Starting phenix.real_space_refine on Wed Jul 23 18:31:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8az7_15756/07_2025/8az7_15756.cif Found real_map, /net/cci-nas-00/data/ceres_data/8az7_15756/07_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_15756/07_2025/8az7_15756.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8az7_15756/07_2025/8az7_15756.map" model { file = "/net/cci-nas-00/data/ceres_data/8az7_15756/07_2025/8az7_15756.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8az7_15756/07_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-5711/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: 3.30, per 1000 atoms: 0.82 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: 0.91 Conformation dependent library (CDL) restraints added in 436.3 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: 0.80 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: 1.65 Time building geometry restraints manager: 1.10 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: 0.07 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: 2.230 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 16.030 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.110 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:20.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.030 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.16975 ( 108) hydrogen bonds : angle 6.67305 ( 324) covalent geometry : bond 0.00264 ( 4050) covalent geometry : angle 0.50779 ( 5490) 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 : 0.506 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: 0.7181 time to fit residues: 65.8489 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 : 0.406 ------------------------------------------------------------------------------- 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: 1.9990 chunk 10 optimal weight: 8.9990 chunk 20 optimal weight: 20.0000 chunk 31 optimal weight: 5.9990 chunk 12 optimal weight: 8.9990 chunk 19 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 36 optimal weight: 0.6980 chunk 11 optimal weight: 8.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- 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** F 21 ASN 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** I 21 ASN ** 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** N 21 ASN 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: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.133950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.086917 restraints weight = 5173.466| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.82 r_work: 0.3135 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 4070 Z= 0.164 Angle : 0.516 3.701 5490 Z= 0.298 Chirality : 0.043 0.136 640 Planarity : 0.002 0.026 720 Dihedral : 4.582 10.863 550 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.50 % Allowed : 5.91 % Favored : 91.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.52 (0.24), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.67 (0.18), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS Q 18 PHE 0.009 0.002 PHE F 15 TYR 0.006 0.001 TYR S 37 ARG 0.003 0.001 ARG F 11 Details of bonding type rmsd hydrogen bonds : bond 0.04591 ( 108) hydrogen bonds : angle 4.72306 ( 324) covalent geometry : bond 0.00367 ( 4050) covalent geometry : angle 0.51643 ( 5490) Misc. bond : bond 0.00114 ( 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 99 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.480 Fit side-chains REVERT: A 10 GLN cc_start: 0.8044 (mt0) cc_final: 0.7804 (mp10) REVERT: A 12 LEU cc_start: 0.8873 (mt) cc_final: 0.8598 (tp) REVERT: E 10 GLN cc_start: 0.7414 (mt0) cc_final: 0.7145 (mp10) REVERT: E 11 ARG cc_start: 0.8084 (mtp-110) cc_final: 0.7822 (mtp85) REVERT: E 12 LEU cc_start: 0.8785 (mt) cc_final: 0.8349 (tm) REVERT: H 31 ASN cc_start: 0.7893 (t0) cc_final: 0.7580 (t0) REVERT: O 31 ASN cc_start: 0.8094 (t0) cc_final: 0.7827 (t0) REVERT: R 11 ARG cc_start: 0.8541 (mtp180) cc_final: 0.8314 (mtp85) outliers start: 11 outliers final: 4 residues processed: 88 average time/residue: 0.6645 time to fit residues: 61.9466 Evaluate side-chains 90 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 86 