Starting phenix.real_space_refine on Wed Feb 4 17:42:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9tgn_55905/02_2026/9tgn_55905.cif Found real_map, /net/cci-nas-00/data/ceres_data/9tgn_55905/02_2026/9tgn_55905.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9tgn_55905/02_2026/9tgn_55905.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9tgn_55905/02_2026/9tgn_55905.map" model { file = "/net/cci-nas-00/data/ceres_data/9tgn_55905/02_2026/9tgn_55905.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9tgn_55905/02_2026/9tgn_55905.cif" } resolution = 2.55 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= 0.008 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: 6 Type Number sf(0) Gaussians P 47 5.49 5 Mg 8 5.21 5 S 60 5.16 5 C 7326 2.51 5 N 2034 2.21 5 O 2465 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11940 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 849 Classifications: {'peptide': 109} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 105} Chain: "B" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 972 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "C" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 849 Classifications: {'peptide': 109} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 105} Chain: "D" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 972 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "E" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 849 Classifications: {'peptide': 109} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 105} Chain: "F" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 972 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "G" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 849 Classifications: {'peptide': 109} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 105} Chain: "H" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 972 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "I" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 849 Classifications: {'peptide': 109} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 105} Chain: "J" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 972 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "K" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 849 Classifications: {'peptide': 109} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 105} Chain: "L" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 972 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "M" Number of atoms: 244 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 12, 243 Classifications: {'DNA': 12} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 11} Conformer: "B" Number of residues, atoms: 12, 243 Classifications: {'DNA': 12} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 11} bond proxies already assigned to first conformer: 270 Chain: "N" Number of atoms: 247 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 12, 246 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Conformer: "B" Number of residues, atoms: 12, 246 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} bond proxies already assigned to first conformer: 273 Chain: "O" Number of atoms: 247 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 12, 246 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Conformer: "B" Number of residues, atoms: 12, 246 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} bond proxies already assigned to first conformer: 273 Chain: "P" Number of atoms: 246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 246 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "M" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 2.97, per 1000 atoms: 0.25 Number of scatterers: 11940 At special positions: 0 Unit cell: (146.858, 99.924, 105.98, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 60 16.00 P 47 15.00 Mg 8 11.99 O 2465 8.00 N 2034 7.00 C 7326 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 23 " - pdb=" SG CYS A 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 98 " distance=2.04 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 98 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 98 " distance=2.04 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 98 " distance=2.04 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 98 " distance=2.04 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 98 " distance=2.04 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: 0.99 Conformation dependent library (CDL) restraints added in 542.6 milliseconds 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2556 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 35 sheets defined 6.8% alpha, 48.3% beta 24 base pairs and 20 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 79 through 83 removed outlier: 3.505A pdb=" N ASP A 82 " --> pdb=" O GLU A 79 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE A 83 " --> pdb=" O GLN A 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 79 through 83' Processing helix chain 'B' and resid 53 through 57 Processing helix chain 'B' and resid 89 through 93 removed outlier: 3.559A pdb=" N THR B 93 " --> pdb=" O THR B 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 83 removed outlier: 3.585A pdb=" N ASP C 82 " --> pdb=" O GLU C 79 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE C 83 " --> pdb=" O GLN C 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 79 through 83' Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.547A pdb=" N THR D 31 " --> pdb=" O THR D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 57 Processing helix chain 'D' and resid 89 through 93 removed outlier: 3.702A pdb=" N THR D 93 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.557A pdb=" N ASP E 82 " --> pdb=" O GLU E 79 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE E 83 " --> pdb=" O GLN E 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 79 through 83' Processing helix chain 'F' and resid 28 through 32 Processing helix chain 'F' and resid 89 through 93 removed outlier: 4.007A pdb=" N THR F 93 " --> pdb=" O THR F 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 83 removed outlier: 3.911A pdb=" N ILE G 83 " --> pdb=" O GLN G 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.503A pdb=" N THR H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 57 Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.655A pdb=" N ASP I 82 " --> pdb=" O GLU I 79 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE I 83 " --> pdb=" O GLN I 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 79 through 83' Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.564A pdb=" N THR J 31 " --> pdb=" O THR J 28 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN J 32 " --> pdb=" O PHE J 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 