Starting phenix.real_space_refine on Mon Feb 10 21:44:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6y1a_10669/02_2025/6y1a_10669.cif Found real_map, /net/cci-nas-00/data/ceres_data/6y1a_10669/02_2025/6y1a_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6y1a_10669/02_2025/6y1a_10669.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6y1a_10669/02_2025/6y1a_10669.map" model { file = "/net/cci-nas-00/data/ceres_data/6y1a_10669/02_2025/6y1a_10669.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6y1a_10669/02_2025/6y1a_10669.cif" } resolution = 4.2 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= 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-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 2.15, per 1000 atoms: 0.73 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: 0.73 Conformation dependent library (CDL) restraints added in 334.6 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: 0.49 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: 0.68 Time building geometry restraints manager: 0.84 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: 0.350 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.470 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.030 ------------------------------------------------------------------------------- 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 : 0.005 0.033 2992 Z= 0.308 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.99 (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 HIS 0.001 0.001 HIS N 18 PHE 0.004 0.001 PHE O 23 TYR 0.004 0.001 TYR P 37 *********************** 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 : 0.360 Fit side-chains REVERT: A 37 TYR cc_start: 0.5198 (m-80) cc_final: 0.4194 (p90) REVERT: B 23 PHE cc_start: 0.5808 (m-80) cc_final: 0.4598 (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: 0.0697 time to fit residues: 11.5153 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 : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 27 optimal weight: 20.0000 chunk 24 optimal weight: 30.0000 chunk 13 optimal weight: 20.0000 chunk 8 optimal weight: 20.0000 chunk 16 optimal weight: 20.0000 chunk 12 optimal weight: 5.9990 chunk 25 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 chunk 15 optimal weight: 20.0000 chunk 18 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- 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 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 = 0.3730 r_free = 0.3730 target = 0.089258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.076271 restraints weight = 8892.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.078568 restraints weight = 4692.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.080144 restraints weight = 3060.267| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.4677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 2992 Z= 0.279 Angle : 0.577 5.026 4064 Z= 0.320 Chirality : 0.041 0.130 480 Planarity : 0.002 0.011 528 Dihedral : 4.629 15.983 400 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 17.83 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 (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: -5.00 (0.26), residues: 368 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.80 (0.20), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 18 PHE 0.024 0.003 PHE L 23 TYR 0.004 0.001 TYR P 37 *********************** 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 57 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 56 time to evaluate : 0.504 Fit side-chains REVERT: C 20 SER cc_start: 0.9097 (p) cc_final: 0.8893 (m) REVERT: C 21 ASN cc_start: 0.7333 (m-40) cc_final: 0.6934 (m-40) REVERT: E 21 ASN cc_start: 0.7630 (m-40) cc_final: 0.7357 (m-40) REVERT: G 36 THR cc_start: 0.9172 (m) cc_final: 0.8902 (p) REVERT: J 36 THR cc_start: 0.9166 (m) cc_final: 0.8949 (p) REVERT: K 36 THR cc_start: 0.9204 (m) cc_final: 0.8897 (t) outliers start: 1 outliers final: 0 residues processed: 57 average time/residue: 0.0695 time to fit residues: 5.8866 Evaluate side-chains 24 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 0 optimal weight: 20.0000 chunk 29 optimal weight: 0.8980 chunk 16 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 23 optimal weight: 20.0000 chunk 24 optimal weight: 20.0000 chunk 30 optimal weight: 0.2980 chunk 2 optimal weight: 20.0000 chunk 25 optimal weight: 10.0000 chunk 22 optimal weight: 20.0000 chunk 15 optimal weight: 3.9990 overall best weight: 5.0388 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.084363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.071593 restraints weight = 10013.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.073775 restraints weight = 4817.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.075323 restraints weight = 3036.844| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.5948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2992 Z= 0.264 Angle : 0.514 4.663 4064 Z= 0.282 Chirality : 0.037 0.112 480 Planarity : 0.002 0.008 528 Dihedral : 4.497 14.970 400 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.30 % Allowed : 1.79 % Favored : 97.