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain D residue 35 ASN 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: 8.9990 chunk 34 optimal weight: 10.0000 chunk 38 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 28 optimal weight: 8.9990 chunk 5 optimal weight: 10.0000 chunk 29 optimal weight: 20.0000 chunk 15 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 overall best weight: 2.6984 ------------------------------------------------------------------------------- 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** ** 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** G 31 ASN ** 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** ** N 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** P 31 ASN ** Q 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.134514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.087033 restraints weight = 5066.430| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.49 r_work: 0.3152 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4070 Z= 0.149 Angle : 0.529 6.656 5490 Z= 0.291 Chirality : 0.043 0.137 640 Planarity : 0.002 0.015 720 Dihedral : 4.588 11.595 550 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 2.27 % Allowed : 7.73 % Favored : 90.00 % 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: -3.57 (0.25), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.72 (0.19), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS R 18 PHE 0.008 0.001 PHE E 15 TYR 0.008 0.001 TYR S 37 ARG 0.004 0.001 ARG M 11 Details of bonding type rmsd hydrogen bonds : bond 0.03716 ( 108) hydrogen bonds : angle 4.68245 ( 324) covalent geometry : bond 0.00336 ( 4050) covalent geometry : angle 0.52851 ( 5490) Misc. bond : bond 0.00077 ( 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 97 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.403 Fit side-chains REVERT: A 10 GLN cc_start: 0.8074 (mt0) cc_final: 0.7804 (mp10) REVERT: A 12 LEU cc_start: 0.8876 (mt) cc_final: 0.8648 (tp) REVERT: E 10 GLN cc_start: 0.7510 (mt0) cc_final: 0.7167 (mp10) REVERT: H 31 ASN cc_start: 0.8037 (t0) cc_final: 0.7712 (t0) REVERT: I 12 LEU cc_start: 0.8767 (mp) cc_final: 0.8260 (tm) REVERT: N 12 LEU cc_start: 0.8737 (mp) cc_final: 0.8257 (tm) REVERT: R 11 ARG cc_start: 0.8753 (mtp180) cc_final: 0.8534 (mtp85) outliers start: 10 outliers final: 4 residues processed: 88 average time/residue: 0.6289 time to fit residues: 58.7187 Evaluate side-chains 90 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 86 time to evaluate : 0.456 ------------------------------------------------------------------------------- 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 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: 20.0000 chunk 26 optimal weight: 0.7980 chunk 38 optimal weight: 10.0000 chunk 16 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 33 optimal weight: 8.9990 chunk 31 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 7 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- 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** ** 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** ** L 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.133627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.087854 restraints weight = 5192.168| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.71 r_work: 0.3102 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4070 Z= 0.147 Angle : 0.545 7.380 5490 Z= 0.293 Chirality : 0.043 0.138 640 Planarity : 0.002 0.026 720 Dihedral : 4.567 11.879 550 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 1.59 % Allowed : 9.55 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.58 (0.25), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.72 (0.19), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS N 18 PHE 0.007 0.001 PHE E 15 TYR 0.008 0.001 TYR S 37 ARG 0.007 0.001 ARG M 11 Details of bonding type rmsd hydrogen bonds : bond 0.03579 ( 108) hydrogen bonds : angle 4.62251 ( 324) covalent geometry : bond 0.00331 ( 4050) covalent geometry : angle 0.54503 ( 5490) Misc. bond : bond 0.00080 ( 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 94 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 0.392 Fit side-chains REVERT: A 10 GLN cc_start: 