Starting phenix.real_space_refine on Wed Jun 3 09:44:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ofw_70445/06_2026/9ofw_70445_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ofw_70445/06_2026/9ofw_70445.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ofw_70445/06_2026/9ofw_70445_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ofw_70445/06_2026/9ofw_70445_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ofw_70445/06_2026/9ofw_70445.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ofw_70445/06_2026/9ofw_70445.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 1480 2.51 5 N 460 2.21 5 O 420 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2360 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 118 Classifications: {'peptide': 15} Link IDs: {'TRANS': 14} Chain: "B" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 118 Classifications: {'peptide': 15} Link IDs: {'TRANS': 14} Chain: "C" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 118 Classifications: {'peptide': 15} Link IDs: {'TRANS': 14} Chain: "D" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 118 Classifications: {'peptide': 15} Link IDs: {'TRANS': 14} Chain: "E" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 118 Classifications: {'peptide': 15} Link IDs: {'TRANS': 14} Chain: "F" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 118 Classifications: {'peptide': 15} Link IDs: {'TRANS': 14} Chain: "G" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 118 Classifications: {'peptide': 15} Link IDs: {'TRANS': 14} Chain: "H" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 118 Classifications: {'peptide': 15} Link IDs: {'TRANS': 14} Chain: "I" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 118 Classifications: {'peptide': 15} Link IDs: {'TRANS': 14} Chain: "J" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 118 Classifications: {'peptide': 15} Link IDs: {'TRANS': 14} Chain: "K" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 118 Classifications: {'peptide': 15} Link IDs: {'TRANS': 14} Chain: "L" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 118 Classifications: {'peptide': 15} Link IDs: {'TRANS': 14} Chain: "M" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 118 Classifications: {'peptide': 15} Link IDs: {'TRANS': 14} Chain: "N" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 118 Classifications: {'peptide': 15} Link IDs: {'TRANS': 14} Chain: "O" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 118 Classifications: {'peptide': 15} Link IDs: {'TRANS': 14} Chain: "P" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 118 Classifications: {'peptide': 15} Link IDs: {'TRANS': 14} Chain: "Q" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 118 Classifications: {'peptide': 15} Link IDs: {'TRANS': 14} Chain: "R" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 118 Classifications: {'peptide': 15} Link IDs: {'TRANS': 14} Chain: "S" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 118 Classifications: {'peptide': 15} Link IDs: {'TRANS': 14} Chain: "T" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 118 Classifications: {'peptide': 15} Link IDs: {'TRANS': 14} Time building chain proxies: 0.96, per 1000 atoms: 0.41 Number of scatterers: 2360 At special positions: 0 Unit cell: (66.456, 92.664, 45.864, 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 420 8.00 N 460 7.00 C 1480 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=0, symmetry=0 Time building additional restraints: 0.19 Conformation dependent library (CDL) restraints added in 82.2 milliseconds 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 560 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 4 sheets defined 0.0% alpha, 78.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 35 removed outlier: 7.015A pdb=" N ILE A 25 " --> pdb=" O GLN E 24 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N LYS E 26 " --> pdb=" O ILE A 25 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ILE A 27 " --> pdb=" O LYS E 26 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N GLY E 28 " --> pdb=" O ILE A 27 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ILE E 25 " --> pdb=" O GLN I 24 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N LYS I 26 " --> pdb=" O ILE E 25 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ILE E 27 " --> pdb=" O LYS I 26 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N GLY I 28 " --> pdb=" O ILE E 27 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ILE I 25 " --> pdb=" O GLN M 24 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N LYS M 26 " --> pdb=" O ILE I 25 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ILE I 27 " --> pdb=" O LYS M 26 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N GLY M 28 " --> pdb=" O ILE I 27 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ILE M 25 " --> pdb=" O GLN Q 24 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N LYS Q 26 " --> pdb=" O ILE M 25 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ILE M 27 " --> pdb=" O LYS Q 26 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N GLY Q 28 " --> pdb=" O ILE M 27 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 23 through 35 removed outlier: 6.381A pdb=" N GLN B 24 " --> pdb=" O ILE F 25 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N ILE F 27 " --> pdb=" O GLN B 24 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LYS B 26 " --> pdb=" O ILE F 27 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N SER F 29 " --> pdb=" O LYS B 26 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLY B 28 " --> pdb=" O SER F 29 " (cutoff:3.500A) removed outlier: 10.116A pdb=" N ASP F 31 " --> pdb=" O GLY B 28 " (cutoff:3.500A) removed outlier: 8.731A pdb=" N LEU B 30 " --> pdb=" O