Starting phenix.real_space_refine on Mon Aug 25 08:21:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jkf_36371/08_2025/8jkf_36371.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jkf_36371/08_2025/8jkf_36371.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jkf_36371/08_2025/8jkf_36371.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jkf_36371/08_2025/8jkf_36371.map" model { file = "/net/cci-nas-00/data/ceres_data/8jkf_36371/08_2025/8jkf_36371.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jkf_36371/08_2025/8jkf_36371.cif" } resolution = 2.83 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 10856 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 11343 2.51 5 N 3201 2.21 5 O 3397 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 81 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18049 Number of models: 1 Model: "" Number of chains: 12 Chain: "H" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 889 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 111} Chain: "L" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 814 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99} Chain: "h" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 889 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 111} Chain: "l" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 814 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99} Chain: "a" Number of atoms: 2768 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 345, 2762 Classifications: {'peptide': 345} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 325} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 345, 2762 Classifications: {'peptide': 345} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 325} Chain breaks: 2 bond proxies already assigned to first conformer: 2830 Chain: "A" Number of atoms: 2855 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 355, 2848 Classifications: {'peptide': 355} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 335} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Conformer: "B" Number of residues, atoms: 355, 2848 Classifications: {'peptide': 355} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 335} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 bond proxies already assigned to first conformer: 2922 Chain: "M" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 889 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 111} Chain: "N" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 814 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99} Chain: "B" Number of atoms: 2845 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 354, 2838 Classifications: {'peptide': 354} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 334} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Conformer: "B" Number of residues, atoms: 354, 2838 Classifications: {'peptide': 354} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 334} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 bond proxies already assigned to first conformer: 2911 Chain: "b" Number of atoms: 2769 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 348, 2763 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'TRP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 16 Conformer: "B" Number of residues, atoms: 348, 2763 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'TRP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 16 bond proxies already assigned to first conformer: 2829 Chain: "m" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 889 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 111} Chain: "n" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 814 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N ASER a 58 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER a 58 " occ=0.50 residue: pdb=" N AVAL A 60 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BVAL A 60 " occ=0.50 residue: pdb=" N AVAL B 60 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BVAL B 60 " occ=0.50 residue: pdb=" N ASER b 58 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER b 58 " occ=0.50 Time building chain proxies: 6.16, per 1000 atoms: 0.34 Number of scatterers: 18049 At special positions: 0 Unit cell: (94.35, 115.6, 170, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 108 16.00 O 3397 8.00 N 3201 7.00 C 11343 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=32, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS h 22 " - pdb=" SG CYS h 95 " distance=2.04 Simple disulfide: pdb=" SG CYS l 23 " - pdb=" SG CYS l 88 " distance=2.04 Simple disulfide: pdb=" SG CYS a 4 " - pdb=" SG CYS a 15 " distance=2.04 Simple disulfide: pdb=" SG CYS a 55 " - pdb=" SG CYS a 143 " distance=2.03 Simple disulfide: pdb=" SG CYS a 179 " - pdb=" SG CYS a 223 " distance=2.03 Simple disulfide: pdb=" SG CYS a 280 " - pdb=" SG CYS a 329 " distance=2.03 Simple disulfide: pdb=" SG CYS a 291 " - pdb=" SG CYS a 312 " distance=2.03 Simple disulfide: pdb=" SG CYS a 313 " - pdb=" SG CYS a 316 " distance=2.03 Simple disulfide: pdb=" SG CYS A 4 " - pdb=" SG CYS A 15 " distance=2.03 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 143 " distance=2.03 Simple disulfide: pdb=" SG CYS A 179 " - pdb=" SG CYS A 223 " distance=2.03 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 329 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 312 " distance=2.04 Simple disulfide: pdb=" SG CYS A 313 " - pdb=" SG CYS A 316 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 95 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 4 " - pdb=" SG CYS B 15 " distance=2.03 Simple disulfide: pdb=" SG CYS B 55 " - pdb=" SG CYS B 143 " distance=2.03 Simple disulfide: pdb=" SG CYS B 179 " - pdb=" SG CYS B 223 " distance=2.03 Simple disulfide: pdb=" SG CYS B 280 " - pdb=" SG CYS B 329 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 312 " distance=2.04 Simple disulfide: pdb=" SG CYS B 313 " - pdb=" SG CYS B 316 " distance=2.03 Simple disulfide: pdb=" SG CYS b 4 " - pdb=" SG CYS b 15 " distance=2.03 Simple disulfide: pdb=" SG CYS b 55 " - pdb=" SG CYS b 143 " distance=2.03 Simple disulfide: pdb=" SG CYS b 179 " - pdb=" SG CYS b 223 " distance=2.03 Simple disulfide: pdb=" SG CYS b 280 " - pdb=" SG CYS b 329 " distance=2.03 Simple disulfide: pdb=" SG CYS b 291 " - pdb=" SG CYS b 312 " distance=2.04 Simple disulfide: pdb=" SG CYS b 313 " - pdb=" SG CYS b 316 " distance=2.03 Simple disulfide: pdb=" SG CYS m 22 " - pdb=" SG CYS m 95 " distance=2.04 Simple disulfide: pdb=" SG CYS n 23 " - pdb=" SG CYS n 88 " 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: 1.97 Conformation dependent library (CDL) restraints added in 995.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4190 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 42 sheets defined 13.8% alpha, 31.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.743A pdb=" N ASN H 32 " --> pdb=" O VAL H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 90 Processing helix chain 'L' and resid 49 through 53 removed outlier: 3.967A pdb=" N SER L 53 " --> pdb=" O ALA L 50 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.081A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'h' and resid 28 through 32 removed outlier: 3.824A pdb=" N ASN h 32 " --> pdb=" O VAL h 29 " (cutoff:3.500A) Processing helix chain 'h' and resid 86 through 90 Processing helix chain 'l' and resid 79 through 83 removed outlier: 4.078A pdb=" N PHE l 83 " --> pdb=" O PRO l 80 " (cutoff:3.500A) Processing helix chain 'a' and resid 38 through 52 Processing helix chain 'a' and resid 61 through 81 removed outlier: 3.699A pdb=" N ASN a 65 " --> pdb=" O SER a 61 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N GLY a 73 " --> pdb=" O ARG a 69 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N GLU a 74 " --> pdb=" O SER a 70 " (cutoff:3.500A) Processing helix chain 'a' and resid 144 through 146 No H-bonds generated for 'chain 'a' and resid 144 through 146' Processing helix chain 'a' and resid 180 through 183 removed outlier: 3.704A pdb=" N VAL a 183 " --> pdb=" O ASP a 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 180 through 183' Processing helix chain 'a' and resid 226 through 230 Processing helix chain 'a' and resid 244 through 248 Processing helix chain 'a' and resid 252 through 256 removed outlier: 3.660A pdb=" N THR a 256 " --> pdb=" O HIS a 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.629A pdb=" N ARG A 31 " --> pdb=" O TRP A 28 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR A 32 " --> pdb=" O ARG A 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 28 through 32' Processing helix chain 'A' and resid 38 through 52 Processing helix chain 'A' and resid 61 through 82 removed outlier: 4.880A pdb=" N GLY A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N GLU A 74 " --> pdb=" O SER A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 146 No H-bonds generated for 'chain 'A' and resid 144 through 146' Processing helix chain 'A' and resid 180 through 183 removed outlier: 3.854A pdb=" N VAL A 183 " --> pdb=" O ASP A 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 180 through 183' Processing helix chain 'A' and resid 237 through 241 removed outlier: 3.870A pdb=" N LEU A 241 " --> pdb=" O GLU