28 through 32' Processing helix chain 'J' and resid 53 through 57 Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.616A pdb=" N ILE K 83 " --> pdb=" O GLN K 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 28 through 32 removed outlier: 3.685A pdb=" N ASN L 32 " --> pdb=" O PHE L 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 53 through 57 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 5 removed outlier: 3.516A pdb=" N ASP A 70 " --> pdb=" O SER A 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 13 removed outlier: 3.639A pdb=" N ILE A 48 " --> pdb=" O TRP A 35 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N GLN A 37 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N LEU A 46 " --> pdb=" O GLN A 37 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 10 through 13 removed outlier: 3.971A pdb=" N THR A 97 " --> pdb=" O GLN A 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'B' and resid 11 through 12 removed outlier: 6.089A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 11 through 12 removed outlier: 3.629A pdb=" N TYR B 111 " --> pdb=" O ARG B 100 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 4 through 5 Processing sheet with id=AA8, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.278A pdb=" N GLN C 37 " --> pdb=" O LEU C 46 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N LEU C 46 " --> pdb=" O GLN C 37 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 10 through 13 removed outlier: 3.896A pdb=" N THR C 97 " --> pdb=" O GLN C 90 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.789A pdb=" N MET D 34 " --> pdb=" O ARG D 50 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ARG D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.541A pdb=" N TYR D 111 " --> pdb=" O ARG D 100 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 4 through 5 Processing sheet with id=AB5, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.830A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 10 through 13 removed outlier: 3.950A pdb=" N THR E 97 " --> pdb=" O GLN E 90 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AB8, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.170A pdb=" N GLY F 10 " --> pdb=" O THR F 119 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N MET F 34 " --> pdb=" O ARG F 50 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ARG F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.170A pdb=" N GLY F 10 " --> pdb=" O THR F 119 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR F 111 " --> pdb=" O ARG F 100 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 4 through 5 Processing sheet with id=AC2, first strand: chain 'G' and resid 10 through 13 Processing sheet with id=AC3, first strand: chain 'G' and resid 53 through 54 removed outlier: 5.568A pdb=" N LEU G 46 " --> pdb=" O GLN G 37 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N GLN G 37 " --> pdb=" O LEU G 46 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE G 48 " --> pdb=" O TRP G 35 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N THR G 97 " --> pdb=" O GLN G 90 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AC5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.085A pdb=" N GLY H 10 " --> pdb=" O THR H 119 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N MET H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ARG H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.085A pdb=" N GLY H 10 " --> pdb=" O THR H 119 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TYR H 111 " --> pdb=" O ARG H 100 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 4 through 5 removed outlier: 3.604A pdb=" N ASP I 70 " --> pdb=" O SER I 67 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 10 through 13 removed outlier: 3.554A pdb=" N ILE I 48 " --> pdb=" O TRP I 35 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N GLN I 37 " --> pdb=" O LEU I 46 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N LEU I 46 " --> pdb=" O GLN I 37 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AD1, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.474A pdb=" N GLY J 10 " --> pdb=" O THR J 119 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N MET J 34 " --> pdb=" O ARG J 50 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ARG J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.474A pdb=" N GLY J 10 " --> pdb=" O THR J 119 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR J 111 " --> pdb=" O ARG J 100 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 4 through 5 Processing sheet with id=AD4, first strand: chain 'K' and resid 10 through 13 removed outlier: 3.595A pdb=" N ILE K 48 " --> pdb=" O TRP K 35 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N GLN K 37 " --> pdb=" O LEU K 46 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N LEU K 46 " --> pdb=" O GLN K 37 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 10 through 13 removed outlier: 3.988A pdb=" N THR K 97 " --> pdb=" O GLN K 90 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 3 through 7 removed outlier: 5.750A pdb=" N GLY L 16 " --> pdb=" O ASN L 87 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 11 through 12 removed outlier: 5.954A pdb=" N ARG L 38 " --> pdb=" O TRP L 47 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N TRP L 47 " --> pdb=" O ARG L 38 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 11 through 12 removed outlier: 6.463A pdb=" N ARG L 100 " --> pdb=" O ASP L 110 " (cutoff:3.500A) 445 hydrogen bonds defined for protein. 1068 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 72 hydrogen bonds 144 hydrogen bond angles 0 basepair planarities 24 basepair parallelities 20 stacking parallelities Total time for adding SS restraints: 1.87 Time building geometry restraints manager: 1.