ASP F 31 " (cutoff:3.500A) removed outlier: 9.781A pdb=" N ILE F 33 " --> pdb=" O LEU B 30 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N ASN B 32 " --> pdb=" O ILE F 33 " (cutoff:3.500A) removed outlier: 10.030A pdb=" N HIS F 35 " --> pdb=" O ASN B 32 " (cutoff:3.500A) removed outlier: 8.945A pdb=" N THR B 34 " --> pdb=" O HIS F 35 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLN F 24 " --> pdb=" O ILE J 25 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N ILE J 27 " --> pdb=" O GLN F 24 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LYS F 26 " --> pdb=" O ILE J 27 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N SER J 29 " --> pdb=" O LYS F 26 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N GLY F 28 " --> pdb=" O SER J 29 " (cutoff:3.500A) removed outlier: 10.116A pdb=" N ASP J 31 " --> pdb=" O GLY F 28 " (cutoff:3.500A) removed outlier: 8.730A pdb=" N LEU F 30 " --> pdb=" O ASP J 31 " (cutoff:3.500A) removed outlier: 9.781A pdb=" N ILE J 33 " --> pdb=" O LEU F 30 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N ASN F 32 " --> pdb=" O ILE J 33 " (cutoff:3.500A) removed outlier: 10.030A pdb=" N HIS J 35 " --> pdb=" O ASN F 32 " (cutoff:3.500A) removed outlier: 8.946A pdb=" N THR F 34 " --> pdb=" O HIS J 35 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N GLN J 24 " --> pdb=" O ILE N 25 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N ILE N 27 " --> pdb=" O GLN J 24 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LYS J 26 " --> pdb=" O ILE N 27 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N SER N 29 " --> pdb=" O LYS J 26 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLY J 28 " --> pdb=" O SER N 29 " (cutoff:3.500A) removed outlier: 10.116A pdb=" N ASP N 31 " --> pdb=" O GLY J 28 " (cutoff:3.500A) removed outlier: 8.730A pdb=" N LEU J 30 " --> pdb=" O ASP N 31 " (cutoff:3.500A) removed outlier: 9.781A pdb=" N ILE N 33 " --> pdb=" O LEU J 30 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N ASN J 32 " --> pdb=" O ILE N 33 " (cutoff:3.500A) removed outlier: 10.031A pdb=" N HIS N 35 " --> pdb=" O ASN J 32 " (cutoff:3.500A) removed outlier: 8.946A pdb=" N THR J 34 " --> pdb=" O HIS N 35 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLN N 24 " --> pdb=" O ILE R 25 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ILE R 27 " --> pdb=" O GLN N 24 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LYS N 26 " --> pdb=" O ILE R 27 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N SER R 29 " --> pdb=" O LYS N 26 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLY N 28 " --> pdb=" O SER R 29 " (cutoff:3.500A) removed outlier: 10.116A pdb=" N ASP R 31 " --> pdb=" O GLY N 28 " (cutoff:3.500A) removed outlier: 8.730A pdb=" N LEU N 30 " --> pdb=" O ASP R 31 " (cutoff:3.500A) removed outlier: 9.781A pdb=" N ILE R 33 " --> pdb=" O LEU N 30 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N ASN N 32 " --> pdb=" O ILE R 33 " (cutoff:3.500A) removed outlier: 10.031A pdb=" N HIS R 35 " --> pdb=" O ASN N 32 " (cutoff:3.500A) removed outlier: 8.946A pdb=" N THR N 34 " --> pdb=" O HIS R 35 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 23 through 35 removed outlier: 9.069A pdb=" N VAL C 23 " --> pdb=" O GLN G 24 " (cutoff:3.500A) removed outlier: 9.950A pdb=" N LYS G 26 " --> pdb=" O VAL C 23 " (cutoff:3.500A) removed outlier: 8.666A pdb=" N ILE C 25 " --> pdb=" O LYS G 26 " (cutoff:3.500A) removed outlier: 9.834A pdb=" N GLY G 28 " --> pdb=" O ILE C 25 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE C 27 " --> pdb=" O GLY G 28 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N LEU G 30 " --> pdb=" O ILE C 27 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N SER C 29 " --> pdb=" O LEU G 30 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ASN G 32 " --> pdb=" O SER C 29 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ASP C 31 " --> pdb=" O ASN G 32 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N THR G 34 " --> pdb=" O ASP C 31 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE C 33 " --> pdb=" O THR G 34 " (cutoff:3.500A) removed outlier: 9.068A pdb=" N VAL G 23 " --> pdb=" O GLN K 24 " (cutoff:3.500A) removed outlier: 9.951A pdb=" N LYS K 26 " --> pdb=" O VAL G 23 " (cutoff:3.500A) removed outlier: 8.666A pdb=" N ILE G 25 " --> pdb=" O LYS K 26 " (cutoff:3.500A) removed outlier: 9.834A pdb=" N GLY K 28 " --> pdb=" O ILE G 25 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ILE G 27 " --> pdb=" O GLY K 28 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N LEU K 30 " --> pdb=" O ILE G 27 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N SER G 29 " --> pdb=" O LEU K 30 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N ASN K 32 " --> pdb=" O SER G 29 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ASP G 31 " --> pdb=" O ASN K 32 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N THR K 34 " --> pdb=" O ASP G 31 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE G 33 " --> pdb=" O THR K 34 " (cutoff:3.500A) removed outlier: 9.068A pdb=" N VAL K 23 " --> pdb=" O GLN O 24 " (cutoff:3.500A) removed outlier: 9.950A pdb=" N LYS O 26 " --> pdb=" O VAL K 23 " (cutoff:3.500A) removed outlier: 8.665A pdb=" N ILE K 25 " --> pdb=" O LYS O 26 " (cutoff:3.500A) removed outlier: 9.835A pdb=" N GLY O 28 " --> pdb=" O ILE K 25 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE K 27 " --> pdb=" O GLY O 28 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N LEU O 30 " --> pdb=" O ILE K 27 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N SER K 29 " --> pdb=" O LEU O 30 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N ASN O 32 " --> pdb=" O SER K 29 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ASP K 31 " --> pdb=" O ASN O 32 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N THR O 34 " --> pdb=" O ASP K 31 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE K 33 " --> pdb=" O THR O 34 " (cutoff:3.500A) removed outlier: 9.068A pdb=" N VAL O 23 " --> pdb=" O GLN S 24 " (cutoff:3.500A) removed outlier: 9.950A pdb=" N LYS S 26 " --> pdb=" O VAL O 23 " (cutoff:3.500A) removed outlier: 8.666A pdb=" N ILE O 25 " --> pdb=" O LYS S 26 " (cutoff:3.500A) removed outlier: 9.834A pdb=" N GLY S 28 " --> pdb=" O ILE O 25 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE O 27 " --> pdb=" O GLY S 28 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N LEU S 30 " --> pdb=" O ILE O 27 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N SER O 29 " --> pdb=" O LEU S 30 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N ASN S 32 " --> pdb=" O SER O 29 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ASP O 31 " --> pdb=" O ASN S 32 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N THR S 34 " --> pdb=" O ASP O 31 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE O 33 " --> pdb=" O THR S 34 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'D' and resid 23 through 35 removed outlier: 9.123A pdb=" N VAL D 23 " --> pdb=" O GLN H 24 " (cutoff:3.500A) removed outlier: 10.384A pdb=" N LYS H 26 " --> pdb=" O VAL D 23 " (cutoff:3.500A) removed outlier: 9.070A pdb=" N ILE D 25 " --> pdb=" O LYS H 26 " (cutoff:3.500A) removed outlier: 10.316A pdb=" N GLY H 28 " --> pdb=" O ILE D 25 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ILE D 27 " --> pdb=" O GLY H 28 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N LEU H 30 " --> pdb=" O ILE D 27 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N SER D 29 " --> pdb=" O LEU H 30 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ASN H 32 " --> pdb=" O SER D 29 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ASP D 31 " --> pdb=" O ASN H 32 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N THR H 34 " --> pdb=" O ASP D 31 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ILE D 33 " --> pdb=" O THR H 34 " (cutoff:3.500A) removed outlier: 9.122A pdb=" N VAL H 23 " --> pdb=" O GLN L 24 " (cutoff:3.500A) removed outlier: 10.384A pdb=" N LYS L 26 " --> pdb=" O VAL H 23 " (cutoff:3.500A) removed outlier: 9.070A pdb=" N ILE H 25 " --> pdb=" O LYS L 26 " (cutoff:3.500A) removed outlier: 10.315A pdb=" N GLY L 28 " --> pdb=" O ILE H 25 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ILE H 27 " --> pdb=" O GLY L 28 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LEU L 30 " --> pdb=" O ILE H 27 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N SER H 29 " --> pdb=" O LEU L 30 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ASN L 32 " --> pdb=" O SER H 29 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ASP H 31 " --> pdb=" O ASN L 32 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N THR L 34 " --> pdb=" O ASP H 31 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ILE H 33 " --> pdb=" O THR L 34 " (cutoff:3.500A) removed outlier: 9.123A pdb=" N VAL L 23 " --> pdb=" O GLN P 24 " (cutoff:3.500A) removed outlier: 10.385A pdb=" N LYS P 26 " --> pdb=" O VAL L 23 " (cutoff:3.500A) removed outlier: 9.070A pdb=" N ILE L 25 " --> pdb=" O LYS P 26 " (cutoff:3.500A) removed outlier: 10.315A pdb=" N GLY P 28 " --> pdb=" O ILE L 25 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ILE L 27 " --> pdb=" O GLY P 28 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N LEU P 30 " --> pdb=" O ILE L 27 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N SER L 29 " --> pdb=" O LEU P 30 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ASN P 32 " --> pdb=" O SER L 29 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ASP L 31 " --> pdb=" O ASN P 32 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N THR P 34 " --> pdb=" O ASP L 31 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ILE L 33 " --> pdb=" O THR P 34 " (cutoff:3.500A) removed outlier: 9.122A pdb=" N VAL P 23 " --> pdb=" O GLN T 24 " (cutoff:3.500A) removed outlier: 10.385A pdb=" N LYS T 26 " --> pdb=" O VAL P 23 " (cutoff:3.500A) removed outlier: 9.069A pdb=" N ILE P 25 " --> pdb=" O LYS T 26 " (cutoff:3.500A) removed outlier: 10.315A pdb=" N GLY T 28 " --> pdb=" O ILE P 25 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ILE P 27 " --> pdb=" O GLY T 28 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N LEU T 30 " --> pdb=" O ILE P 27 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N SER P 29 " --> pdb=" O LEU T 30 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ASN T 32 " --> pdb=" O SER P 29 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ASP P 31 " --> pdb=" O ASN T 32 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N THR T 34 " --> pdb=" O ASP P 31 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ILE P 33 " --> pdb=" O THR T 34 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 28 hydrogen bonds defined for protein. 84 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: 0.27 Time building geometry restraints manager: 0.