A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 248 Processing helix chain 'A' and resid 252 through 256 removed outlier: 3.595A pdb=" N THR A 256 " --> pdb=" O HIS A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 345 removed outlier: 4.099A pdb=" N ASN A 344 " --> pdb=" O PRO A 341 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 32 removed outlier: 3.630A pdb=" N ASN M 32 " --> pdb=" O VAL M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 64 Processing helix chain 'M' and resid 86 through 90 Processing helix chain 'B' and resid 38 through 53 Processing helix chain 'B' and resid 61 through 82 removed outlier: 5.020A pdb=" N GLY B 73 " --> pdb=" O ARG B 69 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N GLU B 74 " --> pdb=" O SER B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 146 No H-bonds generated for 'chain 'B' and resid 144 through 146' Processing helix chain 'B' and resid 180 through 183 removed outlier: 3.793A pdb=" N VAL B 183 " --> pdb=" O ASP B 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 180 through 183' Processing helix chain 'B' and resid 226 through 230 removed outlier: 3.524A pdb=" N THR B 230 " --> pdb=" O LYS B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 241 removed outlier: 3.776A pdb=" N LEU B 241 " --> pdb=" O GLU B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 248 Processing helix chain 'B' and resid 252 through 256 removed outlier: 3.772A pdb=" N THR B 256 " --> pdb=" O HIS B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 345 removed outlier: 3.557A pdb=" N ASN B 344 " --> pdb=" O PRO B 341 " (cutoff:3.500A) Processing helix chain 'b' and resid 38 through 52 Processing helix chain 'b' and resid 61 through 82 removed outlier: 3.592A pdb=" N ASN b 65 " --> pdb=" O SER b 61 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N GLY b 73 " --> pdb=" O ARG b 69 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N GLU b 74 " --> pdb=" O SER b 70 " (cutoff:3.500A) Processing helix chain 'b' and resid 144 through 146 No H-bonds generated for 'chain 'b' and resid 144 through 146' Processing helix chain 'b' and resid 180 through 183 removed outlier: 3.797A pdb=" N VAL b 183 " --> pdb=" O ASP b 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 180 through 183' Processing helix chain 'b' and resid 226 through 230 Processing helix chain 'b' and resid 244 through 248 Processing helix chain 'b' and resid 252 through 256 removed outlier: 3.624A pdb=" N THR b 256 " --> pdb=" O HIS b 253 " (cutoff:3.500A) Processing helix chain 'm' and resid 28 through 32 removed outlier: 3.735A pdb=" N ASN m 31 " --> pdb=" O THR m 28 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN m 32 " --> pdb=" O VAL m 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 28 through 32' Processing helix chain 'm' and resid 86 through 90 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.193A pdb=" N GLY H 10 " --> pdb=" O THR H 112 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N TYR H 33 " --> pdb=" O GLU H 98 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N MET H 34 " --> pdb=" O ILE H 50 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ILE H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.193A pdb=" N GLY H 10 " --> pdb=" O THR H 112 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N TYR H 104 " --> pdb=" O ARG H 97 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.504A pdb=" N THR L 72 " --> pdb=" O GLY L 65 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 13 removed outlier: 7.002A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'L' and resid 45 through 48 removed outlier: 6.751A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'h' and resid 3 through 7 Processing sheet with id=AA8, first strand: chain 'h' and resid 10 through 12 removed outlier: 6.071A pdb=" N GLY h 10 " --> pdb=" O THR h 112 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N TYR h 33 " --> pdb=" O GLU h 98 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N MET h 34 " --> pdb=" O ILE h 50 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ILE h 50 " --> pdb=" O MET h 34 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N TRP h 36 " --> pdb=" O VAL h 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'h' and resid 10 through 12 removed outlier: 6.071A pdb=" N GLY h 10 " --> pdb=" O THR h 112 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N TYR h 104 " --> pdb=" O ARG h 97 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'l' and resid 4 through 7 Processing sheet with id=AB2, first strand: chain 'l' and resid 10 through 13 removed outlier: 3.580A pdb=" N ALA l 13 " --> pdb=" O GLU l 105 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU l 33 " --> pdb=" O TYR l 49 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N TYR l 49 " --> pdb=" O LEU l 33 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N TRP l 35 " --> pdb=" O LEU l 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'l' and resid 10 through 13 removed outlier: 3.580A pdb=" N ALA l 13 " --> pdb=" O GLU l 105 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N THR l 97 " --> pdb=" O GLN l 90 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'a' and resid 1 through 7 removed outlier: 3.795A pdb=" N HIS a 1 " --> pdb=" O GLY a 18 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N HIS A 1 " --> pdb=" O GLY A 18 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N HIS a 2 " --> pdb=" O VAL A 6 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'a' and resid 33 through 36 removed outlier: 6.051A pdb=" N LYS a 33 " --> pdb=" O VAL a 167 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N LEU a 169 " --> pdb=" O LYS a 33 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N HIS a 35 " --> pdb=" O LEU a 169 " (cutoff:3.500A) removed outlier: 8.942A pdb=" N VAL a 171 " --> pdb=" O HIS a 35 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'a' and resid 56 through 57 removed outlier: 7.155A pdb=" N GLY a 56 " --> pdb=" O ALA a 149 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'a' and resid 87 through 89 removed outlier: 6.535A pdb=" N THR a 87 " --> pdb=" O PHE a 133 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'a' and resid 329 through 331 removed outlier: 3.608A pdb=" N GLU a 274 " --> pdb=" O ARG a 324 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N PHE a 277 " --> pdb=" O LYS a 213 " (cutoff:3.500A) removed outlier: 9.214A pdb=" N LYS a 213 " --> pdb=" O PHE a 277 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N LEU a 212 " --> pdb=" O GLU a 205 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N GLU a 205 " --> pdb=" O LEU a 212 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU a 192 " --> pdb=" O LYS a 189 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU A 192 " --> pdb=" O LYS A 189 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N GLU A 205 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N LEU A 212 " --> pdb=" O GLU A 205 " (cutoff:3.500A) removed outlier: 9.091A pdb=" N LYS A 213 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N PHE A 277 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'a' and resid 284 through 287 removed outlier: 6.299A pdb=" N LYS a 284 " --> pdb=" O TRP a 311 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N CYS a 313 " --> pdb=" O LYS a 284 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N HIS a 286 " --> pdb=" O CYS a 313 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 33 through 35 removed outlier: 6.383A pdb=" N LYS A 33 " --> pdb=" O VAL A 167 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LEU A 169 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N HIS A 35 " --> pdb=" O LEU A 169 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N VAL A 171 " --> pdb=" O HIS A 35 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N SER A 166 " --> pdb=" O HIS A 158 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N HIS A 158 " --> pdb=" O SER A 166 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N TRP A 168 " --> pdb=" O GLU A 156 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 56 through 57 removed outlier: 7.334A pdb=" N GLY A 56 " --> pdb=" O ALA A 149 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'A' and resid 87 through 90 removed outlier: 6.316A pdb=" N THR A 87 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N VAL A 135 " --> pdb=" O THR A 87 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N VAL A 89 " --> pdb=" O VAL A 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'A' and resid 284 through 287 Processing sheet with id=AC5, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AC6, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.301A pdb=" N GLY M 10 " --> pdb=" O THR M 112 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N TYR M 33 " --> pdb=" O GLU M 98 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N MET M 34 " --> pdb=" O ILE M 50 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ILE M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.301A pdb=" N GLY M 10 " --> pdb=" O THR M 112 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N TYR M 104 " --> pdb=" O ARG M 97 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AC9, first strand: chain 