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.83 (0.27), residues: 368 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.67 (0.21), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS L 18 PHE 0.018 0.002 PHE L 23 TYR 0.004 0.001 TYR H 37 *********************** 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 44 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 0.342 Fit side-chains REVERT: E 36 THR cc_start: 0.9165 (m) cc_final: 0.8806 (p) REVERT: F 21 ASN cc_start: 0.7388 (m-40) cc_final: 0.6591 (m-40) REVERT: J 36 THR cc_start: 0.9109 (m) cc_final: 0.8796 (p) outliers start: 1 outliers final: 0 residues processed: 44 average time/residue: 0.0697 time to fit residues: 4.6582 Evaluate side-chains 22 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 8 optimal weight: 20.0000 chunk 20 optimal weight: 20.0000 chunk 4 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 11 optimal weight: 20.0000 chunk 30 optimal weight: 20.0000 chunk 14 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 overall best weight: 6.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 ASN D 35 ASN ** H 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 31 ASN J 31 ASN M 31 ASN ** P 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.078560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.067762 restraints weight = 13308.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.069727 restraints weight = 5709.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.071045 restraints weight = 3439.960| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.6845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 2992 Z= 0.336 Angle : 0.559 6.971 4064 Z= 0.305 Chirality : 0.039 0.135 480 Planarity : 0.002 0.010 528 Dihedral : 5.114 17.831 400 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 17.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 0.30 % Allowed : 1.79 % Favored : 97.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.90 (0.28), residues: 368 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.73 (0.22), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS J 18 PHE 0.022 0.002 PHE H 23 TYR 0.007 0.001 TYR C 37 *********************** 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 31 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 30 time to evaluate : 0.335 Fit side-chains REVERT: C 27 LEU cc_start: 0.8830 (mt) cc_final: 0.8512 (tt) REVERT: D 31 ASN cc_start: 0.8499 (m-40) cc_final: 0.8024 (m-40) REVERT: G 27 LEU cc_start: 0.8922 (mt) cc_final: 0.8638 (tt) outliers start: 1 outliers final: 0 residues processed: 31 average time/residue: 0.0665 time to fit residues: 3.3304 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 : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 14 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 19 optimal weight: 7.9990 chunk 17 optimal weight: 4.9990 chunk 25 optimal weight: 9.9990 chunk 23 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 15 optimal weight: 0.9990 chunk 24 optimal weight: 20.0000 chunk 20 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 ASN C 31 ASN D 18 HIS ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 ASN F 31 ASN G 31 ASN H 18 HIS J 31 ASN K 31 ASN P 35 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.079528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.068815 restraints weight = 10448.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.070729 restraints weight = 5088.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.072018 restraints weight = 3236.027| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.7062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2992 Z= 0.249 Angle : 0.508 6.696 4064 Z= 0.269 Chirality : 0.037 0.119 480 Planarity : 0.002 0.010 528 Dihedral : 4.567 17.032 400 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.30 % Allowed : 3.87 % Favored : 95.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.85 (0.28), residues: 368 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.69 (0.21), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS L 18 PHE 0.014 0.002 PHE H 23 TYR 0.004 0.001 TYR D 37 *********************** 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 : 0.308 Fit side-chains REVERT: C 27 LEU cc_start: 0.8836 (mt) cc_final: 0.8593 (tt) REVERT: D 31 ASN cc_start: 0.8053 (m-40) cc_final: 0.6933 (t0) REVERT: F 21 ASN cc_start: 0.6802 (m-40) cc_final: 0.6112 (m-40) outliers start: 1 outliers final: 0 residues processed: 26 average time/residue: 0.0712 time to fit residues: 2.9781 Evaluate side-chains 16 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 3 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 4 optimal weight: 0.9990 chunk 17 optimal weight: 7.9990 chunk 30 optimal weight: 20.0000 chunk 31 optimal weight: 20.0000 chunk 23 optimal weight: 20.0000 chunk 12 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 14 optimal weight: 20.0000 chunk 16 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 31 ASN I 31 ASN J 31 ASN J 35 ASN K 18 HIS M 31 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.078109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.067770 restraints weight = 10260.