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2075 1.32 - 1.45: 3760 1.45 - 1.57: 6227 1.57 - 1.70: 93 1.70 - 1.82: 96 Bond restraints: 12251 Sorted by residual: bond pdb=" CG PRO D 41 " pdb=" CD PRO D 41 " ideal model delta sigma weight residual 1.503 1.200 0.303 3.40e-02 8.65e+02 7.94e+01 bond pdb=" N PRO D 41 " pdb=" CD PRO D 41 " ideal model delta sigma weight residual 1.473 1.514 -0.041 1.40e-02 5.10e+03 8.53e+00 bond pdb=" CA PRO D 41 " pdb=" CB PRO D 41 " ideal model delta sigma weight residual 1.532 1.499 0.034 1.34e-02 5.57e+03 6.34e+00 bond pdb=" N PRO D 41 " pdb=" CA PRO D 41 " ideal model delta sigma weight residual 1.471 1.498 -0.028 1.27e-02 6.20e+03 4.72e+00 bond pdb=" P DC M 9 " pdb=" O5' DC M 9 " ideal model delta sigma weight residual 1.600 1.567 0.033 2.00e-02 2.50e+03 2.64e+00 ... (remaining 12246 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.68: 16766 4.68 - 9.36: 23 9.36 - 14.04: 1 14.04 - 18.72: 0 18.72 - 23.40: 2 Bond angle restraints: 16792 Sorted by residual: angle pdb=" N PRO D 41 " pdb=" CD PRO D 41 " pdb=" CG PRO D 41 " ideal model delta sigma weight residual 103.20 82.34 20.86 1.50e+00 4.44e-01 1.93e+02 angle pdb=" CA PRO D 41 " pdb=" CB PRO D 41 " pdb=" CG PRO D 41 " ideal model delta sigma weight residual 104.50 81.10 23.40 1.90e+00 2.77e-01 1.52e+02 angle pdb=" N PRO D 41 " pdb=" CA PRO D 41 " pdb=" CB PRO D 41 " ideal model delta sigma weight residual 103.17 96.90 6.27 8.90e-01 1.26e+00 4.96e+01 angle pdb=" CA PRO D 41 " pdb=" N PRO D 41 " pdb=" CD PRO D 41 " ideal model delta sigma weight residual 112.00 104.98 7.02 1.40e+00 5.10e-01 2.52e+01 angle pdb=" C TYR A 50 " pdb=" N THR A 51 " pdb=" CA THR A 51 " ideal model delta sigma weight residual 121.54 131.00 -9.46 1.91e+00 2.74e-01 2.45e+01 ... (remaining 16787 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.39: 6512 32.39 - 64.78: 535 64.78 - 97.18: 21 97.18 - 129.57: 4 129.57 - 161.96: 1 Dihedral angle restraints: 7073 sinusoidal: 3035 harmonic: 4038 Sorted by residual: dihedral pdb=" C4' DC N 1 " pdb=" C3' DC N 1 " pdb=" O3' DC N 1 " pdb=" P DG N 2 " ideal model delta sinusoidal sigma weight residual 220.00 58.04 161.96 1 3.50e+01 8.16e-04 1.53e+01 dihedral pdb=" CA TYR F 102 " pdb=" C TYR F 102 " pdb=" N VAL F 103 " pdb=" CA VAL F 103 " ideal model delta harmonic sigma weight residual -180.00 -160.76 -19.24 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" N PRO D 41 " pdb=" CG PRO D 41 " pdb=" CD PRO D 41 " pdb=" CB PRO D 41 " ideal model delta sinusoidal sigma weight residual 30.00 76.98 -46.98 1 1.50e+01 4.44e-03 1.36e+01 ... (remaining 7070 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1200 0.037 - 0.073: 436 0.073 - 0.110: 162 0.110 - 0.147: 43 0.147 - 0.184: 3 Chirality restraints: 1844 Sorted by residual: chirality pdb=" CA THR A 51 " pdb=" N THR A 51 " pdb=" C THR A 51 " pdb=" CB THR A 51 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.18 2.00e-01 2.50e+01 8.44e-01 chirality pdb=" CA VAL L 37 " pdb=" N VAL L 37 " pdb=" C VAL L 37 " pdb=" CB VAL L 37 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.57e-01 chirality pdb=" CA VAL D 37 " pdb=" N VAL D 37 " pdb=" C VAL D 37 " pdb=" CB VAL D 37 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.48e-01 ... (remaining 1841 not shown) Planarity restraints: 1968 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU K 81 " -0.011 2.00e-02 2.50e+03 2.13e-02 4.52e+00 pdb=" C GLU K 81 " 0.037 2.00e-02 2.50e+03 pdb=" O GLU K 81 " -0.014 2.00e-02 2.50e+03 pdb=" N ASP K 82 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 51 " -0.010 2.00e-02 2.50e+03 1.94e-02 3.76e+00 pdb=" C THR C 51 " 0.034 2.00e-02 2.50e+03 pdb=" O THR C 51 " -0.012 2.00e-02 2.50e+03 pdb=" N SER C 52 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR E 51 " -0.009 2.00e-02 2.50e+03 1.74e-02 3.04e+00 pdb=" C THR E 51 " 0.030 2.00e-02 2.50e+03 pdb=" O THR E 51 " -0.011 2.00e-02 2.50e+03 pdb=" N SER E 52 " -0.010 2.00e-02 2.50e+03 ... (remaining 1965 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 767 2.73 - 3.28: 9951 3.28 - 3.82: 18593 3.82 - 4.36: 24908 4.36 - 4.90: 42590 Nonbonded interactions: 96809 Sorted by model distance: nonbonded pdb=" OG SER I 14 " pdb=" OD1 ASP I 17 " model vdw 2.192 3.040 nonbonded pdb=" N GLU J 91 " pdb=" OE1 GLU J 91 " model vdw 2.269 3.120 nonbonded pdb=" NH1 ARG I 61 " pdb=" OD2 ASP I 82 " model vdw 2.276 3.120 nonbonded pdb=" NH1 ARG K 61 " pdb=" OD2 ASP K 82 " model vdw 2.304 3.120 nonbonded pdb=" O THR C 8 " pdb=" OG1 THR C 102 " model vdw 2.318 3.040 ... (remaining 96804 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 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' } ncs_group { reference = (chain 'M' and (resid 1 or resid 3 through 5 or resid 7 through 101)) selection = (chain 'N' and ((resid 1 and (name O5' or name C5' or name C4' or name O4' or na \ me C3' or name O3' or name C2' or name C1' or name N1 or name C2 or name O2 or n \ ame N3 or name C4 or name N4 or name C5 or name C6 )) or resid 3 through 5 or re \ sid 7 through 101)) selection = (chain 'O' and ((resid 1 and (name O5' or name C5' or name C4' or name O4' or na \ me C3' or name O3' or name C2' or name C1' or name N1 or name C2 or name O2 or n \ ame N3 or name C4 or name N4 or name C5 or name C6 )) or resid 3 through 5 or re \ sid 7 through 101)) selection = (chain 'P' and ((resid 1 and (name O5' or name C5' or name C4' or name O4' or na \ me C3' or name O3' or name C2' or name C1' or name N1 or name C2 or name O2 or n \ ame N3 or name C4 or name N4 or name C5 or name C6 )) or resid 3 through 5 or re \ sid 7 through 101)) } 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=0.37 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: 13.870 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: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.060 Process input model: 12.630 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 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 0.303 12263 Z= 0.226 Angle : 0.694 23.402 16816 Z= 0.389 Chirality : 0.045 0.184 1844 Planarity : 0.004 0.034 1968 Dihedral : 20.085 161.959 4481 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 5.28 % Allowed : 26.55 % Favored : 68.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: -0.34 (0.22), residues: 1368 helix: None (None), residues: 0 sheet: 0.08 (0.19), residues: 690 loop : -0.45 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 24 TYR 0.011 0.002 TYR B 111 PHE 0.013 0.002 PHE K 87 TRP 0.009 0.001 TRP L 47 HIS 0.001 0.000 HIS I 55 Details of bonding type rmsd covalent geometry : bond 0.00548 (12251) covalent geometry : angle 0.69094 (16792) SS BOND : bond 0.00828 ( 12) SS BOND : angle 1.77238 ( 24) hydrogen bonds : bond 0.11606 ( 472) hydrogen bonds : angle 5.71097 ( 1212) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 185 time to evaluate : 0.364 Fit side-chains outliers start: 63 outliers final: 59 residues processed: 243 average time/residue: 0.4962 time to fit residues: 131.5463 Evaluate side-chains 243 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 184 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 41 PRO Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain E residue 1 ASP Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 102 TYR Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 100 ARG Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 43 THR Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 102 TYR Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 41 ASP Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain L residue 73 SER Chi-restraints excluded: chain L residue 102 TYR Chi-restraints excluded: chain L residue 120 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.135004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.098879 restraints weight = 12579.050| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.95 r_work: 0.3202 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3086 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3086 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.0473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 12263 Z= 0.300 Angle : 0.724 9.838 16816 Z= 0.396 Chirality : 0.050 0.164 1844 Planarity : 0.004 0.036 1968 Dihedral : 17.429 161.206 2111 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 7.62 % Allowed : 22.86 % Favored : 69.