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 380 1.29 - 1.35: 420 1.35 - 1.41: 73 1.41 - 1.48: 342 1.48 - 1.54: 1145 Bond restraints: 2360 Sorted by residual: bond pdb=" N ARG J 22 " pdb=" CA ARG J 22 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.90e-02 2.77e+03 2.39e+00 bond pdb=" N ARG R 22 " pdb=" CA ARG R 22 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.90e-02 2.77e+03 2.30e+00 bond pdb=" N ARG F 22 " pdb=" CA ARG F 22 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.90e-02 2.77e+03 2.30e+00 bond pdb=" N ARG N 22 " pdb=" CA ARG N 22 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.90e-02 2.77e+03 2.24e+00 bond pdb=" N ARG B 22 " pdb=" CA ARG B 22 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.90e-02 2.77e+03 2.20e+00 ... (remaining 2355 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.03: 3140 5.03 - 10.06: 0 10.06 - 15.09: 5 15.09 - 20.13: 5 20.13 - 25.16: 10 Bond angle restraints: 3160 Sorted by residual: angle pdb=" N VAL F 23 " pdb=" CA VAL F 23 " pdb=" C VAL F 23 " ideal model delta sigma weight residual 107.24 82.08 25.16 1.68e+00 3.54e-01 2.24e+02 angle pdb=" N VAL J 23 " pdb=" CA VAL J 23 " pdb=" C VAL J 23 " ideal model delta sigma weight residual 107.24 82.10 25.14 1.68e+00 3.54e-01 2.24e+02 angle pdb=" N VAL B 23 " pdb=" CA VAL B 23 " pdb=" C VAL B 23 " ideal model delta sigma weight residual 107.24 82.10 25.14 1.68e+00 3.54e-01 2.24e+02 angle pdb=" N VAL R 23 " pdb=" CA VAL R 23 " pdb=" C VAL R 23 " ideal model delta sigma weight residual 107.24 82.13 25.11 1.68e+00 3.54e-01 2.23e+02 angle pdb=" N VAL N 23 " pdb=" CA VAL N 23 " pdb=" C VAL N 23 " ideal model delta sigma weight residual 107.24 82.14 25.10 1.68e+00 3.54e-01 2.23e+02 ... (remaining 3155 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.00: 1185 12.00 - 23.99: 185 23.99 - 35.98: 35 35.98 - 47.98: 30 47.98 - 59.97: 5 Dihedral angle restraints: 1440 sinusoidal: 600 harmonic: 840 Sorted by residual: dihedral pdb=" C VAL J 23 " pdb=" N VAL J 23 " pdb=" CA VAL J 23 " pdb=" CB VAL J 23 " ideal model delta harmonic sigma weight residual -122.00 -110.43 -11.57 0 2.50e+00 1.60e-01 2.14e+01 dihedral pdb=" C VAL R 23 " pdb=" N VAL R 23 " pdb=" CA VAL R 23 " pdb=" CB VAL R 23 " ideal model delta harmonic sigma weight residual -122.00 -110.43 -11.57 0 2.50e+00 1.60e-01 2.14e+01 dihedral pdb=" C VAL F 23 " pdb=" N VAL F 23 " pdb=" CA VAL F 23 " pdb=" CB VAL F 23 " ideal model delta harmonic sigma weight residual -122.00 -110.44 -11.56 0 2.50e+00 1.60e-01 2.14e+01 ... (remaining 1437 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 292 0.058 - 0.116: 123 0.116 - 0.175: 0 0.175 - 0.233: 0 0.233 - 0.291: 5 Chirality restraints: 420 Sorted by residual: chirality pdb=" CA ARG R 22 " pdb=" N ARG R 22 " pdb=" C ARG R 22 " pdb=" CB ARG R 22 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CA ARG F 22 " pdb=" N ARG F 22 " pdb=" C ARG F 22 " pdb=" CB ARG F 22 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CA ARG J 22 " pdb=" N ARG J 22 " pdb=" C ARG J 22 " pdb=" CB ARG J 22 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.11e+00 ... (remaining 417 not shown) Planarity restraints: 380 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG N 22 " -0.385 9.50e-02 1.11e+02 1.73e-01 1.83e+01 pdb=" NE ARG N 22 " 0.024 2.00e-02 2.50e+03 pdb=" CZ ARG N 22 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG N 22 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG N 22 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 22 " -0.385 9.50e-02 1.11e+02 1.72e-01 1.83e+01 pdb=" NE ARG F 22 " 0.024 2.00e-02 2.50e+03 pdb=" CZ ARG F 22 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG F 22 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG F 22 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG R 22 " -0.384 9.50e-02 1.11e+02 1.72e-01 1.83e+01 pdb=" NE ARG R 22 " 0.024 2.00e-02 2.50e+03 pdb=" CZ ARG R 22 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG R 22 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG R 22 " -0.012 2.00e-02 2.50e+03 ... (remaining 377 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 185 2.77 - 3.30: 1928 3.30 - 3.83: 3874 3.83 - 4.37: 4322 4.37 - 4.90: 8238 Nonbonded interactions: 18547 Sorted by model distance: nonbonded pdb=" OE1 GLN J 24 " pdb=" NZ LYS J 26 " model vdw 2.233 3.120 nonbonded pdb=" OE1 GLN B 24 " pdb=" NZ LYS B 26 " model vdw 2.233 3.120 nonbonded pdb=" OE1 GLN N 24 " pdb=" NZ LYS N 26 " model vdw 2.234 3.120 nonbonded pdb=" OE1 GLN F 24 " pdb=" NZ LYS F 26 " model vdw 2.234 3.120 nonbonded pdb=" OE1 GLN R 24 " pdb=" NZ LYS R 26 " model vdw 2.234 3.120 ... (remaining 18542 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' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.050 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.730 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.000 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: 0.010 Load rotamer database and sin/cos tables:8.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 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 0.029 2360 Z= 0.259 Angle : 1.688 25.158 3160 Z= 0.931 Chirality : 0.065 0.291 420 Planarity : 0.020 0.173 380 Dihedral : 13.895 59.975 880 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.79 % Allowed : 14.29 % Favored : 83.93 % Cbeta Deviations : 1.79 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.44), residues: 260 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.29 (0.34), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 22 HIS 0.004 0.002 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.26 ( 2360) covalent geometry : angle 1.68848 / 0.93 ( 3160) hydrogen bonds : bond 0.20575 / 15.87 ( 28) hydrogen bonds : angle 8.76620 / 6.30 ( 84) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.061 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 47 average time/residue: 0.1029 time to fit residues: 5.4114 Evaluate side-chains 36 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 35 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 27 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 12 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 8 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 9 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 6 optimal weight: 0.0270 chunk 4 optimal weight: 10.0000 overall best weight: 2.6044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 ASN ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 ASN ** M 32 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 = 0.5276 r_free = 0.5276 target = 0.359631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.5084 r_free = 0.5084 target = 0.291653 restraints weight = 2046.157| |-----------------------------------------------------------------------------| r_work (start): 0.4465 rms_B_bonded: 1.96 r_work: 0.4224 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.4071 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.4071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 2360 Z= 0.229 Angle : 0.567 4.472 3160 Z= 0.296 Chirality : 0.058 0.133 420 Planarity : 0.003 0.016 380 Dihedral : 6.101 18.205 302 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.21 % Allowed : 17.14 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.43), residues: 260 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.00 (0.33), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG O 22 HIS 0.004 0.001 HIS D 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.23 ( 2360) covalent geometry : angle 0.56694 / 0.30 ( 3160) hydrogen bonds : bond 0.03994 / 3.10 ( 28) hydrogen bonds : angle 6.17494 / 4.15 ( 84) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.110 Fit side-chains REVERT: B 35 HIS cc_start: 0.7509 (t-170) cc_final: 0.7239 (t-90) REVERT: H 26 LYS cc_start: 0.7563 (mttt) cc_final: 0.7067 (mtmp) REVERT: L 26 LYS cc_start: 0.7717 (mttt) cc_final: 0.7148 (mtpp) REVERT: L 32 ASN cc_start: 0.7304 (t0) cc_final: 0.7061 (t0) REVERT: M 32 ASN cc_start: 0.7323 (t0) cc_final: 0.7032 (t0) REVERT: P 29 SER cc_start: 0.7046 (OUTLIER) cc_final: 0.6747 (t) REVERT: P 32 ASN cc_start: 0.7397 (t0) cc_final: 0.7098 (t0) outliers start: 9 outliers final: 5 residues processed: 40 average time/residue: 0.1571 time to fit residues: 6.7408 Evaluate side-chains 39 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain I residue 27 ILE Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain P residue 29 SER Chi-restraints excluded: chain R residue 36 VAL Chi-restraints excluded: chain T residue 29 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 6 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 chunk 14 optimal weight: 0.5980 chunk 5 optimal weight: 10.0000 chunk 10 optimal weight: 0.4980 chunk 4 optimal weight: 20.0000 chunk 8 optimal weight: 4.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 ASN ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 32 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 = 0.5263 r_free = 0.5263 target = 0.359585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.5088 r_free = 0.5088 target = 0.291287 restraints weight = 2052.716| |-----------------------------------------------------------------------------| r_work (start): 0.4551 rms_B_bonded: 1.93 r_work: 0.4322 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.4168 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.4168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6709 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 2360 Z= 0.227 Angle : 0.576 7.193 3160 Z= 0.294 Chirality : 0.058 0.142 420 Planarity : 0.003 0.015 380 Dihedral : 5.968 16.891 300 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.93 % Allowed : 16.43 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.43), residues: 260 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.04 (0.33), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 22 HIS 0.004 0.001 HIS D 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.23 ( 2360) covalent geometry : angle 0.57575 / 0.29 ( 3160) hydrogen bonds : bond 0.03559 / 2.78 ( 28) hydrogen bonds : angle 5.78992 / 3.79 ( 84) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 0.129 Fit side-chains REVERT: B 35 HIS cc_start: 0.7541 (t-170) cc_final: 0.7243 (t-90) REVERT: E 26 LYS cc_start: 0.7083 (mttt) cc_final: 0.6715 (mtmm) REVERT: H 26 LYS cc_start: 0.7606 (mttt) cc_final: 0.6996 (mtmp) REVERT: I 26 LYS cc_start: 0.6980 (mttt) cc_final: 0.6493 (mtmm) REVERT: L 26 LYS cc_start: 0.7621 (mttt) cc_final: 0.6980 (mtpp) REVERT: M 32 ASN cc_start: 0.7293 (t0) cc_final: 0.7065 (t0) REVERT: P 29 SER cc_start: 0.6701 (OUTLIER) cc_final: 0.6397 (t) REVERT: P 32 ASN cc_start: 0.7414 (t0) cc_final: 0.6970 (t0) outliers start: 11 outliers final: 5 residues processed: 45 average time/residue: 0.1683 time to fit residues: 8.1064 Evaluate side-chains 41 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain I residue 27 ILE Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain P residue 29 SER Chi-restraints excluded: chain R residue 36 VAL Chi-restraints excluded: chain T residue 29 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 3 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 chunk 14 optimal weight: 4.9990 chunk 16 optimal weight: 20.0000 chunk 17 optimal weight: 4.9990 chunk 19 optimal weight: 0.0050 chunk 18 optimal weight: 0.9980 chunk 12 optimal weight: 9.9990 chunk 13 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 7 optimal weight: 0.0020 overall best weight: 0.4802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 ASN H 35 HIS ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 35 HIS L 32 ASN ** M 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 35 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5294 r_free = 0.5294 target = 0.365768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.5234 r_free = 0.5234 target = 0.301641 restraints weight = 2038.580| |-----------------------------------------------------------------------------| r_work (start): 0.4894 rms_B_bonded: 1.64 r_work: 0.5085 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.5007 rms_B_bonded: 1.92 restraints_weight: 0.2500 r_work (final): 