Starting phenix.real_space_refine on Tue Mar 3 11:10:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6y1a_10669/03_2026/6y1a_10669.cif Found real_map, /net/cci-nas-00/data/ceres_data/6y1a_10669/03_2026/6y1a_10669.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6y1a_10669/03_2026/6y1a_10669.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6y1a_10669/03_2026/6y1a_10669.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6y1a_10669/03_2026/6y1a_10669.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6y1a_10669/03_2026/6y1a_10669.map" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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 1824 2.51 5 N 528 2.21 5 O 608 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2960 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 184 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "B" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 184 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "C" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 184 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "D" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 184 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "E" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 184 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "F" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 184 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "G" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 184 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "H" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 184 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "I" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 184 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "J" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 184 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "K" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 184 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "L" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 184 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "M" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 184 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "N" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 184 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "O" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 184 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "P" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 184 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.83, per 1000 atoms: 0.28 Number of scatterers: 2960 At special positions: 0 Unit cell: (61.71, 66.385, 55.165, 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 608 8.00 N 528 7.00 C 1824 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=16, symmetry=0 Number of additional bonds: simple=16, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.26 Conformation dependent library (CDL) restraints added in 99.5 milliseconds 736 Ramachandran restraints generated. 368 Oldfield, 0 Emsley, 368 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 736 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 7 sheets defined 0.0% alpha, 40.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 18 removed outlier: 5.958A pdb=" N PHE A 15 " --> pdb=" O LEU C 16 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N HIS C 18 " --> pdb=" O PHE A 15 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL A 17 " --> pdb=" O HIS C 18 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N PHE C 15 " --> pdb=" O LEU E 16 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N HIS E 18 " --> pdb=" O PHE C 15 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL C 17 " --> pdb=" O HIS E 18 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N PHE E 15 " --> pdb=" O LEU G 16 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N HIS G 18 " --> pdb=" O PHE E 15 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL E 17 " --> pdb=" O HIS G 18 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N PHE G 15 " --> pdb=" O LEU I 16 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N HIS I 18 " --> pdb=" O PHE G 15 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL G 17 " --> pdb=" O HIS I 18 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N PHE I 15 " --> pdb=" O LEU K 16 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N HIS K 18 " --> pdb=" O PHE I 15 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL I 17 " --> pdb=" O HIS K 18 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N PHE K 15 " --> pdb=" O LEU M 16 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N HIS M 18 " --> pdb=" O PHE K 15 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N VAL K 17 " --> pdb=" O HIS M 18 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N PHE M 15 " --> pdb=" O LEU O 16 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N HIS O 18 " --> pdb=" O PHE M 15 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL M 17 " --> pdb=" O HIS O 18 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 31 removed outlier: 6.542A pdb=" N ILE A 26 " --> pdb=" O LEU C 27 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N SER C 29 " --> pdb=" O ILE A 26 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N SER A 28 " --> pdb=" O SER C 29 