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: -0.47 (0.21), residues: 1368 helix: None (None), residues: 0 sheet: 0.01 (0.19), residues: 708 loop : -0.56 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 24 TYR 0.014 0.003 TYR B 111 PHE 0.016 0.003 PHE D 29 TRP 0.009 0.002 TRP H 112 HIS 0.001 0.000 HIS I 55 Details of bonding type rmsd covalent geometry : bond 0.00697 (12251) covalent geometry : angle 0.71991 (16792) SS BOND : bond 0.00985 ( 12) SS BOND : angle 2.07009 ( 24) hydrogen bonds : bond 0.04815 ( 472) hydrogen bonds : angle 4.85909 ( 1212) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 186 time to evaluate : 0.452 Fit side-chains REVERT: A 18 ARG cc_start: 0.7685 (OUTLIER) cc_final: 0.6612 (ttm170) REVERT: D 46 GLU cc_start: 0.8855 (OUTLIER) cc_final: 0.8624 (tt0) REVERT: D 89 LYS cc_start: 0.7650 (OUTLIER) cc_final: 0.7372 (mttm) REVERT: G 94 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8272 (mp) REVERT: H 100 ARG cc_start: 0.9165 (OUTLIER) cc_final: 0.7648 (ttm170) REVERT: I 24 ARG cc_start: 0.7548 (OUTLIER) cc_final: 0.7002 (ttp80) REVERT: J 18 LEU cc_start: 0.7581 (OUTLIER) cc_final: 0.7024 (tt) REVERT: J 80 MET cc_start: 0.8144 (mmm) cc_final: 0.7891 (tpp) REVERT: K 73 LEU cc_start: 0.7664 (OUTLIER) cc_final: 0.6948 (tp) REVERT: K 79 GLU cc_start: 0.6203 (OUTLIER) cc_final: 0.4538 (mp0) REVERT: K 103 LYS cc_start: 0.7784 (OUTLIER) cc_final: 0.7015 (tptm) REVERT: L 85 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.8188 (mtp) outliers start: 91 outliers final: 51 residues processed: 253 average time/residue: 0.4984 time to fit residues: 137.4777 Evaluate side-chains 244 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 182 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 89 LYS Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 94 LEU Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 85 MET Chi-restraints excluded: chain H residue 100 ARG Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 24 ARG Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 43 THR Chi-restraints excluded: chain I residue 93 THR Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 43 LYS Chi-restraints excluded: chain J residue 102 TYR Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain K residue 9 SER Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 41 ASP Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 103 LYS Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain L residue 73 SER Chi-restraints excluded: chain L residue 85 MET Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 102 TYR Chi-restraints excluded: chain L residue 110 ASP Chi-restraints excluded: chain L residue 120 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 86 optimal weight: 0.6980 chunk 96 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 121 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 93 optimal weight: 0.4980 chunk 105 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 30 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.138236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.102043 restraints weight = 12545.619| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.97 r_work: 0.3241 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3131 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3131 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.0615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12263 Z= 0.135 Angle : 0.554 8.318 16816 Z= 0.311 Chirality : 0.042 0.146 1844 Planarity : 0.003 0.033 1968 Dihedral : 16.811 162.239 2072 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 5.28 % Allowed : 24.04 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: -0.28 (0.22), residues: 1368 helix: None (None), residues: 0 sheet: 0.19 (0.19), residues: 690 loop : -0.49 (0.22), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 24 TYR 0.008 0.001 TYR C 86 PHE 0.014 0.002 PHE B 29 TRP 0.009 0.001 TRP H 47 HIS 0.001 0.000 HIS I 55 Details of bonding type rmsd covalent geometry : bond 0.00297 (12251) covalent geometry : angle 0.55275 (16792) SS BOND : bond 0.00652 ( 12) SS BOND : angle 1.14377 ( 24) hydrogen bonds : bond 0.03163 ( 472) hydrogen bonds : angle 4.48061 ( 1212) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 191 time to evaluate : 0.461 Fit side-chains REVERT: C 43 THR cc_start: 0.8619 (m) cc_final: 0.8359 (p) REVERT: D 95 MET cc_start: 0.8874 (OUTLIER) cc_final: 0.8587 (tpp) REVERT: F 110 ASP cc_start: 0.8517 (p0) cc_final: 0.8300 (p0) REVERT: G 94 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8242 (mp) REVERT: H 57 ASN cc_start: 0.8238 (OUTLIER) cc_final: 0.7910 (m-40) REVERT: H 100 ARG cc_start: 0.9091 (OUTLIER) cc_final: 0.7369 (ttm170) REVERT: I 24 ARG cc_start: 0.7345 (OUTLIER) cc_final: 0.6788 (ttp80) REVERT: J 80 MET cc_start: 0.8135 (mmm) cc_final: 0.7865 (tpp) REVERT: L 85 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.8173 (mtp) outliers start: 63 outliers final: 35 residues processed: 236 average time/residue: 0.4919 time to fit residues: 126.1805 Evaluate side-chains 223 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 182 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 41 ASP Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 95 MET Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 102 TYR Chi-restraints excluded: chain G residue 94 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 57 ASN Chi-restraints excluded: chain H residue 85 MET Chi-restraints excluded: chain H residue 100 ARG Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain I residue 24 ARG Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 83 ILE Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 102 TYR Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 41 ASP Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 73 SER Chi-restraints excluded: chain L residue 85 MET Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 102 TYR Chi-restraints excluded: chain L residue 120 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 1 optimal weight: 8.9990 chunk 23 optimal weight: 0.8980 chunk 44 optimal weight: 8.9990 chunk 124 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 117 optimal weight: 4.