'N' and resid 10 through 13 Processing sheet with id=AD1, first strand: chain 'N' and resid 53 through 54 removed outlier: 5.549A pdb=" N LEU N 46 " --> pdb=" O GLN N 37 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N GLN N 37 " --> pdb=" O LEU N 46 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N THR N 97 " --> pdb=" O GLN N 90 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1 through 7 removed outlier: 5.306A pdb=" N HIS B 1 " --> pdb=" O GLY B 18 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU B 12 " --> pdb=" O ASP B 7 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N HIS b 2 " --> pdb=" O VAL B 6 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 33 through 35 removed outlier: 6.641A pdb=" N LYS B 33 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N LEU B 169 " --> pdb=" O LYS B 33 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N HIS B 35 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N VAL B 171 " --> pdb=" O HIS B 35 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N SER B 166 " --> pdb=" O HIS B 158 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N HIS B 158 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N TRP B 168 " --> pdb=" O GLU B 156 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 87 through 89 removed outlier: 6.233A pdb=" N THR B 87 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N VAL B 135 " --> pdb=" O THR B 87 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N VAL B 89 " --> pdb=" O VAL B 135 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 321 through 324 removed outlier: 4.696A pdb=" N PHE B 277 " --> pdb=" O LYS B 213 " (cutoff:3.500A) removed outlier: 9.263A pdb=" N LYS B 213 " --> pdb=" O PHE B 277 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N LEU B 212 " --> pdb=" O GLU B 205 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N GLU B 205 " --> pdb=" O LEU B 212 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG B 214 " --> pdb=" O GLU B 203 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU B 192 " --> pdb=" O LYS B 189 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N GLU b 205 " --> pdb=" O LEU b 212 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N LEU b 212 " --> pdb=" O GLU b 205 " (cutoff:3.500A) removed outlier: 9.423A pdb=" N LYS b 213 " --> pdb=" O PHE b 277 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N PHE b 277 " --> pdb=" O LYS b 213 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU b 274 " --> pdb=" O ARG b 324 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY b 328 " --> pdb=" O ALA b 325 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 285 through 287 removed outlier: 6.280A pdb=" N HIS B 286 " --> pdb=" O CYS B 313 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'b' and resid 34 through 36 Processing sheet with id=AD8, first strand: chain 'b' and resid 87 through 89 removed outlier: 6.379A pdb=" N THR b 87 " --> pdb=" O PHE b 133 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N VAL b 135 " --> pdb=" O THR b 87 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL b 89 " --> pdb=" O VAL b 135 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N GLY b 56 " --> pdb=" O ALA b 149 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'b' and resid 285 through 287 Processing sheet with id=AE1, first strand: chain 'm' and resid 3 through 7 removed outlier: 3.534A pdb=" N THR m 77 " --> pdb=" O ASP m 72 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'm' and resid 10 through 12 removed outlier: 4.049A pdb=" N TYR m 33 " --> pdb=" O GLU m 98 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N MET m 34 " --> pdb=" O ILE m 50 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ILE m 50 " --> pdb=" O MET m 34 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N TRP m 36 " --> pdb=" O VAL m 48 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'm' and resid 10 through 12 removed outlier: 4.347A pdb=" N TYR m 104 " --> pdb=" O ARG m 97 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'n' and resid 4 through 7 removed outlier: 3.788A pdb=" N VAL n 19 " --> pdb=" O ILE n 75 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'n' and resid 10 through 13 removed outlier: 3.542A pdb=" N ALA n 13 " --> pdb=" O GLU n 105 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N GLN n 37 " --> pdb=" O LEU n 46 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N LEU n 46 " --> pdb=" O GLN n 37 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'n' and resid 10 through 13 removed outlier: 3.542A pdb=" N ALA n 13 " --> pdb=" O GLU n 105 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N THR n 97 " --> pdb=" O GLN n 90 " (cutoff:3.500A) 582 hydrogen bonds defined for protein. 1464 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.06 Time building geometry restraints manager: 2.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5923 1.34 - 1.46: 4569 1.46 - 1.59: 7872 1.59 - 1.71: 0 1.71 - 1.83: 152 Bond restraints: 18516 Sorted by residual: bond pdb=" N VAL L 51 " pdb=" CA VAL L 51 " ideal model delta sigma weight residual 1.459 1.505 -0.046 1.25e-02 6.40e+03 1.36e+01 bond pdb=" N VAL N 51 " pdb=" CA VAL N 51 " ideal model delta sigma weight residual 1.459 1.501 -0.042 1.25e-02 6.40e+03 1.14e+01 bond pdb=" N VAL l 51 " pdb=" CA VAL l 51 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.25e-02 6.40e+03 1.10e+01 bond pdb=" N VAL n 51 " pdb=" CA VAL n 51 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.25e-02 6.40e+03 1.09e+01 bond pdb=" N GLY N 65 " pdb=" CA GLY N 65 " ideal model delta sigma weight residual 1.447 1.477 -0.030 9.30e-03 1.16e+04 1.03e+01 ... (remaining 18511 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 24388 1.64 - 3.28: 639 3.28 - 4.92: 87 4.92 - 6.56: 12 6.56 - 8.19: 2 Bond angle restraints: 25128 Sorted by residual: angle pdb=" CA ALA N 50 " pdb=" C ALA N 50 " pdb=" O ALA N 50 " ideal model delta sigma weight residual 121.84 117.14 4.70 1.16e+00 7.43e-01 1.64e+01 angle pdb=" CA ALA n 50 " pdb=" C ALA n 50 " pdb=" O ALA n 50 " ideal model delta sigma weight residual 121.84 117.16 4.68 1.16e+00 7.43e-01 1.63e+01 angle pdb=" CA GLY N 64 " pdb=" C GLY N 64 " pdb=" O GLY N 64 " ideal model delta sigma weight residual 121.57 118.08 3.49 8.70e-01 1.32e+00 1.61e+01 angle pdb=" CA ALA L 50 " pdb=" C ALA L 50 " pdb=" O ALA L 50 " ideal model delta sigma weight residual 121.54 116.90 4.64 1.16e+00 7.43e-01 1.60e+01 angle pdb=" CA ALA l 50 " pdb=" C ALA l 50 " pdb=" O ALA l 50 " ideal model delta sigma weight residual 121.84 117.26 4.58 1.16e+00 7.43e-01 1.56e+01 ... (remaining 25123 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 10088 17.85 - 35.70: 763 35.70 - 53.54: 144 53.54 - 71.39: 23 71.39 - 89.24: 6 Dihedral angle restraints: 11024 sinusoidal: 4477 harmonic: 6547 Sorted by residual: dihedral pdb=" CB CYS a 291 " pdb=" SG CYS a 291 " pdb=" SG CYS a 312 " pdb=" CB CYS a 312 " ideal model delta sinusoidal sigma weight residual -86.00 -147.43 61.43 1 1.00e+01 1.00e-02 5.01e+01 dihedral pdb=" CA SER N 28 " pdb=" C SER N 28 " pdb=" N VAL N 29 " pdb=" CA VAL N 29 " ideal model delta harmonic sigma weight residual 180.00 157.95 22.05 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA SER L 28 " pdb=" C SER L 28 " pdb=" N VAL L 29 " pdb=" CA VAL L 29 " ideal model delta harmonic sigma weight residual 180.00 159.65 20.35 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 11021 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 2356 0.068 - 0.135: 314 0.135 - 0.203: 14 0.203 - 0.270: 0 0.270 - 0.338: 1 Chirality restraints: 2685 Sorted by residual: chirality pdb=" CB VAL L 51 " pdb=" CA VAL L 51 " pdb=" CG1 VAL L 51 " pdb=" CG2 VAL L 51 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.85e+00 chirality pdb=" CA ILE N 48 " pdb=" N ILE N 48 " pdb=" C ILE N 48 " pdb=" CB ILE N 48 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA ILE n 48 " pdb=" N ILE n 48 " pdb=" C ILE n 48 " pdb=" CB ILE n 48 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.76e-01 ... (remaining 2682 not shown) Planarity restraints: 3216 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN n 79 " -0.045 5.00e-02 4.00e+02 6.74e-02 7.27e+00 pdb=" N PRO n 80 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO n 80 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO n 80 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR h 33 " -0.015 2.00e-02 2.50e+03 1.63e-02 5.33e+00 pdb=" CG TYR h 33 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR h 33 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR h 33 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR h 33 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR h 33 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR h 33 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR h 33 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 33 " 0.015 2.00e-02 2.50e+03 1.55e-02 4.81e+00 pdb=" CG TYR H 33 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR H 33 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR H 33 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR H 33 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR H 33 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR H 33 