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N ASN C 31 " --> pdb=" O SER A 28 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N THR A 30 " --> pdb=" O ASN C 31 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ILE C 26 " --> pdb=" O LEU E 27 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N SER E 29 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N SER C 28 " --> pdb=" O SER E 29 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N ASN E 31 " --> pdb=" O SER C 28 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N THR C 30 " --> pdb=" O ASN E 31 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE E 26 " --> pdb=" O LEU G 27 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N SER G 29 " --> pdb=" O ILE E 26 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N SER E 28 " --> pdb=" O SER G 29 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N ASN G 31 " --> pdb=" O SER E 28 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N THR E 30 " --> pdb=" O ASN G 31 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE G 26 " --> pdb=" O LEU I 27 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N SER I 29 " --> pdb=" O ILE G 26 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N SER G 28 " --> pdb=" O SER I 29 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N ASN I 31 " --> pdb=" O SER G 28 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N THR G 30 " --> pdb=" O ASN I 31 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ILE I 26 " --> pdb=" O LEU K 27 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N SER K 29 " --> pdb=" O ILE I 26 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N SER I 28 " --> pdb=" O SER K 29 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N ASN K 31 " --> pdb=" O SER I 28 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N THR I 30 " --> pdb=" O ASN K 31 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILE K 26 " --> pdb=" O LEU M 27 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N SER M 29 " --> pdb=" O ILE K 26 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N SER K 28 " --> pdb=" O SER M 29 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N ASN M 31 " --> pdb=" O SER K 28 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N THR K 30 " --> pdb=" O ASN M 31 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE M 26 " --> pdb=" O LEU O 27 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N SER O 29 " --> pdb=" O ILE M 26 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N SER M 28 " --> pdb=" O SER O 29 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N ASN O 31 " --> pdb=" O SER M 28 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N THR M 30 " --> pdb=" O ASN O 31 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 35 through 36 Processing sheet with id=AA4, first strand: chain 'B' and resid 14 through 18 removed outlier: 5.970A pdb=" N PHE B 15 " --> pdb=" O LEU D 16 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N HIS D 18 " --> pdb=" O PHE B 15 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL B 17 " --> pdb=" O HIS D 18 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N PHE D 15 " --> pdb=" O LEU F 16 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N HIS F 18 " --> pdb=" O PHE D 15 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL D 17 " --> pdb=" O HIS F 18 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N PHE F 15 " --> pdb=" O LEU H 16 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N HIS H 18 " --> pdb=" O PHE F 15 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL F 17 " --> pdb=" O HIS H 18 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N PHE H 15 " --> pdb=" O LEU J 16 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N HIS J 18 " --> pdb=" O PHE H 15 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL H 17 " --> pdb=" O HIS J 18 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N PHE J 15 " --> pdb=" O LEU L 16 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N HIS L 18 " --> pdb=" O PHE J 15 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL J 17 " --> pdb=" O HIS L 18 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N PHE L 15 " --> pdb=" O LEU N 16 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N HIS N 18 " --> pdb=" O PHE L 15 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL L 17 " --> pdb=" O HIS N 18 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N PHE N 15 " --> pdb=" O LEU P 16 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N HIS P 18 " --> pdb=" O PHE N 15 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL N 17 " --> pdb=" O HIS P 18 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 26 through 27 removed outlier: 6.376A pdb=" N ILE B 26 " --> pdb=" O LEU D 27 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N SER D 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 26 through 27 removed outlier: 6.376A pdb=" N ILE B 26 " --> pdb=" O LEU D 27 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N SER D 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ILE D 26 " --> pdb=" O LEU F 27 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N SER F 29 " --> pdb=" O ILE D 26 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N SER D 28 " --> pdb=" O SER F 29 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N