0.8069 (mt0) cc_final: 0.7446 (mp10) REVERT: A 11 ARG cc_start: 0.7804 (mtp180) cc_final: 0.6761 (mmm160) REVERT: E 10 GLN cc_start: 0.7465 (mt0) cc_final: 0.7174 (mp10) REVERT: E 12 LEU cc_start: 0.8758 (mp) cc_final: 0.8264 (tm) REVERT: H 31 ASN cc_start: 0.8095 (t0) cc_final: 0.7751 (t0) REVERT: I 12 LEU cc_start: 0.8706 (mp) cc_final: 0.8129 (tm) REVERT: R 11 ARG cc_start: 0.8526 (mtp180) cc_final: 0.8310 (mtp85) outliers start: 7 outliers final: 3 residues processed: 87 average time/residue: 0.6758 time to fit residues: 62.0914 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 : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain L residue 35 ASN Chi-restraints excluded: chain T residue 35 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 29 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 36 optimal weight: 0.0020 chunk 32 optimal weight: 9.9990 chunk 13 optimal weight: 20.0000 chunk 30 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 6 optimal weight: 20.0000 overall best weight: 7.1996 ------------------------------------------------------------------------------- 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 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** K 35 ASN ** L 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 18 HIS M 21 ASN N 18 HIS ** O 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 31 ASN ** P 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 21 ASN T 31 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.130533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.082722 restraints weight = 5887.209| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.57 r_work: 0.3074 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.039 4070 Z= 0.357 Angle : 0.700 6.959 5490 Z= 0.390 Chirality : 0.048 0.151 640 Planarity : 0.003 0.025 720 Dihedral : 5.356 13.470 550 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 1.59 % Allowed : 11.14 % Favored : 87.27 % 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: -3.67 (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 HIS 0.006 0.003 HIS A 18 PHE 0.012 0.002 PHE E 15 TYR 0.011 0.002 TYR S 37 ARG 0.007 0.001 ARG I 11 Details of bonding type rmsd hydrogen bonds : bond 0.05342 ( 108) hydrogen bonds : angle 4.93232 ( 324) covalent geometry : bond 0.00816 ( 4050) covalent geometry : angle 0.69952 ( 5490) Misc. bond : bond 0.00214 ( 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 102 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 95 time to evaluate : 0.462 Fit side-chains REVERT: A 10 GLN cc_start: 0.8188 (mt0) cc_final: 0.7426 (mp10) REVERT: A 11 ARG cc_start: 0.7863 (mtp180) cc_final: 0.6865 (mmm160) REVERT: E 10 GLN cc_start: 0.7582 (mt0) cc_final: 0.7303 (mp10) REVERT: E 12 LEU cc_start: 0.8745 (mp) cc_final: 0.8234 (tm) REVERT: H 31 ASN cc_start: 0.8127 (t0) cc_final: 0.7879 (t0) REVERT: H 34 SER cc_start: 0.8597 (t) cc_final: 0.8338 (t) REVERT: N 12 LEU cc_start: 0.8700 (mp) cc_final: 0.8221 (tm) REVERT: O 34 SER cc_start: 0.8558 (t) cc_final: 0.8335 (t) REVERT: T 31 ASN cc_start: 0.8304 (t0) cc_final: 0.8032 (t160) outliers start: 7 outliers final: 5 residues processed: 95 average time/residue: 0.6486 time to fit residues: 65.1641 Evaluate side-chains 99 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 94 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 0.6980 chunk 12 optimal weight: 20.0000 chunk 10 optimal weight: 0.9990 chunk 36 optimal weight: 20.0000 chunk 11 optimal weight: 0.8980 chunk 14 optimal weight: 20.0000 chunk 38 optimal weight: 20.0000 chunk 28 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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** K 31 ASN ** 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 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 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 = 0.4029 r_free = 0.4029 target = 0.136217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.089615 restraints weight = 5719.458| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.55 r_work: 0.3183 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4070 Z= 0.086 Angle : 0.553 7.570 5490 Z= 0.279 Chirality : 0.042 0.134 640 Planarity : 0.002 0.025 720 Dihedral : 4.390 12.068 550 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.91 % Allowed : 14.09 % 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: -3.59 (0.25), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.73 (0.19), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 18 PHE 0.006 0.001 PHE L 15 TYR 0.010 0.001 TYR S 37 ARG 0.007 0.001 ARG I 11 Details of bonding type rmsd hydrogen bonds : bond 0.01979 ( 108) hydrogen bonds : angle 4.17193 ( 324) covalent geometry : bond 0.00184 ( 4050) covalent geometry : angle 0.55269 ( 5490) Misc. bond : bond 0.00030 ( 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 93 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 89 time to evaluate : 0.441 Fit side-chains REVERT: A 10 GLN cc_start: 0.8101 (mt0) cc_final: 0.7792 (mp10) REVERT: E 10 GLN cc_start: 0.7480 (mt0) cc_final: 0.7269 (mp10) REVERT: E 12 LEU cc_start: 0.8694 (mp) cc_final: 0.8196 (tm) REVERT: F 12 LEU cc_start: 0.8716 (mp) cc_final: 0.8205 (tp) REVERT: G 34 SER cc_start: 0.8609 (m) cc_final: 0.8403 (t) REVERT: H 31 ASN cc_start: 0.8085 (t0) cc_final: 0.7748 (t0) REVERT: I 12 LEU cc_start: 0.8637 (mp) cc_final: 0.8104 (tm) REVERT: O 31 ASN cc_start: 0.8113 (t0) cc_final: 0.7876 (t0) REVERT: T 31 ASN cc_start: 0.8196 (t0) cc_final: 0.7902 (t160) outliers start: 4 outliers final: 2 residues processed: 89 average time/residue: 0.6176 time to fit residues: 58.4348 Evaluate side-chains 87 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 85 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 35 ASN Chi-restraints excluded: chain L 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: 5.9990 chunk 15 optimal weight: 20.0000 chunk 11 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 12 optimal weight: 20.0000 chunk 1 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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** 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** K 31 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.131774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.084816 restraints weight = 5537.577| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.51 r_work: 0.3111 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 4070 Z= 0.198 Angle : 0.597 6.055 5490 Z= 0.320 Chirality : 0.043 0.142 640 Planarity : 0.003 0.041 720 Dihedral : 4.726 12.846 550 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 1.59 % Allowed : 13.86 % Favored : 84.55 % 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: -3.67 (0.24), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.79 (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 J 15 TYR 0.011 0.001 TYR S 37 ARG 0.009 0.001 ARG I 11 Details of bonding type rmsd hydrogen bonds : bond 0.04001 ( 108) hydrogen bonds : angle 4.58491 ( 324) covalent geometry : bond 0.00451 ( 4050) covalent geometry : angle 0.59656 ( 5490) Misc. bond : bond 0.00115 ( 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 95 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.437 Fit side-chains REVERT: A 10 GLN cc_start: 0.8170 (mt0) cc_final: 0.7498 (mp10) REVERT: A 11 ARG cc_start: 0.7710 (mtp180) cc_final: 0.6792 (mmm160) REVERT: E 10 GLN cc_start: 0.7561 (mt0) cc_final: 0.7234 (mp10) REVERT: E 12 LEU cc_start: 0.8745 (mp) cc_final: 0.8228 (tm) REVERT: F 12 LEU cc_start: 0.8702 (mp) cc_final: 0.8149 (tp) REVERT: H 31 ASN cc_start: 0.8113 (t0) cc_final: 0.7781 (t0) REVERT: I 12 LEU cc_start: 0.8743 (mp) cc_final: 0.8148 (tm) REVERT: O 31 ASN cc_start: 0.8165 (t0) cc_final: 0.7915 (t0) REVERT: T 23 PHE cc_start: 0.7741 (t80) cc_final: 0.7532 (t80) REVERT: T 31 ASN cc_start: 0.8244 (t0) cc_final: 0.7894 (t160) outliers start: 7 outliers final: 5 residues processed: 88 average time/residue: 0.7074 time to fit residues: 65.8601 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 : 0.454 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 39 optimal weight: 7.9990 chunk 34 optimal weight: 7.9990 chunk 38 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 25 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 28 optimal weight: 20.0000 chunk 16 optimal weight: 6.9990 chunk 6 optimal weight: 20.0000 chunk 9 optimal weight: 2.