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR H 33 " 0.003 2.00e-02 2.50e+03 ... (remaining 3213 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 133 2.64 - 3.20: 14601 3.20 - 3.77: 25631 3.77 - 4.33: 38965 4.33 - 4.90: 65438 Nonbonded interactions: 144768 Sorted by model distance: nonbonded pdb=" O GLY B 159 " pdb=" OG1 THR B 165 " model vdw 2.069 3.040 nonbonded pdb=" O LEU B 231 " pdb=" OG SER B 252 " model vdw 2.167 3.040 nonbonded pdb=" OG SER B 297 " pdb=" O TYR B 331 " model vdw 2.191 3.040 nonbonded pdb=" OG SER b 297 " pdb=" O TYR b 331 " model vdw 2.200 3.040 nonbonded pdb=" OG SER a 297 " pdb=" O TYR a 331 " model vdw 2.234 3.040 ... (remaining 144763 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' and (resid 1 through 25 or resid 30 through 57 or resid 59 or resid 6 \ 1 through 117 or (resid 118 and (name N or name CA or name C or name O or name C \ B )) or resid 123 through 352)) selection = (chain 'B' and (resid 1 through 25 or resid 30 through 57 or resid 59 or resid 6 \ 1 through 117 or (resid 118 and (name N or name CA or name C or name O or name C \ B )) or resid 123 through 352)) selection = (chain 'a' and (resid 1 through 57 or resid 59 or resid 61 through 117 or (resid \ 118 and (name N or name CA or name C or name O or name CB )) or resid 123 throu \ gh 352)) selection = (chain 'b' and (resid 1 through 57 or resid 59 or resid 61 through 118 or resid \ 123 through 352)) } ncs_group { reference = chain 'H' selection = chain 'M' selection = chain 'h' selection = chain 'm' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'l' selection = chain 'n' } 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=0.50 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: 5.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 19.950 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.060 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:8.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 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 0.048 18548 Z= 0.245 Angle : 0.639 8.194 25192 Z= 0.375 Chirality : 0.046 0.338 2685 Planarity : 0.004 0.067 3216 Dihedral : 12.924 89.239 6738 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.26 % Favored : 95.69 % Rotamer: Outliers : 0.96 % Allowed : 0.76 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % 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 aren not related in a simple way. whole: -0.67 (0.18), residues: 2264 helix: 1.69 (0.41), residues: 148 sheet: -0.55 (0.20), residues: 738 loop : -0.58 (0.17), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG b 31 TYR 0.038 0.002 TYR h 33 PHE 0.009 0.002 PHE n 98 TRP 0.013 0.001 TRP B 115 HIS 0.006 0.001 HIS B 1 Details of bonding type rmsd covalent geometry : bond 0.00474 (18516) covalent geometry : angle 0.63556 (25128) SS BOND : bond 0.00447 ( 32) SS BOND : angle 1.50277 ( 64) hydrogen bonds : bond 0.22738 ( 555) hydrogen bonds : angle 9.09504 ( 1464) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 339 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: h 13 GLN cc_start: 0.8045 (mp10) cc_final: 0.7833 (mm-40) REVERT: l 9 SER cc_start: 0.8266 (m) cc_final: 0.8017 (p) REVERT: N 66 ASP cc_start: 0.6869 (OUTLIER) cc_final: 0.6588 (p0) REVERT: B 0 HIS cc_start: 0.5816 (p-80) cc_final: 0.5364 (p90) REVERT: B 33 LYS cc_start: 0.8348 (ptmt) cc_final: 0.8063 (ptpp) REVERT: B 109 ASN cc_start: 0.7333 (m-40) cc_final: 0.7057 (t0) REVERT: b 31 ARG cc_start: 0.6363 (ttm110) cc_final: 0.6023 (ttt90) REVERT: b 123 PHE cc_start: 0.4408 (OUTLIER) cc_final: 0.3645 (p90) outliers start: 16 outliers final: 3 residues processed: 350 average time/residue: 0.6163 time to fit residues: 238.6148 Evaluate side-chains 239 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 234 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain A residue 0 HIS Chi-restraints excluded: chain N residue 66 ASP Chi-restraints excluded: chain b residue 110 GLU Chi-restraints excluded: chain b residue 123 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 216 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 0.1980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 0.7980 chunk 212 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 100 GLN l 100 GLN a 158 HIS A 147 HIS ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 0 HIS B 286 HIS b 2 HIS m 107 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.143447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.108140 restraints weight = 51849.410| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 3.48 r_work: 0.3043 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3033 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3033 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18548 Z= 0.111 Angle : 0.549 6.990 25192 Z= 0.293 Chirality : 0.043 0.152 2685 Planarity : 0.004 0.039 3216 Dihedral : 5.081 83.565 2521 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.37 % Favored : 96.58 % Rotamer: Outliers : 2.23 % Allowed : 9.43 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % 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 aren not related in a simple way. whole: -0.28 (0.18), residues: 2264 helix: 1.69 (0.41), residues: 153 sheet: -0.09 (0.21), residues: 648 loop : -0.40 (0.17), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG b 41 TYR 0.019 0.001 TYR H 33 PHE 0.010 0.001 PHE L 98 TRP 0.014 0.001 TRP B 115 HIS 0.006 0.001 HIS B 286 Details of bonding type rmsd covalent geometry : bond 0.00251 (18516) covalent geometry : angle 0.54659 (25128) SS BOND : bond 0.00364 ( 32) SS BOND : angle 1.10430 ( 64) hydrogen bonds : bond 0.03971 ( 555) hydrogen bonds : angle 5.92155 ( 1464) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 274 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: h 13 GLN cc_start: 0.8242 (mp10) cc_final: 0.7981 (mm-40) REVERT: A -2 HIS cc_start: 0.4944 (OUTLIER) cc_final: 0.4714 (t70) REVERT: A 12 GLU cc_start: 0.7566 (mm-30) cc_final: 0.7221 (mt-10) REVERT: A 116 LYS cc_start: 0.7995 (OUTLIER) cc_final: 0.7644 (pttm) REVERT: A 284 LYS cc_start: 0.7666 (mtpp) cc_final: 0.7115 (tttp) REVERT: A 286 HIS cc_start: 0.8027 (m-70) cc_final: 0.7707 (m-70) REVERT: M 3 GLN cc_start: 0.8245 (tt0) cc_final: 0.8021 (mm110) REVERT: B 0 HIS cc_start: 0.6199 (p90) cc_final: 0.5855 (p90) REVERT: B 94 LYS cc_start: 0.8177 (mmmm) cc_final: 0.7520 (mtmt) REVERT: B 109 ASN cc_start: 0.7333 (m-40) cc_final: 0.7052 (t0) REVERT: B 340 GLU cc_start: 0.6937 (OUTLIER) cc_final: 0.6718 (mt-10) REVERT: b 31 ARG cc_start: 0.6352 (ttm110) cc_final: 0.5882 (ttt90) REVERT: b 123 PHE cc_start: 0.4528 (OUTLIER) cc_final: 0.3772 (p90) REVERT: b 164 HIS cc_start: 0.6273 (OUTLIER) cc_final: 0.5894 (p90) REVERT: b 289 GLU cc_start: 0.6984 (mt-10) cc_final: 0.6768 (tt0) REVERT: b 331 TYR cc_start: 0.7525 (m-80) cc_final: 0.7286 (m-80) REVERT: m 76 ASN cc_start: 0.8677 (t0) cc_final: 0.8342 (t0) outliers start: 41 outliers final: 14 residues processed: 297 average time/residue: 0.5739 time to fit residues: 190.1467 Evaluate side-chains 251 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 232 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain h residue 6 GLU Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 20 THR Chi-restraints excluded: chain l residue 53 SER Chi-restraints excluded: chain l residue 54 LEU Chi-restraints excluded: chain a residue 168 TRP Chi-restraints excluded: chain A residue -2 HIS Chi-restraints excluded: chain A residue 0 HIS Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain b residue 123 PHE Chi-restraints excluded: chain b residue 164 HIS Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain n residue 5 THR Chi-restraints excluded: chain n residue 9 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 147 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 chunk 157 optimal weight: 6.9990 chunk 150 optimal weight: 0.1980 chunk 68 optimal weight: 2.9990 chunk 47 optimal weight: 0.4980 chunk 50 optimal weight: 9.9990 chunk 4 optimal weight: 5.9990 chunk 179 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 178 optimal weight: 0.