ASN F 31 " --> pdb=" O SER D 28 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N THR D 30 " --> pdb=" O ASN F 31 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ILE F 26 " --> pdb=" O LEU H 27 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N SER H 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N SER F 28 " --> pdb=" O SER H 29 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N ASN H 31 " --> pdb=" O SER F 28 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N THR F 30 " --> pdb=" O ASN H 31 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ILE H 26 " --> pdb=" O LEU J 27 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N SER J 29 " --> pdb=" O ILE H 26 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N SER H 28 " --> pdb=" O SER J 29 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N ASN J 31 " --> pdb=" O SER H 28 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N THR H 30 " --> pdb=" O ASN J 31 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE J 26 " --> pdb=" O LEU L 27 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N SER L 29 " --> pdb=" O ILE J 26 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N SER J 28 " --> pdb=" O SER L 29 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N ASN L 31 " --> pdb=" O SER J 28 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N THR J 30 " --> pdb=" O ASN L 31 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ILE L 26 " --> pdb=" O LEU N 27 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N SER N 29 " --> pdb=" O ILE L 26 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N SER L 28 " --> pdb=" O SER N 29 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N ASN N 31 " --> pdb=" O SER L 28 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N THR L 30 " --> pdb=" O ASN N 31 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE N 26 " --> pdb=" O LEU P 27 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N SER P 29 " --> pdb=" O ILE N 26 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N SER N 28 " --> pdb=" O SER P 29 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N ASN P 31 " --> pdb=" O SER N 28 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N THR N 30 " --> pdb=" O ASN P 31 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 35 through 36 16 hydrogen bonds defined for protein. 45 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: 0.28 Time building geometry restraints manager: 0.29 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: 480 1.29 - 1.36: 512 1.36 - 1.42: 416 1.42 - 1.48: 416 1.48 - 1.55: 1168 Bond restraints: 2992 Sorted by residual: bond pdb=" N ALA M 13 " pdb=" CA ALA M 13 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.02e+00 bond pdb=" N ALA B 13 " pdb=" CA ALA B 13 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.01e+00 bond pdb=" N ALA E 13 " pdb=" CA ALA E 13 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.00e+00 bond pdb=" N ALA N 13 " pdb=" CA ALA N 13 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.94e+00 bond pdb=" N ALA J 13 " pdb=" CA ALA J 13 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.94e+00 ... (remaining 2987 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.95: 3093 0.95 - 1.90: 622 1.90 - 2.85: 168 2.85 - 3.80: 116 3.80 - 4.75: 65 Bond angle restraints: 4064 Sorted by residual: angle pdb=" N THR D 36 " pdb=" CA THR D 36 " pdb=" C THR D 36 " ideal model delta sigma weight residual 109.24 113.99 -4.75 1.67e+00 3.59e-01 8.10e+00 angle pdb=" N THR C 36 " pdb=" CA THR C 36 " pdb=" C THR C 36 " ideal model delta sigma weight residual 109.24 113.97 -4.73 1.67e+00 3.59e-01 8.02e+00 angle pdb=" N THR E 36 " pdb=" CA THR E 36 " pdb=" C THR E 36 " ideal model delta sigma weight residual 109.24 113.96 -4.72 1.67e+00 3.59e-01 8.00e+00 angle pdb=" N THR L 36 " pdb=" CA THR L 36 " pdb=" C THR L 36 " ideal model delta sigma weight residual 109.24 113.95 -4.71 1.67e+00 3.59e-01 7.95e+00 angle pdb=" N THR I 36 " pdb=" CA THR I 36 " pdb=" C THR I 36 " ideal model delta sigma weight residual 109.24 113.92 -4.68 1.67e+00 3.59e-01 7.87e+00 ... (remaining 4059 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 6.00: 1472 6.00 - 12.00: 50 12.00 - 18.00: 46 18.00 - 23.99: 26 23.99 - 29.99: 70 Dihedral angle restraints: 1664 sinusoidal: 528 harmonic: 1136 Sorted by residual: dihedral pdb=" CA ASN L 31 " pdb=" CB ASN L 31 " pdb=" CG ASN L 31 " pdb=" OD1 ASN L 31 " ideal model delta sinusoidal sigma weight residual -30.00 -59.99 29.99 2 2.00e+01 2.50e-03 3.00e+00 dihedral pdb=" CA ASN O 31 " pdb=" CB ASN O 31 " pdb=" CG ASN O 31 " pdb=" OD1 ASN O 31 " ideal model delta sinusoidal sigma weight residual -90.00 -60.02 -29.98 2 2.00e+01 2.50e-03 3.00e+00 dihedral pdb=" CA ASN I 31 " pdb=" CB ASN I 31 " pdb=" CG ASN I 31 " pdb=" OD1 ASN I 31 " ideal model delta sinusoidal sigma weight residual -30.00 -59.98 29.98 2 2.00e+01 2.50e-03 3.00e+00 ... (remaining 1661 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 171 0.035 - 0.069: 167 0.069 - 0.103: 87 0.103 - 0.138: 39 0.138 - 0.172: 16 Chirality restraints: 480 Sorted by residual: chirality pdb=" CA VAL G 32 " pdb=" N VAL G 32 " pdb=" C VAL G 32 " pdb=" CB VAL G 32 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.43e-01 chirality pdb=" CA VAL A 32 " pdb=" N VAL A 32 " pdb=" C VAL A 32 " pdb=" CB VAL A 32 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.36e-01 chirality pdb=" CA VAL E 32 " pdb=" N VAL E 32 " pdb=" C VAL E 32 " pdb=" CB VAL E 32 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.31e-01 ... (remaining 477 not shown) Planarity restraints: 528 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR K 36 " 0.002 2.00e-02 2.50e+03 4.08e-03 1.67e-01 pdb=" C THR K 36 " -0.007 2.00e-02 2.50e+03 pdb=" O THR K 36 " 0.003 2.00e-02 2.50e+03 pdb=" N TYR K 37 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR P 36 " -0.002 2.00e-02 2.50e+03 4.08e-03 1.66e-01 pdb=" C THR P 36 " 0.007 2.00e-02 2.50e+03 pdb=" O THR P 36 " -0.003 2.00e-02 2.50e+03 pdb=" N TYR P 37 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR H 36 " -0.002 2.00e-02 2.50e+03 3.92e-03 1.53e-01 pdb=" C THR H 36 " 0.007 2.00e-02 2.50e+03 pdb=" O THR H 36 " -0.003 2.00e-02 2.50e+03 pdb=" N TYR H 37 " -0.002 2.00e-02 2.50e+03 ... (remaining 525 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 1676 2.99 - 3.47: 2760 3.47 - 3.94: 5099 3.94 - 4.42: 5452 4.42 - 4.90: 10567 Nonbonded interactions: 25554 Sorted by model distance: nonbonded pdb=" OG SER G 19 " pdb=" OD1 ASN G 22 " model vdw 2.509 3.040 nonbonded pdb=" OG SER D 19 " pdb=" OD1 ASN D 22 " model vdw 2.510 3.040 nonbonded pdb=" OG SER H 19 " pdb=" OD1 ASN H 22 " model vdw 2.510 3.040 nonbonded pdb=" OG SER K 19 " pdb=" OD1 ASN K 22 " model vdw 2.510 3.040 nonbonded pdb=" OG SER J 19 " pdb=" OD1 ASN J 22 " model vdw 2.510 3.040 ... (remaining 25549 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.270 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.390 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6387 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 : 0.009 0.101 3008 Z= 0.775 Angle : 1.094 4.752 4064 Z= 0.710 Chirality : 0.067 0.172 480 Planarity : 0.001 0.004 528 Dihedral : 9.418 29.993 928 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.99 (0.21), residues: 368 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.80 (0.16), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR P 37 PHE 0.004 0.001 PHE O 23 HIS 0.001 0.001 HIS N 18 Details of bonding type rmsd covalent geometry : bond 0.00483 ( 2992) covalent geometry : angle 1.09407 ( 4064) hydrogen bonds : bond 0.34558 ( 16) hydrogen bonds : angle 11.42292 ( 45) Misc. bond : bond 0.09912 ( 16) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 736 Ramachandran restraints generated. 368 Oldfield, 0 Emsley, 368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 736 Ramachandran restraints generated. 368 Oldfield, 0 Emsley, 368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.098 Fit side-chains REVERT: A 37 TYR cc_start: 0.5197 (m-80) cc_final: 0.4194 (p90) REVERT: B 23 PHE cc_start: 0.5807 (m-80) cc_final: 0.4599 (p90) REVERT: B 37 TYR cc_start: 0.5717 (m-80) cc_final: 0.4405 (p90) REVERT: C 34 SER cc_start: 0.7377 (m) cc_final: 0.7124 (p) REVERT: N 27 LEU cc_start: 0.8572 (tp) cc_final: 0.8105 (mt) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.0248 time to fit residues: 4.2539 Evaluate side-chains 48 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 24 optimal weight: 8.9990 chunk 26 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 31 optimal weight: 20.0000 chunk 25 optimal weight: 9.9990 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 8.9990 chunk 13 optimal weight: 9.9990 chunk 8 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN B 31 ASN C 31 ASN ** D 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 ASN ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 ASN F 31 ASN G 31 ASN ** H 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 ASN ** I 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 31 ASN K 31 ASN ** L 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 ASN ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 31 ASN N 31 ASN P 31 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.088621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.076082 restraints weight = 9002.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.078352 restraints weight = 4663.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.079747 restraints weight = 3006.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.080839 restraints weight = 2264.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.081630 restraints weight = 1825.616| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.4580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3008 Z= 0.195 Angle : 0.565 4.691 4064 Z= 0.313 Chirality : 0.040 0.125 480 Planarity : 0.002 0.011 528 Dihedral : 4.703 16.019 400 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.30 % Allowed : 3.57 % Favored : 96.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.96 (0.26), residues: 368 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.77 (0.20), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR A 37 PHE 0.024 0.003 PHE L 23 HIS 0.004 0.001 HIS J 18 Details of bonding type rmsd covalent geometry : bond 0.00449 ( 2992) covalent geometry : angle 0.56548 ( 4064) hydrogen bonds : bond 0.04766 ( 16) hydrogen bonds : angle 5.66390 ( 45) Misc. bond : bond 0.00116 ( 16) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 736 Ramachandran restraints generated. 368 Oldfield, 0 Emsley, 368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 736 Ramachandran restraints generated. 