cc_final: 0.7977 (t160) outliers start: 6 outliers final: 7 residues processed: 93 average time/residue: 0.8149 time to fit residues: 80.2854 Evaluate side-chains 99 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 0.428 ------------------------------------------------------------------------------- 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 21 ASN Chi-restraints excluded: chain L residue 35 ASN Chi-restraints excluded: chain N residue 9 THR 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 22 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 38 optimal weight: 20.0000 chunk 13 optimal weight: 20.0000 chunk 29 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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** ** G 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 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** O 31 ASN ** P 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 = 0.3962 r_free = 0.3962 target = 0.131453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.083721 restraints weight = 5996.576| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.62 r_work: 0.3086 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.4039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4050 Z= 0.276 Angle : 0.650 8.311 5490 Z= 0.336 Chirality : 0.044 0.143 640 Planarity : 0.002 0.033 720 Dihedral : 4.818 12.837 550 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 1.59 % Allowed : 15.00 % 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 (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: -3.78 (0.24), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.88 (0.18), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 18 PHE 0.008 0.001 PHE E 15 TYR 0.012 0.001 TYR S 37 ARG 0.009 0.001 ARG I 11 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2690.20 seconds wall clock time: 46 minutes 52.48 seconds (2812.48 seconds total)