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.069546 restraints weight = 5209.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.070730 restraints weight = 3317.025| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.7367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2992 Z= 0.260 Angle : 0.533 7.016 4064 Z= 0.282 Chirality : 0.038 0.122 480 Planarity : 0.002 0.021 528 Dihedral : 4.743 17.367 400 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.60 % Allowed : 2.98 % Favored : 96.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.86 (0.28), residues: 368 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.70 (0.21), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS F 18 PHE 0.013 0.002 PHE H 23 TYR 0.004 0.001 TYR D 37 *********************** 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 33 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 31 time to evaluate : 0.347 Fit side-chains REVERT: C 27 LEU cc_start: 0.8843 (mt) cc_final: 0.8543 (tp) REVERT: K 27 LEU cc_start: 0.9108 (mt) cc_final: 0.8716 (tt) REVERT: P 31 ASN cc_start: 0.7174 (m110) cc_final: 0.6423 (t0) outliers start: 2 outliers final: 1 residues processed: 33 average time/residue: 0.0751 time to fit residues: 3.8154 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 : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 8 optimal weight: 4.9990 chunk 19 optimal weight: 20.0000 chunk 12 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 11 optimal weight: 8.9990 chunk 30 optimal weight: 20.0000 chunk 15 optimal weight: 5.9990 chunk 26 optimal weight: 20.0000 chunk 31 optimal weight: 20.0000 chunk 16 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 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 14 ASN ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 ASN G 18 HIS ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.077633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.067120 restraints weight = 10325.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.068908 restraints weight = 5270.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.070103 restraints weight = 3430.026| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.7649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 2992 Z= 0.305 Angle : 0.549 7.135 4064 Z= 0.297 Chirality : 0.038 0.125 480 Planarity : 0.002 0.016 528 Dihedral : 4.980 18.886 400 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.00 % Allowed : 1.79 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.72 (0.28), residues: 368 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.59 (0.21), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS J 18 PHE 0.015 0.002 PHE F 23 TYR 0.006 0.001 TYR C 37 *********************** 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 26 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.343 Fit side-chains REVERT: G 27 LEU cc_start: 0.8923 (mt) cc_final: 0.8578 (tt) REVERT: J 31 ASN cc_start: 0.8164 (m110) cc_final: 0.6818 (t0) REVERT: P 31 ASN cc_start: 0.7264 (m110) cc_final: 0.6393 (t0) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.0731 time to fit residues: 3.0185 Evaluate side-chains 20 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 9 optimal weight: 20.0000 chunk 16 optimal weight: 20.0000 chunk 25 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 19 optimal weight: 20.0000 chunk 5 optimal weight: 10.0000 chunk 14 optimal weight: 20.0000 chunk 26 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 18 HIS ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 31 ASN ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 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 = 0.3483 r_free = 0.3483 target = 0.075912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.065733 restraints weight = 10702.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.067431 restraints weight = 5287.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.068533 restraints weight = 3398.569| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.8056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 2992 Z= 0.408 Angle : 0.613 7.326 4064 Z= 0.340 Chirality : 0.040 0.124 480 Planarity : 0.003 0.013 528 Dihedral : 5.647 20.168 400 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 19.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.87 % Favored : 89.13 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.55 (0.29), residues: 368 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.46 (0.22), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS F 18 PHE 0.017 0.002 PHE F 23 TYR 0.008 0.002 TYR D 37 *********************** 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 26 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.332 Fit side-chains REVERT: I 26 ILE cc_start: 0.9424 (mm) cc_final: 0.9131 (mm) REVERT: J 31 ASN cc_start: 0.8247 (m110) cc_final: 0.6932 (t0) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.0662 time to fit residues: 2.8039 Evaluate side-chains 20 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 23 optimal weight: 20.0000 chunk 16 optimal weight: 20.0000 chunk 18 optimal weight: 20.0000 chunk 28 optimal weight: 20.0000 chunk 29 optimal weight: 7.9990 chunk 3 optimal weight: 20.0000 chunk 26 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 15 optimal weight: 4.9990 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 ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.076221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.065944 restraints weight = 10363.