368 Oldfield, 0 Emsley, 368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 57 time to evaluate : 0.114 Fit side-chains REVERT: C 21 ASN cc_start: 0.7354 (m-40) cc_final: 0.6978 (m-40) REVERT: G 36 THR cc_start: 0.9146 (m) cc_final: 0.8848 (t) REVERT: I 36 THR cc_start: 0.9181 (m) cc_final: 0.8884 (t) REVERT: J 36 THR cc_start: 0.9188 (m) cc_final: 0.8965 (p) REVERT: K 36 THR cc_start: 0.9202 (m) cc_final: 0.8852 (t) outliers start: 1 outliers final: 0 residues processed: 58 average time/residue: 0.0243 time to fit residues: 2.1794 Evaluate side-chains 25 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 23 optimal weight: 4.9990 chunk 22 optimal weight: 8.9990 chunk 5 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 7 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 24 optimal weight: 20.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN B 14 ASN B 31 ASN C 31 ASN ** D 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 ASN E 31 ASN G 31 ASN ** H 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 31 ASN K 31 ASN M 31 ASN P 35 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.082260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.069811 restraints weight = 11455.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.071996 restraints weight = 5346.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.073406 restraints weight = 3294.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.074443 restraints weight = 2458.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.075087 restraints weight = 1963.570| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.6316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 3008 Z= 0.228 Angle : 0.557 4.710 4064 Z= 0.310 Chirality : 0.038 0.136 480 Planarity : 0.003 0.010 528 Dihedral : 4.925 17.449 400 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.30 % Allowed : 2.38 % Favored : 97.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.84 (0.28), residues: 368 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.68 (0.22), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR D 37 PHE 0.018 0.002 PHE M 23 HIS 0.005 0.002 HIS L 18 Details of bonding type rmsd covalent geometry : bond 0.00489 ( 2992) covalent geometry : angle 0.55684 ( 4064) hydrogen bonds : bond 0.05861 ( 16) hydrogen bonds : angle 6.27546 ( 45) Misc. bond : bond 0.00036 ( 16) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 736 Ramachandran restraints generated. 368 Oldfield, 0 Emsley, 368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 736 Ramachandran restraints generated. 368 Oldfield, 0 Emsley, 368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 0.071 Fit side-chains REVERT: C 27 LEU cc_start: 0.8787 (mt) cc_final: 0.8525 (tt) REVERT: G 36 THR cc_start: 0.9057 (m) cc_final: 0.8752 (p) outliers start: 1 outliers final: 0 residues processed: 38 average time/residue: 0.0271 time to fit residues: 1.6470 Evaluate side-chains 17 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 31 optimal weight: 30.0000 chunk 27 optimal weight: 9.9990 chunk 25 optimal weight: 20.0000 chunk 3 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 20 optimal weight: 20.0000 chunk 7 optimal weight: 6.9990 chunk 28 optimal weight: 20.0000 chunk 24 optimal weight: 5.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 31 ASN E 31 ASN G 31 ASN H 18 HIS I 31 ASN J 31 ASN M 31 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.082856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.070784 restraints weight = 11501.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.072937 restraints weight = 5271.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.074421 restraints weight = 3213.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.075461 restraints weight = 2320.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.076091 restraints weight = 1830.663| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.6633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3008 Z= 0.165 Angle : 0.504 6.101 4064 Z= 0.267 Chirality : 0.037 0.122 480 Planarity : 0.002 0.007 528 Dihedral : 4.432 14.736 400 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.30 % Allowed : 1.49 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.83 (0.29), residues: 368 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.67 (0.22), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR O 37 PHE 0.015 0.002 PHE M 23 HIS 0.004 0.002 HIS J 18 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 2992) covalent geometry : angle 0.50445 ( 4064) hydrogen bonds : bond 0.05370 ( 16) hydrogen bonds : angle 5.91941 ( 45) Misc. bond : bond 0.00018 ( 16) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 736 Ramachandran restraints generated. 368 Oldfield, 0 Emsley, 368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 736 Ramachandran restraints generated. 