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 = 0.3950 r_free = 0.3950 target = 0.130299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.082306 restraints weight = 6090.807| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.62 r_work: 0.3065 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.032 4070 Z= 0.300 Angle : 0.686 7.695 5490 Z= 0.373 Chirality : 0.046 0.148 640 Planarity : 0.003 0.034 720 Dihedral : 5.200 13.567 550 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 1.59 % Allowed : 13.64 % 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: -3.76 (0.24), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.86 (0.18), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS B 18 PHE 0.011 0.002 PHE E 15 TYR 0.012 0.002 TYR S 37 ARG 0.009 0.001 ARG I 11 Details of bonding type rmsd hydrogen bonds : bond 0.04862 ( 108) hydrogen bonds : angle 4.72935 ( 324) covalent geometry : bond 0.00683 ( 4050) covalent geometry : angle 0.68637 ( 5490) Misc. bond : bond 0.00184 ( 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 95 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.437 Fit side-chains REVERT: A 10 GLN cc_start: 0.8195 (mt0) cc_final: 0.7346 (mp10) REVERT: A 11 ARG cc_start: 0.7785 (mtp180) cc_final: 0.6814 (mmm160) REVERT: E 10 GLN cc_start: 0.7598 (mt0) cc_final: 0.7248 (mp10) REVERT: E 12 LEU cc_start: 0.8736 (mp) cc_final: 0.8228 (tm) REVERT: F 12 LEU cc_start: 0.8740 (mp) cc_final: 0.8170 (tp) REVERT: H 31 ASN cc_start: 0.8119 (t0) cc_final: 0.7892 (t0) REVERT: I 12 LEU cc_start: 0.8729 (mp) cc_final: 0.8126 (tm) REVERT: O 31 ASN cc_start: 0.8223 (t0) cc_final: 0.7974 (t0) REVERT: O 34 SER cc_start: 0.8540 (t) cc_final: 0.8323 (t) REVERT: T 31 ASN cc_start: 0.8246 (t0) cc_final: 0.7863 (t160) outliers start: 7 outliers final: 8 residues processed: 90 average time/residue: 0.6195 time to fit residues: 59.1039 Evaluate side-chains 96 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.435 ------------------------------------------------------------------------------- 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 R 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: 4.9990 chunk 27 optimal weight: 1.9990 chunk 20 optimal weight: 20.0000 chunk 14 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 29 optimal weight: 20.0000 chunk 8 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- 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** ** 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** M 14 ASN ** O 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 14 ASN S 14 ASN ** S 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.134431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.086822 restraints weight = 5961.099| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.60 r_work: 0.3151 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 4070 Z= 0.099 Angle : 0.571 8.210 5490 Z= 0.291 Chirality : 0.043 0.138 640 Planarity : 0.002 0.028 720 Dihedral : 4.424 12.550 550 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.91 % Allowed : 15.23 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.67 (0.24), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.79 (0.18), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS I 18 PHE 0.006 0.001 PHE E 15 TYR 0.011 0.001 TYR S 37 ARG 0.008 0.001 ARG I 11 Details of bonding type rmsd hydrogen bonds : bond 0.02493 ( 108) hydrogen bonds : angle 4.16313 ( 324) covalent geometry : bond 0.00222 ( 4050) covalent geometry : angle 0.57131 ( 5490) Misc. bond : bond 0.00047 ( 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 91 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 87 time to evaluate : 0.387 Fit side-chains REVERT: A 10 GLN cc_start: 0.8127 (mt0) cc_final: 0.7771 (mp10) REVERT: E 10 GLN cc_start: 0.7538 (mt0) cc_final: 0.7222 (mp10) REVERT: E 12 LEU cc_start: 0.8696 (mp) cc_final: 0.8206 (tm) REVERT: F 12 LEU cc_start: 0.8709 (mp) cc_final: 0.8200 (tp) REVERT: G 34 SER cc_start: 0.8609 (m) cc_final: 0.8398 (t) REVERT: H 31 ASN cc_start: 0.8108 (t0) cc_final: 0.7776 (t0) REVERT: I 12 LEU cc_start: 0.8727 (mp) cc_final: 0.8117 (tm) REVERT: O 31 ASN cc_start: 0.8105 (t0) cc_final: 0.7860 (t0) REVERT: T 31 ASN cc_start: 0.8243 (t0) cc_final: 0.7936 (t160) outliers start: 