Starting phenix.real_space_refine on Wed Mar 5 16:43:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6y1a_10669/03_2025/6y1a_10669.cif Found real_map, /net/cci-nas-00/data/ceres_data/6y1a_10669/03_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_10669/03_2025/6y1a_10669.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6y1a_10669/03_2025/6y1a_10669.map" model { file = "/net/cci-nas-00/data/ceres_data/6y1a_10669/03_2025/6y1a_10669.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6y1a_10669/03_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-5624/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: 2.18, per 1000 atoms: 0.74 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: 0.74 Conformation dependent library (CDL) restraints added in 331.6 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: 0.48 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: 0.64 Time building geometry restraints manager: 0.87 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: 0.370 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.000 Find NCS groups from input model: 0.170 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.630 ------------------------------------------------------------------------------- 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 : 0.316 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: 0.0663 time to fit residues: 10.9914 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 : 0.377 ------------------------------------------------------------------------------- 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 = 0.3466 r_free = 0.3466 target = 0.076267 restraints weight = 8892.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.078566 restraints weight = 4693.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.080154 restraints weight = 3060.679| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- 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 : 0.329 Fit side-chains REVERT: C 20 SER cc_start: 0.9096 (p) cc_final: 0.8892 (m) REVERT: C 21 ASN cc_start: 0.7333 (m-40) cc_final: 0.6934 (m-40) REVERT: E 21 ASN cc_start: 0.7629 (m-40) cc_final: 0.7356 (m-40) REVERT: G 36 THR cc_start: 0.9173 (m) cc_final: 0.8903 (p) REVERT: J 36 THR cc_start: 0.9167 (m) cc_final: 0.8948 (p) REVERT: K 36 THR cc_start: 0.9205 (m) cc_final: 0.8897 (t) outliers start: 1 outliers final: 0 residues processed: 57 average time/residue: 0.0674 time to fit residues: 5.6496 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 : 0.326 ------------------------------------------------------------------------------- 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: 10.0000 chunk 13 optimal weight: 8.9990 chunk 23 optimal weight: 20.0000 chunk 24 optimal weight: 20.0000 chunk 30 optimal weight: 20.0000 chunk 2 optimal weight: 20.0000 chunk 25 optimal weight: 10.0000 chunk 22 optimal weight: 20.0000 chunk 15 optimal weight: 5.9990 overall best weight: 7.1792 ------------------------------------------------------------------------------- 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 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.082531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.070222 restraints weight = 11885.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.072322 restraints weight = 5267.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.073685 restraints weight = 3194.637| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.6322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 2992 Z= 0.360 Angle : 0.568 4.518 4064 Z= 0.319 Chirality : 0.038 0.149 480 Planarity : 0.003 0.012 528 Dihedral : 5.120 17.774 400 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 18.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % 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: -4.94 (0.28), residues: 368 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.76 (0.21), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS L 18 PHE 0.022 0.003 PHE M 23 TYR 0.007 0.001 TYR D 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 39 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.355 Fit side-chains REVERT: C 27 LEU cc_start: 0.8785 (mt) cc_final: 0.8534 (tt) REVERT: G 27 LEU cc_start: 0.8855 (mt) cc_final: 0.8639 (tt) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.0695 time to fit residues: 4.1928 Evaluate side-chains 15 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.353 ------------------------------------------------------------------------------- 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: 6.9990 chunk 4 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 11 optimal weight: 0.3980 chunk 30 optimal weight: 20.0000 chunk 14 optimal weight: 20.0000 chunk 1 optimal weight: 20.0000 chunk 15 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 overall best weight: 3.8788 ------------------------------------------------------------------------------- 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 D 31 ASN E 31 ASN G 31 ASN H 18 HIS I 31 ASN J 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 = 0.3604 r_free = 0.3604 target = 0.083648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.071767 restraints weight = 12041.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.073859 restraints weight = 5349.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.075421 restraints weight = 3243.976| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.6572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2992 Z= 0.213 Angle : 0.496 6.016 4064 Z= 0.259 Chirality : 0.037 0.121 480 Planarity : 0.002 0.006 528 Dihedral : 4.333 13.299 400 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.60 % Allowed : 1.49 % 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: -4.94 (0.28), residues: 368 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.76 (0.21), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS J 18 PHE 0.012 0.002 PHE I 23 TYR 0.004 0.001 TYR O 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 36 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.319 Fit side-chains REVERT: C 27 LEU cc_start: 0.8861 (mt) cc_final: 0.8614 (tt) REVERT: F 21 ASN cc_start: 0.7163 (m-40) cc_final: 0.6424 (m-40) REVERT: J 36 THR cc_start: 0.9097 (m) cc_final: 0.8788 (p) outliers start: 2 outliers final: 0 residues processed: 36 average time/residue: 0.0722 time to fit residues: 4.0245 Evaluate side-chains 23 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.318 ------------------------------------------------------------------------------- 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: 9.9990 chunk 5 optimal weight: 20.0000 chunk 19 optimal weight: 5.9990 chunk 17 optimal weight: 20.0000 chunk 25 optimal weight: 20.0000 chunk 23 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 15 optimal weight: 5.9990 chunk 24 optimal weight: 20.0000 chunk 20 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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 I 31 ASN J 31 ASN ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 31 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.078562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.068047 restraints weight = 10525.