368 Oldfield, 0 Emsley, 368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 36 time to evaluate : 0.084 Fit side-chains REVERT: C 27 LEU cc_start: 0.8842 (mt) cc_final: 0.8593 (tt) REVERT: F 21 ASN cc_start: 0.7043 (m-40) cc_final: 0.6337 (m-40) REVERT: G 36 THR cc_start: 0.9027 (m) cc_final: 0.8695 (p) REVERT: I 26 ILE cc_start: 0.9433 (mm) cc_final: 0.9216 (mm) REVERT: J 36 THR cc_start: 0.9117 (m) cc_final: 0.8813 (p) REVERT: P 31 ASN cc_start: 0.7352 (m110) cc_final: 0.6554 (t0) outliers start: 1 outliers final: 0 residues processed: 37 average time/residue: 0.0229 time to fit residues: 1.3460 Evaluate side-chains 26 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 31 optimal weight: 0.9980 chunk 29 optimal weight: 8.9990 chunk 19 optimal weight: 9.9990 chunk 26 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 5 optimal weight: 20.0000 chunk 7 optimal weight: 7.9990 chunk 8 optimal weight: 20.0000 chunk 25 optimal weight: 3.9990 chunk 17 optimal weight: 20.0000 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 ASN D 31 ASN K 31 ASN M 31 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.079035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.067969 restraints weight = 11865.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.069946 restraints weight = 5532.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.071268 restraints weight = 3418.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.072136 restraints weight = 2480.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.072829 restraints weight = 1976.082| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.7083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3008 Z= 0.195 Angle : 0.525 6.665 4064 Z= 0.280 Chirality : 0.037 0.120 480 Planarity : 0.002 0.015 528 Dihedral : 4.720 17.688 400 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.30 % Allowed : 3.57 % Favored : 96.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.75 (0.29), residues: 368 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.61 (0.22), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR C 37 PHE 0.014 0.002 PHE G 23 HIS 0.005 0.002 HIS J 18 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 2992) covalent geometry : angle 0.52545 ( 4064) hydrogen bonds : bond 0.05480 ( 16) hydrogen bonds : angle 6.22720 ( 45) Misc. bond : bond 0.00019 ( 16) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 736 Ramachandran restraints generated. 368 Oldfield, 0 Emsley, 368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 736 Ramachandran restraints generated. 368 Oldfield, 0 Emsley, 368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 25 time to evaluate : 0.068 Fit side-chains REVERT: C 27 LEU cc_start: 0.8869 (mt) cc_final: 0.8537 (tt) REVERT: J 36 THR cc_start: 0.9058 (m) cc_final: 0.8714 (p) REVERT: P 31 ASN cc_start: 0.7467 (m110) cc_final: 0.6454 (t0) outliers start: 1 outliers final: 0 residues processed: 26 average time/residue: 0.0267 time to fit residues: 1.1417 Evaluate side-chains 18 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 15 optimal weight: 8.9990 chunk 11 optimal weight: 0.9990 chunk 19 optimal weight: 8.9990 chunk 14 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 12 optimal weight: 20.0000 chunk 28 optimal weight: 20.0000 chunk 26 optimal weight: 30.0000 chunk 7 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 8 optimal weight: 9.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 31 ASN D 18 HIS E 18 HIS E 31 ASN F 31 ASN ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 31 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.076814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.066422 restraints weight = 10249.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.068193 restraints weight = 5121.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.069337 restraints weight = 3272.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.070180 restraints weight = 2434.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.070644 restraints weight = 1982.162| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.7607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 3008 Z= 0.273 Angle : 0.609 7.257 4064 Z= 0.326 Chirality : 0.039 0.122 480 Planarity : 0.002 0.009 528 Dihedral : 5.331 18.704 400 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 0.30 % Allowed : 2.98 % Favored : 96.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.78 (0.28), residues: 368 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.64 (0.21), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR G 37 PHE 0.014 0.002 PHE G 23 HIS 0.005 0.003 HIS L 18 Details of bonding type rmsd covalent geometry : bond 0.00588 ( 2992) covalent geometry : angle 0.60875 ( 4064) hydrogen bonds : bond 0.06294 ( 16) hydrogen bonds : angle 6.70610 ( 45) Misc. bond : bond 0.00051 ( 16) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 736 Ramachandran restraints generated. 368 Oldfield, 0 Emsley, 368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 736 Ramachandran restraints generated. 368 Oldfield, 0 Emsley, 368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 24 time to evaluate : 0.079 Fit side-chains REVERT: K 27 LEU cc_start: 0.9008 (mt) cc_final: 0.8715 (tp) REVERT: P 31 ASN cc_start: 0.7642 (m110) cc_final: 0.6502 (t0) outliers start: 1 outliers final: 0 residues processed: 25 average time/residue: 0.0273 time to fit residues: 1.1121 Evaluate side-chains 19 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 21 optimal weight: 9.9990 chunk 29 optimal weight: 30.0000 chunk 23 optimal weight: 20.0000 chunk 20 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 2 optimal weight: 20.0000 chunk 1 optimal weight: 20.0000 chunk 14 optimal weight: 0.9990 chunk 10 optimal weight: 8.9990 chunk 9 optimal weight: 10.0000 chunk 24 optimal weight: 0.9990 overall best weight: 6.