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.135861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.099863 restraints weight = 12585.141| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.94 r_work: 0.3207 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3097 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3097 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.0576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 12263 Z= 0.249 Angle : 0.674 10.285 16816 Z= 0.371 Chirality : 0.047 0.157 1844 Planarity : 0.004 0.035 1968 Dihedral : 16.956 162.191 2056 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 6.78 % Allowed : 23.12 % Favored : 70.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: -0.36 (0.21), residues: 1368 helix: None (None), residues: 0 sheet: 0.12 (0.19), residues: 690 loop : -0.53 (0.22), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 24 TYR 0.014 0.002 TYR F 111 PHE 0.015 0.002 PHE K 87 TRP 0.009 0.001 TRP H 47 HIS 0.001 0.000 HIS I 55 Details of bonding type rmsd covalent geometry : bond 0.00576 (12251) covalent geometry : angle 0.67070 (16792) SS BOND : bond 0.00893 ( 12) SS BOND : angle 1.77106 ( 24) hydrogen bonds : bond 0.04249 ( 472) hydrogen bonds : angle 4.63098 ( 1212) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 186 time to evaluate : 0.385 Fit side-chains REVERT: D 46 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8615 (tt0) REVERT: D 89 LYS cc_start: 0.7650 (OUTLIER) cc_final: 0.7428 (mttm) REVERT: D 95 MET cc_start: 0.8943 (OUTLIER) cc_final: 0.8589 (tpp) REVERT: G 33 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8556 (tm) REVERT: G 61 ARG cc_start: 0.7844 (ptt-90) cc_final: 0.7597 (ptt90) REVERT: G 94 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8260 (mp) REVERT: H 100 ARG cc_start: 0.9122 (OUTLIER) cc_final: 0.7390 (ttm170) REVERT: I 24 ARG cc_start: 0.7528 (OUTLIER) cc_final: 0.6967 (ttp80) REVERT: J 80 MET cc_start: 0.8168 (mmm) cc_final: 0.7941 (tpp) REVERT: K 73 LEU cc_start: 0.7598 (OUTLIER) cc_final: 0.6872 (tp) REVERT: K 79 GLU cc_start: 0.6080 (OUTLIER) cc_final: 0.4392 (mp0) REVERT: L 46 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8313 (tt0) REVERT: L 85 MET cc_start: 0.8433 (OUTLIER) cc_final: 0.8199 (mtp) REVERT: L 91 GLU cc_start: 0.6352 (OUTLIER) cc_final: 0.6088 (pm20) outliers start: 81 outliers final: 44 residues processed: 242 average time/residue: 0.5261 time to fit residues: 137.7677 Evaluate side-chains 242 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 186 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 41 ASP Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 89 LYS Chi-restraints excluded: chain D residue 95 MET Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 94 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 100 ARG Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 24 ARG Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 102 TYR Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 41 ASP Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 46 GLU Chi-restraints excluded: chain L residue 73 SER Chi-restraints excluded: chain L residue 85 MET Chi-restraints excluded: chain L residue 91 GLU Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 102 TYR Chi-restraints excluded: chain L residue 120 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 16 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.135577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.099290 restraints weight = 12580.177| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.96 r_work: 0.3201 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3089 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3089 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.0637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 12263 Z= 0.252 Angle : 0.677 9.837 16816 Z= 0.373 Chirality : 0.047 0.166 1844 Planarity : 0.004 0.034 1968 Dihedral : 16.961 162.431 2056 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 7.37 % Allowed : 23.70 % Favored : 68.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: -0.39 (0.21), residues: 1368 helix: None (None), residues: 0 sheet: 0.11 (0.19), residues: 690 loop : -0.55 (0.22), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 24 TYR 0.013 0.002 TYR H 97 PHE 0.015 0.002 PHE K 87 TRP 0.009 0.002 TRP H 47 HIS 0.001 0.000 HIS I 55 Details of bonding type rmsd covalent geometry : bond 0.00582 (12251) covalent geometry : angle 0.67398 (16792) SS BOND : bond 0.00911 ( 12) SS BOND : angle 1.79430 ( 24) hydrogen bonds : bond 0.04254 ( 472) hydrogen bonds : angle 4.63306 ( 1212) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 184 time to evaluate : 0.317 Fit side-chains REVERT: A 18 ARG cc_start: 0.7631 (OUTLIER) cc_final: 0.6586 (ttm170) REVERT: A 103 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7876 (ttmt) REVERT: D 46 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.8595 (tt0) REVERT: D 89 LYS cc_start: 0.7570 (OUTLIER) cc_final: 0.7325 (mttm) REVERT: D 95 MET cc_start: 0.8885 (OUTLIER) cc_final: 0.8540 (tpp) REVERT: G 33 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8546 (tm) REVERT: G 94 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8215 (mp) REVERT: H 57 ASN cc_start: 0.8237 (m110) cc_final: 0.7928 (m-40) REVERT: H 100 ARG cc_start: 0.9080 (OUTLIER) cc_final: 0.7318 (ttm170) REVERT: I 24 ARG cc_start: 0.7469 (OUTLIER) cc_final: 0.6907 (ttp80) REVERT: K 73 LEU cc_start: 0.7495 (OUTLIER) cc_final: 0.6776 (tp) REVERT: K 79 GLU cc_start: 0.5972 (OUTLIER) cc_final: 0.4318 (mp0) REVERT: L 46 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8280 (tt0) REVERT: L 85 MET cc_start: 0.8361 (OUTLIER) cc_final: 0.8119 (mtp) REVERT: L 91 GLU cc_start: 0.6324 (OUTLIER) cc_final: 0.6020 (pm20) outliers start: 88 outliers final: 52 residues processed: 248 average time/residue: 0.4678 time to fit residues: 125.7033 Evaluate side-chains 248 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 182 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 41 ASP Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 89 LYS Chi-restraints excluded: chain D residue 95 MET Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 94 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 85 MET Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 100 ARG Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 24 ARG Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 77 TYR Chi-restraints excluded: chain I residue 93 THR Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 102 TYR Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 41 ASP Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 46 GLU Chi-restraints excluded: chain L residue 73 SER Chi-restraints excluded: chain L residue 85 MET Chi-restraints excluded: chain L residue 91 GLU Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 102 TYR Chi-restraints excluded: chain L residue 120 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 47 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 76 optimal weight: 8.9990 chunk 38 optimal weight: 0.3980 chunk 104 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 102 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.137726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.100892 restraints weight = 12403.127| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.00 r_work: 0.3203 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3098 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3098 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.0722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12263 Z= 0.143 Angle : 0.565 9.067 16816 Z= 0.316 Chirality : 0.042 0.147 1844 Planarity : 0.003 0.033 1968 Dihedral : 16.649 163.749 2055 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 5.36 % Allowed : 25.63 % Favored : 69.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: -0.33 (0.22), residues: 1368 helix: None (None), residues: 0 sheet: 0.04 (0.18), residues: 726 loop : -0.40 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 24 TYR 0.009 0.001 TYR H 97 PHE 0.015 0.002 PHE B 29 TRP 0.010 0.001 TRP H 47 HIS 0.001 0.000 HIS C 55 Details of bonding type rmsd covalent geometry : bond 0.00318 (12251) covalent geometry : angle 0.56310 (16792) SS BOND : bond 0.00664 ( 12) SS BOND : angle 1.22007 ( 24) hydrogen bonds : bond 0.03175 ( 472) hydrogen bonds : angle 4.39450 ( 1212) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 186 time to evaluate : 0.515 Fit side-chains REVERT: D 95 MET cc_start: 0.8918 (OUTLIER) cc_final: 0.8591 (tpp) REVERT: G 33 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8464 (tm) REVERT: G 61 ARG cc_start: 0.7842 (ptt-90) cc_final: 0.7603 (ptt90) REVERT: G 94 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8282 (mp) REVERT: H 57 ASN cc_start: 0.8240 (m110) cc_final: 0.7949 (m-40) REVERT: H 100 ARG cc_start: 0.9075 (OUTLIER) cc_final: 0.7185 (ttm170) REVERT: I 24 ARG cc_start: 0.7410 (OUTLIER) cc_final: 0.6846 (ttp80) REVERT: K 18 ARG cc_start: 0.6547 (OUTLIER) cc_final: 0.5785 (ptm160) REVERT: K 73 LEU cc_start: 0.7575 (OUTLIER) cc_final: 0.6886 (tp) REVERT: K 79 GLU cc_start: 0.5861 (OUTLIER) cc_final: 0.4156 (mp0) REVERT: L 46 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8329 (tt0) REVERT: L 85 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.8189 (mtp) REVERT: L 91 GLU cc_start: 0.6388 (OUTLIER) cc_final: 0.6116 (pm20) outliers start: 64 outliers final: 35 residues processed: 232 average time/residue: 0.5420 time to fit residues: 136.0428 Evaluate side-chains 229 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 183 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 41 ASP Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 95 MET Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 102 TYR Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 94 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 85 MET Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 100 ARG Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain I residue 24 ARG Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 102 TYR Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 41 ASP Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 46 GLU Chi-restraints excluded: chain L residue 85 MET Chi-restraints excluded: chain L residue 91 GLU Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 102 TYR Chi-restraints excluded: chain L residue 110 ASP Chi-restraints excluded: chain L residue 120 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 12 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 67 optimal weight: 10.0000 chunk 86 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.134926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.097917 restraints weight = 12496.712| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.00 r_work: 0.3162 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3060 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3060 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.0703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 12263 Z= 0.270 Angle : 0.698 8.920 16816 Z= 0.383 Chirality : 0.048 0.159 1844 Planarity : 0.004 0.036 1968 Dihedral : 16.924 163.358 2053 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 6.53 % Allowed : 24.79 % Favored : 68.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: -0.45 (0.21), residues: 1368 helix: None (None), residues: 0 sheet: 0.01 (0.18), residues: 720 loop : -0.55 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 24 TYR 0.014 0.002 TYR H 97 PHE 0.016 0.002 PHE K 87 TRP 0.009 0.002 TRP H 112 HIS 0.001 0.000 HIS E 55 Details of bonding type rmsd covalent geometry : bond 0.00628 (12251) covalent geometry : angle 0.69462 (16792) SS BOND : bond 0.00937 ( 12) SS BOND : angle 1.95009 ( 24) hydrogen bonds : bond 0.04404 ( 472) hydrogen bonds : angle 4.63470 ( 1212) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 182 time to evaluate : 0.442 Fit side-chains REVERT: A 18 ARG cc_start: 0.7662 (OUTLIER) cc_final: 0.6619 (ttm170) REVERT: A 103 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.7980 (ttmt) REVERT: D 46 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.8661 (tt0) REVERT: D 89 LYS cc_start: 0.7661 (OUTLIER) cc_final: 0.7424 (mttm) REVERT: E 33 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8121 (tm) REVERT: G 33 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8596 (tm) REVERT: G 94 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8279 (mp) REVERT: H 57 ASN cc_start: 0.8244 (m110) cc_final: 0.7950 (m-40) REVERT: H 100 ARG cc_start: 0.9115 (OUTLIER) cc_final: 0.7303 (ttm170) REVERT: I 24 ARG cc_start: 0.7580 (OUTLIER) cc_final: 0.7035 (ttp80) REVERT: K 73 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.6901 (tp) REVERT: K 79 GLU cc_start: 0.6129 (OUTLIER) cc_final: 0.4428 (mp0) REVERT: L 46 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8332 (tt0) REVERT: L 85 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.8188 (mtp) REVERT: L 91 GLU cc_start: 0.6368 (OUTLIER) cc_final: 0.6111 (pm20) outliers start: 78 outliers final: 49 residues processed: 234 average time/residue: 0.5471 time to fit residues: 138.6048 Evaluate side-chains 245 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 182 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 89 LYS Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 94 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 100 