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 27 GLN l 100 GLN a 0 HIS a 263 GLN N 100 GLN b 131 ASN m 107 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.139938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.105004 restraints weight = 47949.408| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.90 r_work: 0.2970 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2955 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2955 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 18548 Z= 0.160 Angle : 0.614 8.214 25192 Z= 0.325 Chirality : 0.044 0.195 2685 Planarity : 0.004 0.043 3216 Dihedral : 5.038 38.984 2516 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.91 % Favored : 96.05 % Rotamer: Outliers : 2.94 % Allowed : 11.36 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % 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 aren not related in a simple way. whole: -0.34 (0.18), residues: 2264 helix: 1.63 (0.41), residues: 153 sheet: -0.20 (0.20), residues: 757 loop : -0.40 (0.17), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG b 41 TYR 0.023 0.002 TYR H 33 PHE 0.011 0.002 PHE n 62 TRP 0.019 0.001 TRP a 168 HIS 0.006 0.001 HIS b 158 Details of bonding type rmsd covalent geometry : bond 0.00382 (18516) covalent geometry : angle 0.61132 (25128) SS BOND : bond 0.00488 ( 32) SS BOND : angle 1.35506 ( 64) hydrogen bonds : bond 0.04838 ( 555) hydrogen bonds : angle 5.78900 ( 1464) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 249 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8144 (OUTLIER) cc_final: 0.7580 (mt0) REVERT: H 29 VAL cc_start: 0.8919 (m) cc_final: 0.8669 (t) REVERT: L 78 LEU cc_start: 0.8120 (tp) cc_final: 0.7861 (tm) REVERT: L 79 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.7143 (mp10) REVERT: a 264 MET cc_start: 0.8655 (tpt) cc_final: 0.8412 (mmp) REVERT: a 333 MET cc_start: 0.8672 (mtp) cc_final: 0.8390 (mtm) REVERT: A 12 GLU cc_start: 0.7613 (mm-30) cc_final: 0.7338 (mt-10) REVERT: A 116 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7812 (pttm) REVERT: A 128 LYS cc_start: 0.7937 (ttmm) cc_final: 0.7601 (tttt) REVERT: A 220 MET cc_start: 0.8671 (OUTLIER) cc_final: 0.7223 (mmt) REVERT: A 284 LYS cc_start: 0.7815 (mtpp) cc_final: 0.7377 (tttp) REVERT: A 286 HIS cc_start: 0.8021 (m-70) cc_final: 0.7755 (m-70) REVERT: B 33 LYS cc_start: 0.8264 (ptmt) cc_final: 0.7916 (ptpp) REVERT: B 94 LYS cc_start: 0.8261 (mmmm) cc_final: 0.7500 (mtmt) REVERT: B 109 ASN cc_start: 0.7288 (m-40) cc_final: 0.7046 (t0) REVERT: B 340 GLU cc_start: 0.6873 (OUTLIER) cc_final: 0.6615 (mt-10) REVERT: b 31 ARG cc_start: 0.6363 (ttm110) cc_final: 0.6008 (ttt90) REVERT: b 164 HIS cc_start: 0.6355 (OUTLIER) cc_final: 0.6001 (p90) REVERT: b 261 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.8092 (mtt-85) REVERT: b 289 GLU cc_start: 0.7039 (mt-10) cc_final: 0.6820 (mt-10) REVERT: m 76 ASN cc_start: 0.8698 (t0) cc_final: 0.8318 (t0) REVERT: n 75 ILE cc_start: 0.7257 (OUTLIER) cc_final: 0.7055 (mm) outliers start: 55 outliers final: 24 residues processed: 280 average time/residue: 0.5668 time to fit residues: 176.9228 Evaluate side-chains 257 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 225 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain l residue 22 THR Chi-restraints excluded: chain l residue 53 SER Chi-restraints excluded: chain l residue 54 LEU Chi-restraints excluded: chain a residue 168 TRP Chi-restraints excluded: chain A residue -2 HIS Chi-restraints excluded: chain A residue 0 HIS Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 112 THR Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain b residue 164 HIS Chi-restraints excluded: chain b residue 261 ARG Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain m residue 112 THR Chi-restraints excluded: chain n residue 5 THR Chi-restraints excluded: chain n residue 9 SER Chi-restraints excluded: chain n residue 63 SER Chi-restraints excluded: chain n residue 75 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 45 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 114 optimal weight: 7.9990 chunk 95 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 16 optimal weight: 0.1980 chunk 193 optimal weight: 4.9990 chunk 203 optimal weight: 8.9990 chunk 97 optimal weight: 3.9990 chunk 163 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 107 GLN L 27 GLN L 100 GLN l 100 GLN a 0 HIS a 263 GLN A 113 HIS M 31 ASN N 100 GLN B 0 HIS m 107 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.138154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.114361 restraints weight = 56773.042| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 5.18 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3310 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3310 r_free = 0.3310 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3310 r_free = 0.3310 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3310 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 18548 Z= 0.197 Angle : 0.641 8.647 25192 Z= 0.337 Chirality : 0.046 0.217 2685 Planarity : 0.005 0.046 3216 Dihedral : 5.173 38.925 2514 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.09 % Favored : 95.87 % Rotamer: Outliers : 3.45 % Allowed : 12.73 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % 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 aren not related in a simple way. whole: -0.48 (0.18), residues: 2264 helix: 1.51 (0.39), residues: 153 sheet: -0.28 (0.19), residues: 763 loop : -0.50 (0.17), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG b 41 TYR 0.018 0.002 TYR N 49 PHE 0.014 0.002 PHE A 323 TRP 0.023 0.002 TRP a 168 HIS 0.011 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00477 (18516) covalent geometry : angle 0.63723 (25128) SS BOND : bond 0.00535 ( 32) SS BOND : angle 1.47551 ( 64) hydrogen bonds : bond 0.04776 ( 555) hydrogen bonds : angle 5.70457 ( 1464) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 239 time to evaluate : 0.724 Fit side-chains revert: symmetry clash REVERT: H 3 GLN cc_start: 0.7894 (OUTLIER) cc_final: 0.7300 (mt0) REVERT: H 29 VAL cc_start: 0.8936 (m) cc_final: 0.8695 (t) REVERT: L 78 LEU cc_start: 0.8167 (tp) cc_final: 0.7883 (tm) REVERT: L 79 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7195 (mp10) REVERT: a 40 ARG cc_start: 0.6679 (mtm-85) cc_final: 0.6391 (ttm110) REVERT: A 12 GLU cc_start: 0.7439 (mm-30) cc_final: 0.7155 (mt-10) REVERT: A 116 LYS cc_start: 0.8098 (OUTLIER) cc_final: 0.7668 (pttm) REVERT: A 220 MET cc_start: 0.8232 (OUTLIER) cc_final: 0.6737 (mmt) REVERT: A 284 LYS cc_start: 0.7756 (mtpp) cc_final: 0.7385 (tttp) REVERT: A 286 HIS cc_start: 0.8123 (m-70) cc_final: 0.7871 (m-70) REVERT: N 55 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7819 (mm110) REVERT: B 33 LYS cc_start: 0.8303 (ptmt) cc_final: 0.8016 (ptpp) REVERT: B 40 ARG cc_start: 0.6294 (OUTLIER) cc_final: 0.5863 (mtm180) REVERT: B 63 MET cc_start: 0.8053 (OUTLIER) cc_final: 0.7741 (ttp) REVERT: B 94 LYS cc_start: 0.8278 (mmmm) cc_final: 0.7503 (mtmt) REVERT: B 116 LYS cc_start: 0.8011 (OUTLIER) cc_final: 0.7665 (ttmm) REVERT: B 340 GLU cc_start: 0.6951 (OUTLIER) cc_final: 0.6634 (mt-10) REVERT: b 31 ARG cc_start: 0.6316 (ttm110) cc_final: 0.5959 (ttt90) REVERT: b 164 HIS cc_start: 0.6178 (OUTLIER) cc_final: 0.5925 (p90) REVERT: b 261 ARG cc_start: 0.7707 (OUTLIER) cc_final: 0.7403 (mtt-85) REVERT: m 76 ASN cc_start: 0.8632 (t0) cc_final: 0.8246 (t0) REVERT: n 75 ILE cc_start: 0.7644 (OUTLIER) cc_final: 0.7422 (mm) outliers start: 65 outliers final: 31 residues processed: 274 average time/residue: 0.5894 time to fit residues: 179.7550 Evaluate side-chains 270 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 227 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain h residue 2 VAL Chi-restraints excluded: chain h residue 46 GLU Chi-restraints excluded: chain l residue 22 THR Chi-restraints excluded: chain l residue 54 LEU Chi-restraints excluded: chain l residue 70 ASP Chi-restraints excluded: chain a residue 168 TRP Chi-restraints excluded: chain A residue 0 HIS Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 112 THR Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 55 GLN Chi-restraints excluded: chain B residue 40 ARG Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 116 LYS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain b residue 164 HIS Chi-restraints excluded: chain b residue 261 ARG Chi-restraints excluded: chain b residue 346 VAL Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain m residue 112 THR Chi-restraints excluded: chain n residue 5 THR Chi-restraints excluded: chain n residue 9 SER Chi-restraints excluded: chain n residue 10 SER Chi-restraints excluded: chain n residue 63 SER Chi-restraints excluded: chain n residue 75 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 152 optimal weight: 4.9990 chunk 175 optimal weight: 7.9990 chunk 79 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 186 optimal weight: 3.9990 chunk 43 optimal weight: 8.9990 chunk 153 optimal weight: 0.9990 chunk 144 optimal weight: 10.0000 chunk 99 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 107 GLN L 27 GLN L 100 GLN l 100 GLN a 0 HIS a 263 GLN A 164 HIS N 100 GLN B 0 HIS m 107 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.137054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.101904 restraints weight = 52351.041| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 3.31 r_work: 0.2924 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2905 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2905 r_free = 0.2905 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2905 r_free = 0.2905 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2905 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 18548 Z= 0.239 Angle : 0.684 9.466 25192 Z= 0.359 Chirality : 0.047 0.241 2685 Planarity : 0.005 0.049 3216 Dihedral : 5.415 40.715 2514 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.40 % Favored : 95.56 % Rotamer: Outliers : 3.70 % Allowed : 14.45 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % 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 aren not related in a simple way. whole: -0.65 (0.17), residues: 2264 helix: 1.39 (0.39), residues: 153 sheet: -0.36 (0.19), residues: 763 loop : -0.64 (0.17), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG b 41 TYR 0.020 0.002 TYR N 49 PHE 0.016 0.002 PHE A 323 