4 outliers final: 3 residues processed: 88 average time/residue: 0.6227 time to fit residues: 58.2089 Evaluate side-chains 88 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 85 time to evaluate : 0.460 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 39 optimal weight: 6.9990 chunk 31 optimal weight: 9.9990 chunk 37 optimal weight: 20.0000 chunk 38 optimal weight: 2.9990 chunk 4 optimal weight: 20.0000 chunk 22 optimal weight: 8.9990 chunk 6 optimal weight: 0.2980 chunk 17 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 chunk 13 optimal weight: 8.9990 overall best weight: 5.2588 ------------------------------------------------------------------------------- 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** ** 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 = 0.3955 r_free = 0.3955 target = 0.130611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.083500 restraints weight = 5594.139| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.51 r_work: 0.3083 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.3953 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= 0.267 Angle : 0.666 7.520 5490 Z= 0.359 Chirality : 0.045 0.148 640 Planarity : 0.003 0.038 720 Dihedral : 4.986 13.090 550 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 1.36 % Allowed : 14.77 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 HIS 0.004 0.002 HIS B 18 PHE 0.019 0.002 PHE T 23 TYR 0.012 0.001 TYR S 37 ARG 0.009 0.001 ARG I 11 Details of bonding type rmsd hydrogen bonds : bond 0.04555 ( 108) hydrogen bonds : angle 4.62682 ( 324) covalent geometry : bond 0.00608 ( 4050) covalent geometry : angle 0.66567 ( 5490) Misc. bond : bond 0.00163 ( 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: 6 poor density : 89 time to evaluate : 0.405 Fit side-chains REVERT: A 10 GLN cc_start: 0.8163 (mt0) cc_final: 0.7403 (mp10) REVERT: A 11 ARG cc_start: 0.7748 (mtp180) cc_final: 0.6760 (mmm160) REVERT: E 10 GLN cc_start: 0.7563 (mt0) cc_final: 0.7226 (mp10) REVERT: F 12 LEU cc_start: 0.8723 (mp) cc_final: 0.8160 (tp) REVERT: H 31 ASN cc_start: 0.8156 (t0) cc_final: 0.7901 (t0) REVERT: I 12 LEU cc_start: 0.8772 (mp) cc_final: 0.8202 (tm) REVERT: O 31 ASN cc_start: 0.8175 (t0) cc_final: 0.7932 (t0) REVERT: O 34 SER cc_start: 0.8530 (t) cc_final: 0.8315 (t) REVERT: T 31 ASN cc_start: 0.8254 (t0) cc_final: 0.7894 (t160) outliers start: 6 outliers final: 4 residues processed: 90 average time/residue: 0.6286 time to fit residues: 59.9675 Evaluate side-chains 93 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 89 time to evaluate : 0.404 ------------------------------------------------------------------------------- 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 22 optimal weight: 20.0000 chunk 8 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 38 optimal weight: 20.0000 chunk 13 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 5 optimal weight: 8.9990 chunk 35 optimal weight: 0.5980 overall best weight: 3.5188 ------------------------------------------------------------------------------- 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 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 = 0.3969 r_free = 0.3969 target = 0.131665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.083879 restraints weight = 5979.268| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.61 r_work: 0.3091 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4070 Z= 0.185 Angle : 0.638 8.260 5490 Z= 0.335 Chirality : 0.044 0.145 640 Planarity : 0.003 0.035 720 Dihedral : 4.842 13.055 550 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 0.91 % Allowed : 15.91 % Favored : 83.18 % 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: -3.80 (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 HIS 0.003 0.001 HIS B 18 PHE 0.019 0.002 PHE T 23 TYR 0.012 0.001 TYR S 37 ARG 0.009 0.001 ARG I 11 Details of bonding type rmsd hydrogen bonds : bond 0.03893 ( 108) hydrogen bonds : angle 4.48278 ( 324) covalent geometry : bond 0.00422 ( 4050) covalent geometry : angle 0.63796 ( 5490) Misc. bond : bond 0.00111 ( 20) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2777.53 seconds wall clock time: 49 minutes 4.27 seconds (2944.27 seconds total)