ARG Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 24 ARG Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 77 TYR Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 102 TYR Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 41 ASP Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 46 GLU Chi-restraints excluded: chain L residue 85 MET Chi-restraints excluded: chain L residue 91 GLU Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 102 TYR Chi-restraints excluded: chain L residue 110 ASP Chi-restraints excluded: chain L residue 120 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 38 optimal weight: 0.1980 chunk 82 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 110 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 128 optimal weight: 4.9990 chunk 121 optimal weight: 0.3980 chunk 12 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.135625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.098655 restraints weight = 12413.785| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.00 r_work: 0.3173 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3065 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3065 r_free = 0.3065 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3065 r_free = 0.3065 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3065 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.0703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 12263 Z= 0.225 Angle : 0.657 8.708 16816 Z= 0.362 Chirality : 0.046 0.149 1844 Planarity : 0.004 0.035 1968 Dihedral : 16.863 163.683 2053 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 6.37 % Allowed : 25.29 % Favored : 68.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: -0.40 (0.21), residues: 1368 helix: None (None), residues: 0 sheet: 0.10 (0.19), residues: 690 loop : -0.57 (0.22), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 24 TYR 0.012 0.002 TYR B 111 PHE 0.015 0.002 PHE B 29 TRP 0.009 0.001 TRP H 47 HIS 0.001 0.000 HIS I 55 Details of bonding type rmsd covalent geometry : bond 0.00520 (12251) covalent geometry : angle 0.65445 (16792) SS BOND : bond 0.00859 ( 12) SS BOND : angle 1.76821 ( 24) hydrogen bonds : bond 0.03980 ( 472) hydrogen bonds : angle 4.57782 ( 1212) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 185 time to evaluate : 0.510 Fit side-chains REVERT: A 18 ARG cc_start: 0.7651 (OUTLIER) cc_final: 0.6619 (ttm170) REVERT: A 103 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.7962 (ttmt) REVERT: D 89 LYS cc_start: 0.7649 (OUTLIER) cc_final: 0.7411 (mttm) REVERT: E 3 GLN cc_start: 0.7898 (OUTLIER) cc_final: 0.7340 (mt0) REVERT: E 33 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8103 (tm) REVERT: F 3 GLN cc_start: 0.8351 (mm-40) cc_final: 0.8093 (mm-40) REVERT: G 33 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8566 (tm) REVERT: G 94 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8284 (mp) REVERT: H 57 ASN cc_start: 0.8236 (m110) cc_final: 0.7934 (m-40) REVERT: H 100 ARG cc_start: 0.9103 (OUTLIER) cc_final: 0.7263 (ttm170) REVERT: I 24 ARG cc_start: 0.7556 (OUTLIER) cc_final: 0.6939 (ttp80) REVERT: K 18 ARG cc_start: 0.6569 (OUTLIER) cc_final: 0.5607 (ptm160) REVERT: K 73 LEU cc_start: 0.7634 (OUTLIER) cc_final: 0.6896 (tp) REVERT: K 79 GLU cc_start: 0.6034 (OUTLIER) cc_final: 0.4362 (mp0) REVERT: L 46 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8343 (tt0) REVERT: L 85 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.8190 (mtp) REVERT: L 91 GLU cc_start: 0.6365 (OUTLIER) cc_final: 0.6088 (pm20) outliers start: 76 outliers final: 49 residues processed: 240 average time/residue: 0.5585 time to fit residues: 145.3430 Evaluate side-chains 246 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 182 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain C residue 1 ASP Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 41 ASP Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 89 LYS Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 94 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 100 ARG Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 24 ARG Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 77 TYR Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 43 LYS Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 102 TYR Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 41 ASP Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 46 GLU Chi-restraints excluded: chain L residue 73 SER Chi-restraints excluded: chain L residue 85 MET Chi-restraints excluded: chain L residue 91 GLU Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 102 TYR Chi-restraints excluded: chain L residue 120 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 117 optimal weight: 4.9990 chunk 99 optimal weight: 0.0980 chunk 74 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.135417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.098433 restraints weight = 12400.748| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.99 r_work: 0.3170 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3062 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3062 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.0737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 12263 Z= 0.236 Angle : 0.670 8.578 16816 Z= 0.369 Chirality : 0.047 0.164 1844 Planarity : 0.004 0.035 1968 Dihedral : 16.898 163.856 2053 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 5.70 % Allowed : 26.05 % Favored : 68.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: -0.42 (0.21), residues: 1368 helix: None (None), residues: 0 sheet: 0.09 (0.19), residues: 690 loop : -0.58 (0.22), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 24 TYR 0.013 0.002 TYR H 97 PHE 0.014 0.002 PHE K 87 TRP 0.009 0.001 TRP H 47 HIS 0.001 0.000 HIS I 55 Details of bonding type rmsd covalent geometry : bond 0.00545 (12251) covalent geometry : angle 0.66660 (16792) SS BOND : bond 0.00904 ( 12) SS BOND : angle 1.85416 ( 24) hydrogen bonds : bond 0.04099 ( 472) hydrogen bonds : angle 4.57834 ( 1212) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 184 time to evaluate : 0.365 Fit side-chains REVERT: A 18 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.6625 (ttm170) REVERT: A 103 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.7975 (ttmt) REVERT: D 89 LYS cc_start: 0.7655 (OUTLIER) cc_final: 0.7422 (mttm) REVERT: E 3 GLN cc_start: 0.7923 (OUTLIER) cc_final: 0.7357 (mt0) REVERT: E 33 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8119 (tm) REVERT: E 104 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.7883 (mp) REVERT: G 33 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8559 (tm) REVERT: G 94 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8289 (mp) REVERT: H 57 ASN cc_start: 0.8242 (m110) cc_final: 