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 ASN F 31 ASN ** H 31 ASN ** 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 = 0.3499 r_free = 0.3499 target = 0.077911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.067679 restraints weight = 10164.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.069423 restraints weight = 5046.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.070453 restraints weight = 3217.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.071342 restraints weight = 2466.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.071938 restraints weight = 1992.876| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.7790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 3008 Z= 0.218 Angle : 0.580 7.061 4064 Z= 0.305 Chirality : 0.038 0.125 480 Planarity : 0.002 0.018 528 Dihedral : 5.041 16.645 400 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 0.30 % Allowed : 1.49 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.70 (0.28), residues: 368 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.58 (0.21), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR C 37 PHE 0.017 0.002 PHE G 23 HIS 0.005 0.002 HIS F 18 Details of bonding type rmsd covalent geometry : bond 0.00474 ( 2992) covalent geometry : angle 0.58002 ( 4064) hydrogen bonds : bond 0.05979 ( 16) hydrogen bonds : angle 6.50260 ( 45) Misc. bond : bond 0.00021 ( 16) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 736 Ramachandran restraints generated. 368 Oldfield, 0 Emsley, 368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 736 Ramachandran restraints generated. 368 Oldfield, 0 Emsley, 368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 23 time to evaluate : 0.113 Fit side-chains REVERT: C 27 LEU cc_start: 0.8907 (mp) cc_final: 0.8417 (tt) REVERT: I 21 ASN cc_start: 0.6904 (m-40) cc_final: 0.6606 (m-40) REVERT: P 31 ASN cc_start: 0.7860 (m110) cc_final: 0.6730 (t0) outliers start: 1 outliers final: 1 residues processed: 24 average time/residue: 0.0269 time to fit residues: 1.0872 Evaluate side-chains 20 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 19 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 7 optimal weight: 6.9990 chunk 1 optimal weight: 20.0000 chunk 22 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 29 optimal weight: 30.0000 chunk 28 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 chunk 26 optimal weight: 8.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.078377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.067831 restraints weight = 10052.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.069680 restraints weight = 5060.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.070860 restraints weight = 3214.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.071650 restraints weight = 2406.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.072082 restraints weight = 1984.563| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.7848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3008 Z= 0.176 Angle : 0.550 7.171 4064 Z= 0.285 Chirality : 0.038 0.125 480 Planarity : 0.002 0.016 528 Dihedral : 4.764 15.187 400 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 0.30 % Allowed : 0.30 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.58 (0.28), residues: 368 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.48 (0.21), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR G 37 PHE 0.014 0.002 PHE G 23 HIS 0.005 0.002 HIS J 18 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 2992) covalent geometry : angle 0.54969 ( 4064) hydrogen bonds : bond 0.05602 ( 16) hydrogen bonds : angle 6.24305 ( 45) Misc. bond : bond 0.00023 ( 16) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 736 Ramachandran restraints generated. 368 Oldfield, 0 Emsley, 368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 736 Ramachandran restraints generated. 368 Oldfield, 0 Emsley, 368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 31 time to evaluate : 0.138 Fit side-chains REVERT: C 27 LEU cc_start: 0.8914 (mp) cc_final: 0.8409 (tt) outliers start: 1 outliers final: 1 residues processed: 32 average time/residue: 0.0272 time to fit residues: 1.3521 Evaluate side-chains 23 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 24 optimal weight: 9.9990 chunk 30 optimal weight: 20.0000 chunk 28 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 22 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 31 ASN H 31 ASN ** J 31 ASN ** 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 = 0.3481 r_free = 0.3481 target = 0.076368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.066075 restraints weight = 10571.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.067747 restraints weight = 5254.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.068929 restraints weight = 3370.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.069710 restraints weight = 2502.