0.5007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6810 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 2360 Z= 0.075 Angle : 0.454 5.731 3160 Z= 0.229 Chirality : 0.054 0.126 420 Planarity : 0.001 0.005 380 Dihedral : 5.194 13.238 300 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.93 % Allowed : 16.79 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.46), residues: 260 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.66 (0.35), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG N 22 HIS 0.007 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00150 / 0.08 ( 2360) covalent geometry : angle 0.45447 / 0.23 ( 3160) hydrogen bonds : bond 0.02365 / 1.82 ( 28) hydrogen bonds : angle 5.29131 / 3.45 ( 84) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.111 Fit side-chains REVERT: P 29 SER cc_start: 0.7609 (OUTLIER) cc_final: 0.7375 (t) REVERT: T 29 SER cc_start: 0.7712 (OUTLIER) cc_final: 0.7437 (t) outliers start: 11 outliers final: 4 residues processed: 46 average time/residue: 0.1596 time to fit residues: 7.8091 Evaluate side-chains 39 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain N residue 36 VAL Chi-restraints excluded: chain P residue 29 SER Chi-restraints excluded: chain T residue 29 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 14 optimal weight: 6.9990 chunk 17 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 chunk 7 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 2 optimal weight: 0.0770 chunk 6 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 8 optimal weight: 9.9990 overall best weight: 2.4942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 ASN E 32 ASN ** F 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 ASN H 35 HIS I 32 ASN M 32 ASN M 35 HIS P 32 ASN T 32 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5273 r_free = 0.5273 target = 0.362372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 99)----------------| | r_work = 0.5101 r_free = 0.5101 target = 0.293397 restraints weight = 2055.430| |-----------------------------------------------------------------------------| r_work (start): 0.4584 rms_B_bonded: 1.94 r_work: 0.4338 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.4170 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.4170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6754 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2360 Z= 0.215 Angle : 0.553 7.858 3160 Z= 0.280 Chirality : 0.057 0.136 420 Planarity : 0.003 0.012 380 Dihedral : 5.759 16.265 300 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.93 % Allowed : 19.29 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.45), residues: 260 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.74 (0.34), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 22 HIS 0.014 0.002 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.21 ( 2360) covalent geometry : angle 0.55335 / 0.28 ( 3160) hydrogen bonds : bond 0.02645 / 2.02 ( 28) hydrogen bonds : angle 5.53682 / 3.66 ( 84) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 33 time to evaluate : 0.099 Fit side-chains REVERT: E 27 ILE cc_start: 0.7416 (OUTLIER) cc_final: 0.7173 (mm) REVERT: H 26 LYS cc_start: 0.7656 (tttp) cc_final: 0.6927 (mtmp) REVERT: L 26 LYS cc_start: 0.7738 (mtpp) cc_final: 0.7482 (mtpp) REVERT: M 32 ASN cc_start: 0.7293 (t0) cc_final: 0.7035 (t0) REVERT: M 35 HIS cc_start: 0.7247 (OUTLIER) cc_final: 0.7032 (t-90) REVERT: P 29 SER cc_start: 0.6770 (OUTLIER) cc_final: 0.6456 (t) REVERT: P 32 ASN cc_start: 0.7369 (t0) cc_final: 0.7085 (t0) REVERT: T 29 SER cc_start: 0.7645 (OUTLIER) cc_final: 0.7427 (t) outliers start: 11 outliers final: 6 residues processed: 39 average time/residue: 0.1765 time to fit residues: 7.3423 Evaluate side-chains 43 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 33 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain E residue 27 ILE Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain I residue 26 LYS Chi-restraints excluded: chain M residue 35 HIS Chi-restraints excluded: chain N residue 36 VAL Chi-restraints excluded: chain P residue 29 SER Chi-restraints excluded: chain Q residue 26 LYS Chi-restraints excluded: chain R residue 36 VAL Chi-restraints excluded: chain T residue 29 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 1 optimal weight: 3.9990 chunk 12 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 16 optimal weight: 0.0030 chunk 19 optimal weight: 7.9990 chunk 8 optimal weight: 0.9980 overall best weight: 1.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 ASN D 32 ASN E 32 ASN H 32 ASN H 35 HIS I 32 ASN M 35 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5283 r_free = 0.5283 target = 0.365207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.5122 r_free = 0.5122 target = 0.296704 restraints weight = 2015.456| |-----------------------------------------------------------------------------| r_work (start): 0.4823 rms_B_bonded: 1.90 r_work: 0.5091 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.5029 rms_B_bonded: 1.81 restraints_weight: 0.2500 r_work (final): 0.5029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6848 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2360 Z= 0.136 Angle : 0.500 7.203 3160 Z= 0.252 Chirality : 0.055 0.131 420 Planarity : 0.002 0.008 380 Dihedral : 5.559 15.398 300 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 3.93 % Allowed : 18.21 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.46), residues: 260 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.62 (0.35), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG N 22 HIS 0.007 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.14 ( 2360) covalent geometry : angle 0.50008 / 0.25 ( 3160) hydrogen bonds : bond 0.02338 / 1.79 ( 28) hydrogen