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.067658 restraints weight = 5182.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.068734 restraints weight = 3326.184| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.8179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 2992 Z= 0.342 Angle : 0.582 6.816 4064 Z= 0.318 Chirality : 0.039 0.122 480 Planarity : 0.002 0.010 528 Dihedral : 5.409 18.647 400 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.45 (0.29), residues: 368 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.38 (0.22), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS F 18 PHE 0.015 0.002 PHE H 23 TYR 0.007 0.001 TYR D 37 *********************** 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 22 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 21 time to evaluate : 0.322 Fit side-chains REVERT: C 27 LEU cc_start: 0.8881 (mp) cc_final: 0.8383 (tt) REVERT: D 31 ASN cc_start: 0.8293 (m110) cc_final: 0.6902 (t0) REVERT: G 27 LEU cc_start: 0.9101 (mp) cc_final: 0.8617 (tt) REVERT: J 31 ASN cc_start: 0.8206 (m110) cc_final: 0.6942 (t0) outliers start: 1 outliers final: 0 residues processed: 22 average time/residue: 0.0699 time to fit residues: 2.5314 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 : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 1 optimal weight: 20.0000 chunk 23 optimal weight: 20.0000 chunk 12 optimal weight: 9.9990 chunk 20 optimal weight: 20.0000 chunk 16 optimal weight: 1.9990 chunk 28 optimal weight: 20.0000 chunk 5 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 31 ASN ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 31 ASN ** 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 = 0.3495 r_free = 0.3495 target = 0.076975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.066537 restraints weight = 11675.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.068278 restraints weight = 5619.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.069378 restraints weight = 3565.844| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.8177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2992 Z= 0.266 Angle : 0.545 7.258 4064 Z= 0.292 Chirality : 0.038 0.120 480 Planarity : 0.002 0.009 528 Dihedral : 5.074 16.912 400 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 13.59 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.45 (0.29), residues: 368 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.39 (0.22), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS J 18 PHE 0.013 0.002 PHE H 23 TYR 0.006 0.001 TYR D 37 ********************** 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 21 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 20 time to evaluate : 0.323 Fit side-chains REVERT: E 26 ILE cc_start: 0.9453 (mm) cc_final: 0.9209 (mm) REVERT: G 27 LEU cc_start: 0.9090 (mp) cc_final: 0.8591 (tt) REVERT: J 31 ASN cc_start: 0.8250 (m110) cc_final: 0.6963 (t0) outliers start: 1 outliers final: 0 residues processed: 21 average time/residue: 0.0694 time to fit residues: 2.4311 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 : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 7 optimal weight: 3.9990 chunk 4 optimal weight: 20.0000 chunk 22 optimal weight: 6.9990 chunk 28 optimal weight: 20.0000 chunk 11 optimal weight: 9.9990 chunk 10 optimal weight: 20.0000 chunk 3 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 chunk 24 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 31 ASN ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 31 ASN ** 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 = 0.3500 r_free = 0.3500 target = 0.076642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.066097 restraints weight = 11154.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.067847 restraints weight = 5473.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.069006 restraints weight = 3487.908| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.8320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 2992 Z= 0.342 Angle : 0.572 7.302 4064 Z= 0.316 Chirality : 0.039 0.130 480 Planarity : 0.002 0.009 528 Dihedral : 5.461 17.944 400 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.87 % Favored : 89.13 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.42 (0.30), residues: 368 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.36 (0.23), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS J 18 PHE 0.015 0.002 PHE H 23 TYR 0.008 0.002 TYR D 37 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 979.59 seconds wall clock time: 19 minutes 13.54 seconds (1153.54 seconds total)