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.069915 restraints weight = 2232.451| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.8102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 3008 Z= 0.251 Angle : 0.617 7.221 4064 Z= 0.324 Chirality : 0.039 0.150 480 Planarity : 0.002 0.010 528 Dihedral : 5.275 16.252 400 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.87 % Favored : 89.13 % Rotamer: Outliers : 0.60 % Allowed : 0.60 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.44 (0.29), residues: 368 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.37 (0.22), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.001 TYR G 37 PHE 0.016 0.002 PHE G 23 HIS 0.006 0.002 HIS F 18 Details of bonding type rmsd covalent geometry : bond 0.00554 ( 2992) covalent geometry : angle 0.61666 ( 4064) hydrogen bonds : bond 0.06253 ( 16) hydrogen bonds : angle 6.65094 ( 45) Misc. bond : bond 0.00037 ( 16) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 736 Ramachandran restraints generated. 368 Oldfield, 0 Emsley, 368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 736 Ramachandran restraints generated. 368 Oldfield, 0 Emsley, 368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 25 time to evaluate : 0.091 Fit side-chains REVERT: C 27 LEU cc_start: 0.8936 (mp) cc_final: 0.8423 (tt) outliers start: 2 outliers final: 1 residues processed: 27 average time/residue: 0.0203 time to fit residues: 0.8747 Evaluate side-chains 19 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 21 optimal weight: 0.8980 chunk 31 optimal weight: 20.0000 chunk 26 optimal weight: 20.0000 chunk 29 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 25 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 12 optimal weight: 20.0000 chunk 15 optimal weight: 20.0000 chunk 10 optimal weight: 9.9990 chunk 6 optimal weight: 4.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 ASN H 31 ASN J 31 ASN ** N 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.077713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.067210 restraints weight = 10228.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.068928 restraints weight = 5094.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.070143 restraints weight = 3274.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.070683 restraints weight = 2431.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.070690 restraints weight = 2102.454| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.8066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 3008 Z= 0.182 Angle : 0.565 7.802 4064 Z= 0.293 Chirality : 0.038 0.138 480 Planarity : 0.002 0.009 528 Dihedral : 4.853 12.765 400 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 0.89 % Allowed : 0.00 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.43 (0.29), residues: 368 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.37 (0.22), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR G 37 PHE 0.014 0.002 PHE G 23 HIS 0.005 0.002 HIS J 18 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 2992) covalent geometry : angle 0.56477 ( 4064) hydrogen bonds : bond 0.05780 ( 16) hydrogen bonds : angle 6.32307 ( 45) Misc. bond : bond 0.00026 ( 16) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 736 Ramachandran restraints generated. 368 Oldfield, 0 Emsley, 368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 736 Ramachandran restraints generated. 368 Oldfield, 0 Emsley, 368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 27 time to evaluate : 0.140 Fit side-chains REVERT: C 27 LEU cc_start: 0.8901 (mp) cc_final: 0.8390 (tt) REVERT: I 26 ILE cc_start: 0.9587 (mm) cc_final: 0.9331 (mm) outliers start: 3 outliers final: 1 residues processed: 30 average time/residue: 0.0243 time to fit residues: 1.2251 Evaluate side-chains 22 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 21 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 16 optimal weight: 20.0000 chunk 10 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 24 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 5 optimal weight: 8.9990 chunk 27 optimal weight: 20.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 31 ASN H 31 ASN J 31 ASN ** N 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.078097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.067463 restraints weight = 9801.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.069254 restraints weight = 5052.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.070370 restraints weight = 3234.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.071211 restraints weight = 2468.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.071805 restraints weight = 2012.244| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.8104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3008 Z= 0.165 Angle : 0.550 7.297 4064 Z= 0.282 Chirality : 0.038 0.139 480 Planarity : 0.002 0.009 528 Dihedral : 4.636 13.015 400 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.24 % Favored : 90.76 % Rotamer: Outliers : 0.30 % Allowed : 0.00 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.43 (0.29), residues: 368 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.37 (0.22), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR G 37 PHE 0.013 0.002 PHE G 23 HIS 0.005 0.002 HIS J 18 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 2992) covalent geometry : angle 0.54992 ( 4064) hydrogen bonds : bond 0.05528 ( 16) hydrogen bonds : angle 6.20174 ( 45) Misc. bond : bond 0.00024 ( 16) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 548.31 seconds wall clock time: 10 minutes 29.21 seconds (629.21 seconds total)