bonds : angle 5.36474 / 3.54 ( 84) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 34 time to evaluate : 0.106 Fit side-chains REVERT: M 35 HIS cc_start: 0.7009 (OUTLIER) cc_final: 0.6655 (t-90) REVERT: P 29 SER cc_start: 0.7681 (OUTLIER) cc_final: 0.7363 (t) REVERT: T 29 SER cc_start: 0.7774 (OUTLIER) cc_final: 0.7473 (t) outliers start: 11 outliers final: 5 residues processed: 40 average time/residue: 0.1945 time to fit residues: 8.2983 Evaluate side-chains 42 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 34 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain M residue 35 HIS Chi-restraints excluded: chain N residue 36 VAL Chi-restraints excluded: chain P residue 29 SER Chi-restraints excluded: chain Q residue 26 LYS Chi-restraints excluded: chain T residue 29 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 20.0000 chunk 17 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 5 optimal weight: 0.9980 chunk 3 optimal weight: 0.3980 chunk 6 optimal weight: 7.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 ASN D 32 ASN E 32 ASN H 32 ASN H 35 HIS I 32 ASN M 35 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5275 r_free = 0.5275 target = 0.361984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.5102 r_free = 0.5102 target = 0.292407 restraints weight = 2075.751| |-----------------------------------------------------------------------------| r_work (start): 0.4804 rms_B_bonded: 1.93 r_work: 0.5066 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.5008 rms_B_bonded: 1.84 restraints_weight: 0.2500 r_work (final): 0.5008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 2360 Z= 0.255 Angle : 0.586 7.702 3160 Z= 0.297 Chirality : 0.059 0.144 420 Planarity : 0.003 0.015 380 Dihedral : 5.878 16.423 300 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.29 % Allowed : 18.21 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.46), residues: 260 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.76 (0.35), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 22 HIS 0.012 0.002 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.25 ( 2360) covalent geometry : angle 0.58551 / 0.30 ( 3160) hydrogen bonds : bond 0.02933 / 2.19 ( 28) hydrogen bonds : angle 5.70647 / 3.77 ( 84) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 31 time to evaluate : 0.099 Fit side-chains revert: symmetry clash REVERT: P 29 SER cc_start: 0.7796 (OUTLIER) cc_final: 0.7406 (t) outliers start: 12 outliers final: 9 residues processed: 37 average time/residue: 0.1704 time to fit residues: 6.7562 Evaluate side-chains 41 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 31 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain M residue 35 HIS Chi-restraints excluded: chain N residue 36 VAL Chi-restraints excluded: chain P residue 29 SER Chi-restraints excluded: chain Q residue 26 LYS Chi-restraints excluded: chain R residue 36 VAL Chi-restraints excluded: chain T residue 29 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 5 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 chunk 3 optimal weight: 9.9990 chunk 2 optimal weight: 0.6980 chunk 9 optimal weight: 0.2980 chunk 11 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 12 optimal weight: 8.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 ASN D 32 ASN E 32 ASN H 35 HIS I 32 ASN M 35 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5288 r_free = 0.5288 target = 0.365038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.5112 r_free = 0.5112 target = 0.295162 restraints weight = 2057.782| |-----------------------------------------------------------------------------| r_work (start): 0.4815 rms_B_bonded: 1.94 r_work: 0.5083 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.4990 rms_B_bonded: 1.92 restraints_weight: 0.2500 r_work (final): 0.4990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6878 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2360 Z= 0.137 Angle : 0.514 7.206 3160 Z= 0.257 Chirality : 0.056 0.136 420 Planarity : 0.002 0.007 380 Dihedral : 5.619 15.680 300 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 2.86 % Allowed : 20.36 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.47), residues: 260 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.62 (0.36), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG N 22 HIS 0.008 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.14 ( 2360) covalent geometry : angle 0.51365 / 0.26 ( 3160) hydrogen bonds : bond 0.02385 / 1.81 ( 28) hydrogen bonds : angle 5.53067 / 3.65 ( 84) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 32 time to evaluate : 0.095 Fit side-chains revert: symmetry clash REVERT: E 26 LYS cc_start: 0.7488 (mtmm) cc_final: 0.7198 (mtmm) REVERT: M 35 HIS cc_start: 0.6990 (OUTLIER) cc_final: 0.6636 (t-90) REVERT: P 29 SER cc_start: 0.7685 (OUTLIER) cc_final: 0.7378 (t) REVERT: T 29 SER cc_start: 0.7729 (OUTLIER) cc_final: 0.7453 (t) outliers start: 8 outliers final: 5 residues processed: 37 average time/residue: 0.1660 time to fit residues: 6.6096 Evaluate side-chains 39 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 31 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain M residue 35 HIS Chi-restraints excluded: chain N residue 36 VAL Chi-restraints excluded: chain P residue 29 SER Chi-restraints excluded: chain Q residue 26 LYS Chi-restraints excluded: chain T residue 29 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 17 optimal weight: 4.9990 chunk 12 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 15 optimal weight: 20.0000 chunk 10 optimal weight: 4.9990 chunk 9 optimal weight: 0.0870 chunk 11 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 overall best weight: 4.