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.069855 restraints weight = 5240.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.071009 restraints weight = 3332.613| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.7156 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= 0.340 Angle : 0.557 6.885 4064 Z= 0.303 Chirality : 0.038 0.118 480 Planarity : 0.002 0.013 528 Dihedral : 5.071 16.062 400 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 0.00 % Allowed : 3.87 % 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: -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 0.006 0.003 HIS F 18 PHE 0.016 0.002 PHE K 23 TYR 0.007 0.001 TYR C 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 24 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.341 Fit side-chains REVERT: C 27 LEU cc_start: 0.8875 (mt) cc_final: 0.8595 (tp) REVERT: K 27 LEU cc_start: 0.9036 (mt) cc_final: 0.8833 (tt) REVERT: P 31 ASN cc_start: 0.7344 (m110) cc_final: 0.6603 (t0) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0729 time to fit residues: 2.8273 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 : 0.331 ------------------------------------------------------------------------------- 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: 9.9990 chunk 0 optimal weight: 20.0000 chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 30 optimal weight: 30.0000 chunk 31 optimal weight: 20.0000 chunk 23 optimal weight: 9.9990 chunk 12 optimal weight: 20.0000 chunk 20 optimal weight: 20.0000 chunk 14 optimal weight: 10.0000 chunk 16 optimal weight: 8.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 31 ASN D 31 ASN E 31 ASN F 31 ASN G 31 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.077666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.066686 restraints weight = 10225.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.068442 restraints weight = 5266.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.069632 restraints weight = 3481.164| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.7437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 2992 Z= 0.312 Angle : 0.573 7.148 4064 Z= 0.303 Chirality : 0.038 0.121 480 Planarity : 0.002 0.020 528 Dihedral : 5.007 15.800 400 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.30 % Allowed : 2.68 % Favored : 97.02 % 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: -4.93 (0.27), residues: 368 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.75 (0.21), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS F 18 PHE 0.012 0.002 PHE F 23 TYR 0.005 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 27 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 26 time to evaluate : 0.330 Fit side-chains REVERT: K 27 LEU cc_start: 0.9054 (mt) cc_final: 0.8759 (tt) REVERT: P 31 ASN cc_start: 0.7100 (m110) cc_final: 0.6348 (t0) outliers start: 1 outliers final: 0 residues processed: 27 average time/residue: 0.0741 time to fit residues: 3.1801 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 : 0.333 ------------------------------------------------------------------------------- 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: 20.0000 chunk 19 optimal weight: 0.0670 chunk 12 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 chunk 30 optimal weight: 20.0000 chunk 15 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 31 optimal weight: 20.0000 chunk 16 optimal weight: 5.9990 chunk 5 optimal weight: 20.0000 overall best weight: 4.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 ASN B 31 ASN F 31 ASN G 18 HIS ** J 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.079803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.069006 restraints weight = 10056.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.070901 restraints weight = 5017.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.072053 restraints weight = 3218.266| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.7552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2992 Z= 0.227 Angle : 0.540 6.708 4064 Z= 0.276 Chirality : 0.037 0.130 480 Planarity : 0.002 0.014 528 Dihedral : 4.541 12.638 400 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 0.60 % Allowed : 1.79 % Favored : 97.62 % 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 : -3.68 (0.21), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS J 18 PHE 0.011 0.002 PHE F 23 TYR 0.004 0.001 TYR D 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 29 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 27 time to evaluate : 0.354 Fit side-chains REVERT: C 27 LEU cc_start: 0.8890 (mp) cc_final: 0.8460 (tt) REVERT: K 27 LEU cc_start: 0.9105 (mt) cc_final: 0.8839 (tt) REVERT: N 26 ILE cc_start: 0.9158 (mm) cc_final: 0.8922 (mm) REVERT: P 31 ASN cc_start: 0.7240 (m110) cc_final: 0.6530 (t0) outliers start: 2 outliers final: 2 residues processed: 29 average time/residue: 0.0724 time to fit residues: 3.2944 Evaluate side-chains 24 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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: 20.0000 chunk 22 optimal weight: 2.9990 chunk 4 optimal weight: 20.0000 chunk 19 optimal weight: 8.9990 chunk 5 optimal weight: 9.9990 chunk 14 optimal weight: 7.9990 chunk 26 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 31 ASN D 31 ASN E 31 ASN ** J 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 = 0.3568 r_free = 0.3568 target = 0.079829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.068627 restraints weight = 10176.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.070579 restraints weight = 5081.