TRP 0.025 0.002 TRP a 168 HIS 0.012 0.002 HIS A 164 Details of bonding type rmsd covalent geometry : bond 0.00580 (18516) covalent geometry : angle 0.67974 (25128) SS BOND : bond 0.00607 ( 32) SS BOND : angle 1.62951 ( 64) hydrogen bonds : bond 0.05188 ( 555) hydrogen bonds : angle 5.81088 ( 1464) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 232 time to evaluate : 0.842 Fit side-chains revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7614 (mt0) REVERT: H 29 VAL cc_start: 0.8962 (m) cc_final: 0.8656 (t) REVERT: L 79 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7201 (mp10) REVERT: a 40 ARG cc_start: 0.6989 (mtm-85) cc_final: 0.6707 (ttm110) REVERT: a 74 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7911 (tt0) REVERT: A -2 HIS cc_start: 0.5988 (OUTLIER) cc_final: 0.5537 (t-90) REVERT: A 12 GLU cc_start: 0.7650 (mm-30) cc_final: 0.7397 (mt-10) REVERT: A 116 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7816 (pttm) REVERT: A 220 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.7267 (mmt) REVERT: A 284 LYS cc_start: 0.7883 (mtpp) cc_final: 0.7432 (tttp) REVERT: A 286 HIS cc_start: 0.8013 (m-70) cc_final: 0.7781 (m-70) REVERT: B 33 LYS cc_start: 0.8344 (ptmt) cc_final: 0.7989 (ptpp) REVERT: B 63 MET cc_start: 0.8319 (OUTLIER) cc_final: 0.7989 (ttp) REVERT: B 94 LYS cc_start: 0.8230 (mmmm) cc_final: 0.7465 (mtmt) REVERT: B 116 LYS cc_start: 0.8044 (OUTLIER) cc_final: 0.7774 (ttmm) REVERT: B 340 GLU cc_start: 0.6853 (OUTLIER) cc_final: 0.6526 (mt-10) REVERT: b 31 ARG cc_start: 0.6397 (ttm110) cc_final: 0.6033 (ttt90) REVERT: b 33 LYS cc_start: 0.5678 (tmtt) cc_final: 0.4657 (tmmt) REVERT: b 261 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.8164 (mtt-85) REVERT: m 76 ASN cc_start: 0.8747 (t0) cc_final: 0.8362 (t0) REVERT: n 75 ILE cc_start: 0.7580 (OUTLIER) cc_final: 0.7252 (mm) outliers start: 69 outliers final: 40 residues processed: 266 average time/residue: 0.5925 time to fit residues: 176.1645 Evaluate side-chains 274 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 223 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain h residue 2 VAL Chi-restraints excluded: chain h residue 6 GLU Chi-restraints excluded: chain h residue 46 GLU Chi-restraints excluded: chain l residue 22 THR Chi-restraints excluded: chain l residue 54 LEU Chi-restraints excluded: chain l residue 70 ASP Chi-restraints excluded: chain l residue 74 THR Chi-restraints excluded: chain l residue 100 GLN Chi-restraints excluded: chain a residue 74 GLU Chi-restraints excluded: chain a residue 168 TRP Chi-restraints excluded: chain A residue -2 HIS Chi-restraints excluded: chain A residue 0 HIS Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 112 THR Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 116 LYS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain b residue 261 ARG Chi-restraints excluded: chain b residue 346 VAL Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain m residue 109 THR Chi-restraints excluded: chain m residue 112 THR Chi-restraints excluded: chain n residue 5 THR Chi-restraints excluded: chain n residue 9 SER Chi-restraints excluded: chain n residue 10 SER Chi-restraints excluded: chain n residue 63 SER Chi-restraints excluded: chain n residue 74 THR Chi-restraints excluded: chain n residue 75 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 139 optimal weight: 5.9990 chunk 205 optimal weight: 5.9990 chunk 203 optimal weight: 7.9990 chunk 120 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 197 optimal weight: 7.9990 chunk 56 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 219 optimal weight: 0.8980 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 107 GLN L 27 GLN L 100 GLN l 100 GLN a 0 HIS a 263 GLN A 164 HIS N 100 GLN B 0 HIS m 107 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.136686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.113285 restraints weight = 55460.418| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 4.86 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3283 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3283 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 18548 Z= 0.251 Angle : 0.694 9.253 25192 Z= 0.365 Chirality : 0.048 0.253 2685 Planarity : 0.005 0.051 3216 Dihedral : 5.512 42.437 2514 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.62 % Favored : 95.34 % Rotamer: Outliers : 3.60 % Allowed : 15.16 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % 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 aren not related in a simple way. whole: -0.76 (0.17), residues: 2264 helix: 1.29 (0.39), residues: 153 sheet: -0.43 (0.19), residues: 753 loop : -0.72 (0.17), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG b 41 TYR 0.020 0.002 TYR N 49 PHE 0.017 0.002 PHE A 323 TRP 0.026 0.002 TRP a 168 HIS 0.011 0.002 HIS A 164 Details of bonding type rmsd covalent geometry : bond 0.00610 (18516) covalent geometry : angle 0.69007 (25128) SS BOND : bond 0.00626 ( 32) SS BOND : angle 1.68131 ( 64) hydrogen bonds : bond 0.05263 ( 555) hydrogen bonds : angle 5.83212 ( 1464) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 225 time to evaluate : 0.529 Fit side-chains REVERT: H 3 GLN cc_start: 0.7959 (OUTLIER) cc_final: 0.7364 (mt0) REVERT: H 29 VAL cc_start: 0.8968 (m) cc_final: 0.8719 (t) REVERT: L 78 LEU cc_start: 0.8229 (tp) cc_final: 0.7924 (tm) REVERT: L 79 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7274 (mp10) REVERT: a 74 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7360 (tt0) REVERT: A -2 HIS cc_start: 0.5886 (OUTLIER) cc_final: 0.5445 (t-90) REVERT: A 12 GLU cc_start: 0.7404 (mm-30) cc_final: 0.7159 (mt-10) REVERT: A 116 LYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7717 (pttm) REVERT: A 220 MET cc_start: 0.8242 (OUTLIER) cc_final: 0.6746 (mmt) REVERT: A 284 LYS cc_start: 0.7831 (mtpp) cc_final: 0.7424 (tttp) REVERT: A 286 HIS cc_start: 0.8100 (m-70) cc_final: 0.7892 (m-70) REVERT: M 98 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.7963 (tt0) REVERT: B 63 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.7738 (ttp) REVERT: B 340 GLU cc_start: 0.6994 (OUTLIER) cc_final: 0.6615 (mt-10) REVERT: b 31 ARG cc_start: 0.6335 (ttm110) cc_final: 0.6045 (ttt90) REVERT: b 33 LYS cc_start: 0.5997 (tmtt) cc_final: 0.5772 (tmmm) REVERT: b 261 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.7489 (mtt-85) REVERT: b 274 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7384 (tm-30) REVERT: m 76 ASN cc_start: 0.8664 (t0) cc_final: 0.8294 (t0) REVERT: n 75 ILE cc_start: 0.7802 (OUTLIER) cc_final: 0.7468 (mm) outliers start: 67 outliers final: 45 residues processed: 260 average time/residue: 0.5836 time to fit residues: 169.3656 Evaluate side-chains 276 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 219 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain h residue 2 VAL Chi-restraints excluded: chain h residue 6 GLU Chi-restraints excluded: chain h residue 46 GLU Chi-restraints excluded: chain l residue 22 THR Chi-restraints excluded: chain l residue 54 LEU Chi-restraints excluded: chain l residue 70 ASP Chi-restraints excluded: chain l residue 74 THR Chi-restraints excluded: chain l residue 100 GLN Chi-restraints excluded: chain a residue 74 GLU Chi-restraints excluded: chain a residue 168 TRP Chi-restraints excluded: chain A residue -2 HIS Chi-restraints excluded: chain A residue 0 HIS Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 98 GLU Chi-restraints excluded: chain M residue 112 THR Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain b residue 261 ARG Chi-restraints excluded: chain b residue 274 GLU Chi-restraints excluded: chain b residue 346 VAL Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain m residue 87 VAL Chi-restraints excluded: chain m residue 109 THR Chi-restraints excluded: chain m residue 112 THR Chi-restraints excluded: chain n residue 5 THR Chi-restraints excluded: chain n residue 9 SER Chi-restraints excluded: chain n residue 10 SER Chi-restraints excluded: chain n residue 63 SER Chi-restraints excluded: chain n residue 74 THR Chi-restraints excluded: chain n residue 75 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 82 optimal weight: 0.5980 chunk 213 optimal weight: 9.9990 chunk 148 optimal weight: 6.9990 chunk 42 optimal weight: 10.0000 chunk 80 optimal weight: 0.3980 chunk 53 optimal weight: 8.9990 chunk 41 optimal weight: 0.4980 chunk 149 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 27 GLN L 100 GLN l 100 GLN a 0 HIS a 147 HIS a 263 GLN m 107 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.139751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.104369 restraints weight = 63808.604| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 3.42 r_work: 0.2940 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2924 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2924 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 18548 Z= 0.119 Angle : 0.566 8.780 25192 Z= 0.299 Chirality : 0.042 0.188 2685 Planarity : 0.004 0.044 3216 Dihedral : 4.991 39.280 2514 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.64 % Favored : 96.31 % Rotamer: Outliers : 2.43 % Allowed : 16.48 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % 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 aren not related in a simple way. whole: -0.46 (0.18), residues: 2264 helix: 1.86 (0.40), residues: 153 sheet: -0.17 (0.20), residues: 702 loop : -0.60 (0.16), residues: 1409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG b 41 TYR 0.012 0.001 TYR A 175 PHE 0.012 0.001 PHE b 123 TRP 0.022 0.001 TRP a 168 HIS 0.004 0.001 HIS B 195 Details of bonding type rmsd covalent geometry : bond 0.00279 (18516) covalent geometry : angle 0.56130 (25128) SS BOND : bond 0.00443 ( 32) SS BOND : angle 1.57303 ( 64) hydrogen bonds : bond 0.03850 ( 555) hydrogen bonds : angle 5.40929 ( 1464) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 238 time to evaluate : 0.741 Fit side-chains revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7549 (mt0) REVERT: H 29 VAL cc_start: 0.8917 (m) cc_final: 0.8614 (t) REVERT: L 78 LEU cc_start: 0.8069 (tp) cc_final: 0.7756 (tm) REVERT: L 79 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7222 (mp10) REVERT: A -2 HIS cc_start: 0.6156 (OUTLIER) cc_final: 0.5685 (t-90) REVERT: A 12 GLU cc_start: 0.7619 (mm-30) cc_final: 0.7356 (mt-10) REVERT: A 116 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7825 (pttm) REVERT: A 220 MET cc_start: 0.8650 (OUTLIER) cc_final: 0.7283 (mmt) REVERT: A 284 LYS cc_start: 0.7771 (mtpp) cc_final: 0.7344 (tttp) REVERT: A 286 HIS cc_start: 0.7969 (m-70) cc_final: 0.7729 (m-70) REVERT: B 33 LYS cc_start: 0.8281 (ptmt) cc_final: 0.7969 (ptpp) REVERT: B 63 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.8022 (ttp) REVERT: B 94 LYS cc_start: 0.8195 (mmmm) cc_final: 0.7504 (mtmt) REVERT: B 340 GLU cc_start: 0.6754 (OUTLIER) cc_final: 0.6428 (mt-10) REVERT: b 31 ARG cc_start: 0.6359 (ttm110) cc_final: 0.6080 (ttt90) REVERT: b 274 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7827 (tm-30) REVERT: m 76 ASN cc_start: 0.8706 (t0) cc_final: 0.8319 (t0) REVERT: n 75 ILE cc_start: 0.7454 (OUTLIER) cc_final: 0.7158 (mm) REVERT: n 103 LYS cc_start: 0.8128 (ttpm) cc_final: 0.7758 (tttp) outliers start: 44 outliers final: 27 residues processed: 261 average time/residue: 0.5993 time to fit residues: 173.5871 Evaluate side-chains 264 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 228 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain l residue 22 THR Chi-restraints excluded: chain l residue 70 ASP Chi-restraints excluded: chain l residue 100 GLN Chi-restraints excluded: chain a residue 168 TRP Chi-restraints excluded: chain A residue -2 HIS Chi-restraints excluded: chain A residue 0 HIS Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain B residue 0 HIS Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain b residue 274 GLU Chi-restraints excluded: chain b residue 346 VAL Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain m residue 87 VAL Chi-restraints excluded: chain m residue 112 THR Chi-restraints excluded: chain n residue 5 THR Chi-restraints excluded: chain n residue 9 SER Chi-restraints excluded: chain n residue 10 SER Chi-restraints excluded: chain n residue 74 THR Chi-restraints excluded: chain n residue 75 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 187 optimal weight: 3.9990 chunk 71 optimal weight: 9.9990 chunk 189 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 209 optimal weight: 0.5980 chunk 26 optimal weight: 4.9990 chunk 141 optimal weight: 0.9980 chunk 218 optimal weight: 4.9990 chunk 115 optimal weight: 6.9990 chunk 137 optimal weight: 2.9990 chunk 112 optimal weight: 0.0670 overall best weight: 1.7322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 107 GLN L 27 GLN L 100 GLN l 100 GLN a 0 HIS m 31 ASN m 107 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.138683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.115831 restraints weight = 57971.855| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 5.05 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3329 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3329 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18548 Z= 0.155 Angle : 0.602 9.183 25192 Z= 0.316 Chirality : 0.044 0.209 2685 Planarity : 0.004 0.045 3216 Dihedral : 5.063 38.370 2514 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.00 % Favored : 95.96 % Rotamer: Outliers : 2.89 % Allowed : 16.28 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % 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 aren not related in a simple way. whole: -0.48 (0.18), residues: 2264 helix: 1.85 (0.40), residues: 153 sheet: -0.23 (0.20), residues: 726 loop : -0.58 (0.17), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG b 41 TYR 0.014 0.001 TYR N 49 PHE 0.012 0.002 PHE l 98 TRP 0.022 0.001 TRP a 168 HIS 0.005 0.001 HIS A 2 Details of bonding type rmsd covalent geometry : bond 0.00373 (18516) covalent geometry : angle 0.59791 (25128) SS BOND : bond 0.00488 ( 32) SS BOND : angle 1.55287 ( 64) hydrogen bonds : bond 0.04273 ( 555) hydrogen bonds : angle 5.47138 ( 1464) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 228 time to evaluate : 0.519 Fit side-chains revert: symmetry clash REVERT: H 3 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7305 (mt0) REVERT: H 29 VAL cc_start: 0.8911 (m) cc_final: 0.8688 (t) REVERT: L 45 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7845 (ttpt) REVERT: L 78 LEU cc_start: 0.8141 (tp) cc_final: 0.7887 (tm) REVERT: L 79 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7337 (mp10) REVERT: A -2 HIS cc_start: 0.5987 (OUTLIER) cc_final: 0.5543 (t-90) REVERT: A 12 GLU cc_start: 0.7373 (mm-30) cc_final: 0.7120 (mt-10) REVERT: A 116 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7688 (pttm) REVERT: A 284 LYS cc_start: 0.7693 (mtpp) cc_final: 0.7330 (tttp) REVERT: A 286 HIS cc_start: 0.8070 (m-70) cc_final: 0.7864 (m-70) REVERT: B 33 LYS cc_start: 0.8336 (ptmt) cc_final: 0.8069 (ptpp) REVERT: B 63 MET cc_start: 0.7993 (OUTLIER) cc_final: 0.7656 (ttp) REVERT: B 94 LYS cc_start: 0.8136 (mmmm) cc_final: 0.7435 (mtmt) REVERT: B 128 LYS cc_start: 0.7664 (tmmt) cc_final: 0.6745 (tmtt) REVERT: B 340 GLU cc_start: 0.6848 (OUTLIER) cc_final: 0.6459 (mt-10) REVERT: b 31 ARG cc_start: 0.6324 (ttm110) cc_final: 0.6057 (ttt90) REVERT: b 274 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7541 (tm-30) REVERT: m 76 ASN cc_start: 0.8595 (t0) cc_final: 0.8224 (t0) REVERT: n 75 ILE cc_start: 0.7620 (OUTLIER) cc_final: 0.7313 (mm) REVERT: n 103 LYS cc_start: 0.8279 (ttpm) cc_final: 0.8021 (tttp) outliers start: 53 outliers final: 30 residues processed: 256 average time/residue: 0.5821 time to fit residues: 166.5385 Evaluate side-chains 262 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 223 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain h residue 2 VAL Chi-restraints excluded: chain l residue 22 THR Chi-restraints excluded: chain l residue 100 GLN Chi-restraints excluded: chain a residue 168 TRP Chi-restraints excluded: chain A residue -2 HIS Chi-restraints excluded: chain A residue 0 HIS Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 112 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain b residue 274 GLU Chi-restraints excluded: chain b residue 346 VAL Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain m residue 87 VAL Chi-restraints excluded: chain m residue 112 THR Chi-restraints excluded: chain n residue 5 THR Chi-restraints excluded: chain n residue 9 SER Chi-restraints excluded: chain n residue 10 SER Chi-restraints excluded: chain n residue 74 THR Chi-restraints excluded: chain n residue 75 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 220 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 208 optimal weight: 6.9990 chunk 198 optimal weight: 9.9990 chunk 171 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 165 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 102 optimal weight: 0.7980 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 107 GLN L 27 GLN L 100 GLN l 100 GLN a 0 HIS m 107 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.137245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.101881 restraints weight = 62656.062| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 3.56 r_work: 0.2908 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2910 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2910 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 18548 Z= 0.222 Angle : 0.675 9.644 25192 Z= 0.353 Chirality : 0.047 0.244 2685 Planarity : 0.005 0.049 3216 Dihedral : 5.376 40.317 2514 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.44 % Favored : 95.52 % Rotamer: Outliers : 3.09 % Allowed : 16.43 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % 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 aren not related in a simple way. whole: -0.64 (0.18), residues: 2264 helix: 1.60 (0.39), residues: 153 sheet: -0.36 (0.19), residues: 763 loop : -0.66 (0.17), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG b 41 TYR 0.019 0.002 TYR N 49 PHE 0.013 0.002 PHE A 323 TRP 0.025 0.002 TRP a 168 HIS 0.007 0.001 HIS b 158 Details of bonding type rmsd covalent geometry : bond 0.00542 (18516) covalent geometry : angle 0.66998 (25128) SS BOND : bond 0.00601 ( 32) SS BOND : angle 1.77978 ( 64) hydrogen bonds : bond 0.04952 ( 555) hydrogen bonds : angle 5.67667 ( 