0.7941 (m-40) REVERT: H 100 ARG cc_start: 0.9111 (OUTLIER) cc_final: 0.7271 (ttm170) REVERT: I 24 ARG cc_start: 0.7544 (OUTLIER) cc_final: 0.6990 (ttp80) REVERT: K 18 ARG cc_start: 0.6583 (OUTLIER) cc_final: 0.5749 (ptm160) REVERT: K 73 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.6901 (tp) REVERT: K 79 GLU cc_start: 0.6069 (OUTLIER) cc_final: 0.4406 (mp0) REVERT: L 46 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8337 (tt0) REVERT: L 85 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.8180 (mtp) REVERT: L 91 GLU cc_start: 0.6385 (OUTLIER) cc_final: 0.6117 (pm20) outliers start: 68 outliers final: 50 residues processed: 233 average time/residue: 0.5797 time to fit residues: 146.1740 Evaluate side-chains 249 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 183 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain C residue 1 ASP Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 41 ASP Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 89 LYS Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 94 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 100 ARG Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 24 ARG Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 77 TYR Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 43 LYS Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 102 TYR Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 41 ASP Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 46 GLU Chi-restraints excluded: chain L residue 73 SER Chi-restraints excluded: chain L residue 85 MET Chi-restraints excluded: chain L residue 91 GLU Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 102 TYR Chi-restraints excluded: chain L residue 120 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 129 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.136063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.099078 restraints weight = 12457.303| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.00 r_work: 0.3177 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3070 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3070 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.0724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 12263 Z= 0.205 Angle : 0.642 8.525 16816 Z= 0.355 Chirality : 0.045 0.151 1844 Planarity : 0.004 0.035 1968 Dihedral : 16.828 164.153 2053 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 5.70 % Allowed : 26.13 % Favored : 68.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: -0.41 (0.21), residues: 1368 helix: None (None), residues: 0 sheet: 0.09 (0.19), residues: 690 loop : -0.57 (0.22), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 24 TYR 0.011 0.002 TYR B 111 PHE 0.015 0.002 PHE B 29 TRP 0.010 0.001 TRP H 47 HIS 0.001 0.000 HIS I 55 Details of bonding type rmsd covalent geometry : bond 0.00472 (12251) covalent geometry : angle 0.63921 (16792) SS BOND : bond 0.00834 ( 12) SS BOND : angle 1.75921 ( 24) hydrogen bonds : bond 0.03793 ( 472) hydrogen bonds : angle 4.50009 ( 1212) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 182 time to evaluate : 0.415 Fit side-chains REVERT: A 18 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.6622 (ttm170) REVERT: D 89 LYS cc_start: 0.7644 (OUTLIER) cc_final: 0.7404 (mttm) REVERT: E 3 GLN cc_start: 0.7910 (OUTLIER) cc_final: 0.7342 (mt0) REVERT: E 33 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8089 (tm) REVERT: G 33 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8528 (tm) REVERT: G 94 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8289 (mp) REVERT: H 57 ASN cc_start: 0.8233 (m110) cc_final: 0.7931 (m-40) REVERT: H 100 ARG cc_start: 0.9078 (OUTLIER) cc_final: 0.7195 (ttm170) REVERT: I 24 ARG cc_start: 0.7504 (OUTLIER) cc_final: 0.6910 (ttp80) REVERT: K 18 ARG cc_start: 0.6556 (OUTLIER) cc_final: 0.5627 (ptm160) REVERT: K 73 LEU cc_start: 0.7624 (OUTLIER) cc_final: 0.6900 (tp) REVERT: K 79 GLU cc_start: 0.6014 (OUTLIER) cc_final: 0.4341 (mp0) REVERT: L 46 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8336 (tt0) REVERT: L 85 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.8178 (mtp) REVERT: L 91 GLU cc_start: 0.6384 (OUTLIER) cc_final: 0.6101 (pm20) outliers start: 68 outliers final: 48 residues processed: 229 average time/residue: 0.5091 time to fit residues: 126.4974 Evaluate side-chains 243 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 181 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain C residue 1 ASP Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 89 LYS Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 94 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 100 ARG Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 24 ARG Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 77 TYR Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 102 TYR Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 41 ASP Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 46 GLU Chi-restraints excluded: chain L residue 73 SER Chi-restraints excluded: chain L residue 85 MET Chi-restraints excluded: chain L residue 91 GLU Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 102 TYR Chi-restraints excluded: chain L residue 120 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 135 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 112 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 70 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.136081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.099087 restraints weight = 12418.056| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.00 r_work: 0.3178 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3070 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3070 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.0749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 12263 Z= 0.206 Angle : 0.644 8.437 16816 Z= 0.355 Chirality : 0.045 0.150 1844 Planarity : 0.004 0.035 1968 Dihedral : 16.797 164.153 2051 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 5.70 % Allowed : 26.05 % Favored : 68.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: -0.40 (0.21), residues: 1368 helix: None (None), residues: 0 sheet: 0.09 (0.19), residues: 690 loop : -0.56 (0.22), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 24 TYR 0.012 0.002 TYR A 32 PHE 0.013 0.002 PHE B 29 TRP 0.010 0.001 TRP H 47 HIS 0.001 0.000 HIS I 55 Details of bonding type rmsd covalent geometry : bond 0.00473 (12251) covalent geometry : angle 0.64134 (16792) SS BOND : bond 0.00838 ( 12) SS BOND : angle 1.77865 ( 24) hydrogen bonds : bond 0.03809 ( 472) hydrogen bonds : angle 4.48882 ( 1212) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5461.90 seconds wall clock time: 93 minutes 25.21 seconds (5605.21 seconds total)