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 ASN D 32 ASN E 32 ASN H 32 ASN H 35 HIS I 32 ASN M 35 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5273 r_free = 0.5273 target = 0.361536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.5105 r_free = 0.5105 target = 0.291833 restraints weight = 2123.586| |-----------------------------------------------------------------------------| r_work (start): 0.4805 rms_B_bonded: 1.91 r_work: 0.5078 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.5031 rms_B_bonded: 1.75 restraints_weight: 0.2500 r_work (final): 0.5031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 2360 Z= 0.321 Angle : 0.625 7.391 3160 Z= 0.323 Chirality : 0.061 0.153 420 Planarity : 0.003 0.021 380 Dihedral : 6.028 17.411 300 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.29 % Allowed : 18.21 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.46), residues: 260 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.92 (0.35), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG N 22 HIS 0.016 0.002 HIS M 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00674 / 0.32 ( 2360) covalent geometry : angle 0.62546 / 0.32 ( 3160) hydrogen bonds : bond 0.03202 / 2.39 ( 28) hydrogen bonds : angle 5.91187 / 3.88 ( 84) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 34 time to evaluate : 0.062 Fit side-chains REVERT: P 29 SER cc_start: 0.7754 (OUTLIER) cc_final: 0.7339 (t) outliers start: 12 outliers final: 10 residues processed: 40 average time/residue: 0.2268 time to fit residues: 9.5101 Evaluate side-chains 43 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 32 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain M residue 35 HIS Chi-restraints excluded: chain N residue 36 VAL Chi-restraints excluded: chain P residue 29 SER Chi-restraints excluded: chain Q residue 26 LYS Chi-restraints excluded: chain R residue 36 VAL Chi-restraints excluded: chain T residue 29 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 1 optimal weight: 2.9990 chunk 8 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 19 optimal weight: 0.0170 chunk 3 optimal weight: 0.8980 chunk 2 optimal weight: 0.0270 chunk 7 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 12 optimal weight: 10.0000 overall best weight: 1.3880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 ASN D 32 ASN E 32 ASN H 35 HIS I 32 ASN M 35 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5312 r_free = 0.5312 target = 0.366779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.5171 r_free = 0.5171 target = 0.297437 restraints weight = 2105.175| |-----------------------------------------------------------------------------| r_work (start): 0.4858 rms_B_bonded: 1.89 r_work: 0.5147 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.5061 rms_B_bonded: 1.78 restraints_weight: 0.2500 r_work (final): 0.5061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2360 Z= 0.141 Angle : 0.542 6.872 3160 Z= 0.272 Chirality : 0.056 0.137 420 Planarity : 0.002 0.014 380 Dihedral : 5.728 16.106 300 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 3.93 % Allowed : 20.00 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.46), residues: 260 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.80 (0.35), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG N 22 HIS 0.008 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 ( 2360) covalent geometry : angle 0.54165 / 0.27 ( 3160) hydrogen bonds : bond 0.02312 / 1.74 ( 28) hydrogen bonds : angle 5.60935 / 3.68 ( 84) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 32 time to evaluate : 0.104 Fit side-chains REVERT: M 35 HIS cc_start: 0.7048 (OUTLIER) cc_final: 0.6684 (t-90) REVERT: P 29 SER cc_start: 0.7725 (OUTLIER) cc_final: 0.7399 (t) REVERT: T 29 SER cc_start: 0.7726 (OUTLIER) cc_final: 0.7439 (t) outliers start: 11 outliers final: 6 residues processed: 37 average time/residue: 0.1667 time to fit residues: 6.6422 Evaluate side-chains 40 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 31 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain M residue 35 HIS Chi-restraints excluded: chain N residue 36 VAL Chi-restraints excluded: chain P residue 29 SER Chi-restraints excluded: chain Q residue 26 LYS Chi-restraints excluded: chain R residue 36 VAL Chi-restraints excluded: chain T residue 29 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 13 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 ASN D 32 ASN E 32 ASN H 35 HIS I 32 ASN M 35 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5316 r_free = 0.5316 target = 0.366010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.5167 r_free = 0.5167 target = 0.295839 restraints weight = 2147.441| |-----------------------------------------------------------------------------| r_work (start): 0.4852 rms_B_bonded: 1.92 r_work: 0.5148 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.5061 rms_B_bonded: 1.76 restraints_weight: 0.2500 r_work (final): 0.5061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6878 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2360 Z= 0.186 Angle : 0.557 6.947 3160 Z= 0.281 Chirality : 0.056 0.135 420 Planarity : 0.002 0.011 380 Dihedral : 5.782 16.597 300 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.21 % Allowed : 20.36 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.46), residues: 260 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.76 (0.35), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 22 HIS 0.010 0.001 HIS M 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.19 ( 2360) covalent geometry : angle 0.55722 / 0.28 ( 3160) hydrogen bonds : bond 0.02508 / 1.90 ( 28) hydrogen bonds : angle 5.68213 / 3.74 ( 84) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 991.46 seconds wall clock time: 17 minutes 57.87 seconds (1077.87 seconds total)