1464) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 223 time to evaluate : 0.495 Fit side-chains revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7580 (mt0) REVERT: H 29 VAL cc_start: 0.8920 (m) cc_final: 0.8616 (t) REVERT: L 78 LEU cc_start: 0.8151 (tp) cc_final: 0.7765 (tm) REVERT: L 79 GLN cc_start: 0.8143 (OUTLIER) cc_final: 0.7212 (mp10) REVERT: a 74 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7951 (tt0) REVERT: A -2 HIS cc_start: 0.6196 (OUTLIER) cc_final: 0.5519 (t-90) REVERT: A 12 GLU cc_start: 0.7614 (mm-30) cc_final: 0.7346 (mt-10) REVERT: A 116 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7834 (pttm) REVERT: A 284 LYS cc_start: 0.7829 (mtpp) cc_final: 0.7449 (tttp) REVERT: A 286 HIS cc_start: 0.7995 (m-70) cc_final: 0.7757 (m-70) REVERT: B 33 LYS cc_start: 0.8340 (ptmt) cc_final: 0.7988 (ptpp) REVERT: B 63 MET cc_start: 0.8351 (OUTLIER) cc_final: 0.8040 (ttp) REVERT: B 128 LYS cc_start: 0.7633 (tmmt) cc_final: 0.6834 (tmtt) REVERT: B 340 GLU cc_start: 0.6783 (OUTLIER) cc_final: 0.6371 (mt-10) REVERT: b 31 ARG cc_start: 0.6381 (ttm110) cc_final: 0.6061 (ttt90) REVERT: b 164 HIS cc_start: 0.6303 (OUTLIER) cc_final: 0.6083 (p90) REVERT: b 261 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.8168 (mtt-85) REVERT: b 293 THR cc_start: 0.7489 (OUTLIER) cc_final: 0.7126 (p) REVERT: m 76 ASN cc_start: 0.8754 (t0) cc_final: 0.8379 (t0) REVERT: n 75 ILE cc_start: 0.7642 (OUTLIER) cc_final: 0.7362 (mm) REVERT: n 103 LYS cc_start: 0.8143 (ttpm) cc_final: 0.7778 (tttp) outliers start: 57 outliers final: 38 residues processed: 255 average time/residue: 0.5650 time to fit residues: 160.2952 Evaluate side-chains 272 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 223 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain h residue 2 VAL Chi-restraints excluded: chain h residue 6 GLU Chi-restraints excluded: chain l residue 22 THR Chi-restraints excluded: chain l residue 70 ASP Chi-restraints excluded: chain l residue 74 THR Chi-restraints excluded: chain l residue 100 GLN Chi-restraints excluded: chain a residue 74 GLU Chi-restraints excluded: chain a residue 168 TRP Chi-restraints excluded: chain A residue -2 HIS Chi-restraints excluded: chain A residue 0 HIS Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 112 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain b residue 37 ASP Chi-restraints excluded: chain b residue 164 HIS Chi-restraints excluded: chain b residue 261 ARG Chi-restraints excluded: chain b residue 293 THR Chi-restraints excluded: chain b residue 346 VAL Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain m residue 87 VAL Chi-restraints excluded: chain m residue 112 THR Chi-restraints excluded: chain n residue 5 THR Chi-restraints excluded: chain n residue 9 SER Chi-restraints excluded: chain n residue 10 SER Chi-restraints excluded: chain n residue 63 SER Chi-restraints excluded: chain n residue 74 THR Chi-restraints excluded: chain n residue 75 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 153 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 187 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 62 optimal weight: 0.0980 chunk 0 optimal weight: 7.9990 chunk 147 optimal weight: 2.9990 chunk 174 optimal weight: 9.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 107 GLN L 27 GLN L 100 GLN l 100 GLN a 0 HIS N 100 GLN m 107 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.138361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.103408 restraints weight = 53414.121| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 3.37 r_work: 0.2949 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2924 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2924 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 18548 Z= 0.162 Angle : 0.616 9.942 25192 Z= 0.323 Chirality : 0.044 0.218 2685 Planarity : 0.004 0.048 3216 Dihedral : 5.197 39.366 2514 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.95 % Favored : 96.00 % Rotamer: Outliers : 2.59 % Allowed : 17.14 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % 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 aren not related in a simple way. whole: -0.53 (0.18), residues: 2264 helix: 1.77 (0.40), residues: 153 sheet: -0.20 (0.20), residues: 702 loop : -0.65 (0.16), residues: 1409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG b 41 TYR 0.014 0.001 TYR N 49 PHE 0.011 0.002 PHE b 163 TRP 0.024 0.001 TRP a 168 HIS 0.005 0.001 HIS b 158 Details of bonding type rmsd covalent geometry : bond 0.00391 (18516) covalent geometry : angle 0.61256 (25128) SS BOND : bond 0.00492 ( 32) SS BOND : angle 1.47601 ( 64) hydrogen bonds : bond 0.04363 ( 555) hydrogen bonds : angle 5.52585 ( 1464) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 222 time to evaluate : 0.518 Fit side-chains revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8143 (OUTLIER) cc_final: 0.7546 (mt0) REVERT: H 29 VAL cc_start: 0.8919 (m) cc_final: 0.8630 (t) REVERT: L 78 LEU cc_start: 0.8121 (tp) cc_final: 0.7785 (tm) REVERT: L 79 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7230 (mp10) REVERT: A -2 HIS cc_start: 0.6237 (OUTLIER) cc_final: 0.5596 (t-90) REVERT: A 12 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7294 (mt-10) REVERT: A 116 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7823 (pttm) REVERT: A 284 LYS cc_start: 0.7820 (mtpp) cc_final: 0.7368 (tttp) REVERT: A 286 HIS cc_start: 0.7979 (m-70) cc_final: 0.7743 (m-70) REVERT: N 33 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8434 (tp) REVERT: B 33 LYS cc_start: 0.8311 (ptmt) cc_final: 0.7970 (ptpp) REVERT: B 63 MET cc_start: 0.8351 (OUTLIER) cc_final: 0.8034 (ttp) REVERT: B 128 LYS cc_start: 0.7565 (tmmt) cc_final: 0.6787 (tmtt) REVERT: B 340 GLU cc_start: 0.6768 (OUTLIER) cc_final: 0.6395 (mt-10) REVERT: b 31 ARG cc_start: 0.6380 (ttm110) cc_final: 0.6094 (ttt90) REVERT: b 164 HIS cc_start: 0.6305 (OUTLIER) cc_final: 0.6061 (p90) REVERT: b 293 THR cc_start: 0.7473 (OUTLIER) cc_final: 0.7107 (p) REVERT: n 75 ILE cc_start: 0.7580 (OUTLIER) cc_final: 0.7296 (mm) REVERT: n 103 LYS cc_start: 0.8133 (ttpm) cc_final: 0.7780 (tttp) outliers start: 47 outliers final: 33 residues processed: 251 average time/residue: 0.5881 time to fit residues: 164.6894 Evaluate side-chains 263 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 220 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain h residue 2 VAL Chi-restraints excluded: chain l residue 22 THR Chi-restraints excluded: chain l residue 70 ASP Chi-restraints excluded: chain l residue 100 GLN Chi-restraints excluded: chain a residue 168 TRP Chi-restraints excluded: chain A residue -2 HIS Chi-restraints excluded: chain A residue 0 HIS Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 112 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain b residue 164 HIS Chi-restraints excluded: chain b residue 293 THR Chi-restraints excluded: chain b residue 346 VAL Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain m residue 87 VAL Chi-restraints excluded: chain m residue 112 THR Chi-restraints excluded: chain n residue 5 THR Chi-restraints excluded: chain n residue 9 SER Chi-restraints excluded: chain n residue 10 SER Chi-restraints excluded: chain n residue 74 THR Chi-restraints excluded: chain n residue 75 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 196 optimal weight: 0.0470 chunk 39 optimal weight: 6.9990 chunk 116 optimal weight: 0.9980 chunk 54 optimal weight: 0.0030 chunk 218 optimal weight: 7.9990 chunk 137 optimal weight: 0.9990 chunk 82 optimal weight: 0.0570 chunk 146 optimal weight: 0.0970 chunk 173 optimal weight: 0.9980 chunk 213 optimal weight: 20.0000 chunk 56 optimal weight: 0.7980 overall best weight: 0.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 107 GLN L 27 GLN L 100 GLN l 100 GLN N 100 GLN m 107 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.144890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.111152 restraints weight = 48070.805| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 3.19 r_work: 0.3076 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3066 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3066 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 18548 Z= 0.087 Angle : 0.510 9.108 25192 Z= 0.269 Chirality : 0.041 0.169 2685 Planarity : 0.004 0.038 3216 Dihedral : 4.488 33.248 2514 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.20 % Favored : 96.76 % Rotamer: Outliers : 1.83 % Allowed : 17.85 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % 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 aren not related in a simple way. whole: -0.21 (0.18), residues: 2264 helix: 2.10 (0.41), residues: 153 sheet: 0.04 (0.21), residues: 676 loop : -0.45 (0.16), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG b 41 TYR 0.014 0.001 TYR A 175 PHE 0.012 0.001 PHE l 98 TRP 0.025 0.001 TRP B 115 HIS 0.003 0.000 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00196 (18516) covalent geometry : angle 0.50813 (25128) SS BOND : bond 0.00251 ( 32) SS BOND : angle 0.90451 ( 64) hydrogen bonds : bond 0.03005 ( 555) hydrogen bonds : angle 4.99289 ( 1464) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5425.07 seconds wall clock time: 93 minutes 5.07 seconds (5585.07 seconds total)