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.071890 restraints weight = 3254.398| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.7713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2992 Z= 0.238 Angle : 0.533 6.648 4064 Z= 0.276 Chirality : 0.038 0.133 480 Planarity : 0.002 0.011 528 Dihedral : 4.621 13.466 400 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.30 % Allowed : 0.60 % 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 (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: -4.73 (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 0.011 0.002 PHE K 23 TYR 0.004 0.001 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 28 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 27 time to evaluate : 0.320 Fit side-chains REVERT: C 27 LEU cc_start: 0.8899 (mp) cc_final: 0.8434 (tt) REVERT: D 31 ASN cc_start: 0.8487 (OUTLIER) cc_final: 0.8283 (m-40) REVERT: G 21 ASN cc_start: 0.6913 (m-40) cc_final: 0.5167 (t0) REVERT: K 27 LEU cc_start: 0.9104 (mt) cc_final: 0.8791 (tt) REVERT: N 26 ILE cc_start: 0.9213 (mm) cc_final: 0.8987 (mm) REVERT: P 31 ASN cc_start: 0.7383 (m110) cc_final: 0.6611 (t0) outliers start: 1 outliers final: 0 residues processed: 28 average time/residue: 0.0709 time to fit residues: 3.1145 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 : 0.390 ------------------------------------------------------------------------------- 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: 9.9990 chunk 16 optimal weight: 30.0000 chunk 18 optimal weight: 5.9990 chunk 28 optimal weight: 20.0000 chunk 29 optimal weight: 7.9990 chunk 3 optimal weight: 0.9980 chunk 26 optimal weight: 30.0000 chunk 5 optimal weight: 7.9990 chunk 7 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 chunk 15 optimal weight: 20.0000 overall best weight: 6.1988 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.078751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.068012 restraints weight = 10023.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.069796 restraints weight = 5017.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.070996 restraints weight = 3207.287| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.7944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 2992 Z= 0.303 Angle : 0.571 6.965 4064 Z= 0.300 Chirality : 0.039 0.137 480 Planarity : 0.002 0.010 528 Dihedral : 5.051 13.893 400 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.51 % Favored : 90.49 % Rotamer: Outliers : 0.30 % Allowed : 0.60 % 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 (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: -4.57 (0.29), residues: 368 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.48 (0.22), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS F 18 PHE 0.014 0.002 PHE K 23 TYR 0.006 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 25 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 24 time to evaluate : 0.364 Fit side-chains REVERT: C 27 LEU cc_start: 0.8899 (mp) cc_final: 0.8395 (tt) REVERT: G 21 ASN cc_start: 0.6973 (m-40) cc_final: 0.5337 (t0) outliers start: 1 outliers final: 1 residues processed: 25 average time/residue: 0.0749 time to fit residues: 3.0158 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 : 0.357 ------------------------------------------------------------------------------- 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: 0.3980 chunk 12 optimal weight: 6.9990 chunk 20 optimal weight: 20.0000 chunk 16 optimal weight: 0.9980 chunk 28 optimal weight: 20.0000 chunk 5 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 chunk 11 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 overall best weight: 4.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 ASN D 31 ASN ** H 31 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.079306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.068141 restraints weight = 11118.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.070071 restraints weight = 5281.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.071345 restraints weight = 3305.759| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.7981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 2992 Z= 0.248 Angle : 0.551 7.027 4064 Z= 0.286 Chirality : 0.038 0.145 480 Planarity : 0.002 0.012 528 Dihedral : 4.782 13.092 400 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 0.60 % Allowed : 0.30 % 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 (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: -4.53 (0.29), residues: 368 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.45 (0.22), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS F 18 PHE 0.011 0.002 PHE G 23 TYR 0.005 0.001 TYR L 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 30 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 28 time to evaluate : 0.374 Fit side-chains REVERT: G 21 ASN cc_start: 0.7037 (m-40) cc_final: 0.5278 (t0) REVERT: K 27 LEU cc_start: 0.9076 (mp) cc_final: 0.8499 (tt) outliers start: 2 outliers final: 1 residues processed: 30 average time/residue: 0.0759 time to fit residues: 3.5543 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 : 0.361 ------------------------------------------------------------------------------- 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: 6.9990 chunk 4 optimal weight: 20.0000 chunk 22 optimal weight: 5.9990 chunk 28 optimal weight: 20.0000 chunk 11 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 3 optimal weight: 0.0970 chunk 31 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 12 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 overall best weight: 4.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 31 ASN F 31 ASN ** H 31 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.079886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.068986 restraints weight = 11055.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.070881 restraints weight = 5138.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.072179 restraints weight = 3203.130| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.8031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 2992 Z= 0.250 Angle : 0.547 7.309 4064 Z= 0.282 Chirality : 0.039 0.152 480 Planarity : 0.002 0.009 528 Dihedral : 4.693 13.166 400 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % 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: -4.55 (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 0.004 0.002 HIS F 18 PHE 0.012 0.002 PHE K 23 TYR 0.004 0.001 TYR D 37 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1116.25 seconds wall clock time: 20 minutes 43.27 seconds (1243.27 seconds total)