Starting phenix.real_space_refine on Sun May 25 07:14:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jkf_36371/05_2025/8jkf_36371.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jkf_36371/05_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_36371/05_2025/8jkf_36371.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jkf_36371/05_2025/8jkf_36371.map" model { file = "/net/cci-nas-00/data/ceres_data/8jkf_36371/05_2025/8jkf_36371.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jkf_36371/05_2025/8jkf_36371.cif" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'TYR:plan': 1, 'TRP: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: {'TYR:plan': 1, 'TRP: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: 20.30, per 1000 atoms: 1.12 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: 4.25 Conformation dependent library (CDL) restraints added in 3.8 seconds 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: 4.66 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: 10.29 Time building geometry restraints manager: 5.08 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: 4.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.190 Construct map_model_manager: 0.010 Extract box with map and model: 0.790 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 62.040 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.120 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:13.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.180 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.013 0.001 TRP B 115 HIS 0.006 0.001 HIS B 1 PHE 0.009 0.002 PHE n 98 TYR 0.038 0.002 TYR h 33 ARG 0.015 0.000 ARG b 31 Details of bonding type rmsd hydrogen bonds : bond 0.22738 ( 555) hydrogen bonds : angle 9.09504 ( 1464) SS BOND : bond 0.00447 ( 32) SS BOND : angle 1.50277 ( 64) covalent geometry : bond 0.00474 (18516) covalent geometry : angle 0.63556 (25128) *********************** 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 : 2.069 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: 1.4013 time to fit residues: 543.2349 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 : 2.147 ------------------------------------------------------------------------------- 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 187 optimal weight: 4.9990 chunk 168 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 113 optimal weight: 9.9990 chunk 89 optimal weight: 3.9990 chunk 174 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 chunk 105 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 chunk 201 optimal weight: 10.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 1 HIS B 0 HIS B 286 HIS b 2 HIS m 107 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.137609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.101752 restraints weight = 67028.790| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 3.69 r_work: 0.2885 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2881 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2880 r_free = 0.2880 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2880 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 18548 Z= 0.272 Angle : 0.738 10.274 25192 Z= 0.389 Chirality : 0.049 0.239 2685 Planarity : 0.006 0.053 3216 Dihedral : 5.934 68.955 2521 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.31 % Favored : 95.65 % Rotamer: Outliers : 3.09 % Allowed : 10.29 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.18), residues: 2264 helix: 1.09 (0.39), residues: 153 sheet: -0.37 (0.20), residues: 736 loop : -0.65 (0.17), residues: 1375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP a 168 HIS 0.009 0.002 HIS B 286 PHE 0.016 0.002 PHE A 323 TYR 0.034 0.002 TYR H 33 ARG 0.010 0.001 ARG b 41 Details of bonding type rmsd hydrogen bonds : bond 0.05879 ( 555) hydrogen bonds : angle 6.37214 ( 1464) SS BOND : bond 0.00686 ( 32) SS BOND : angle 1.87018 ( 64) covalent geometry : bond 0.00657 (18516) covalent geometry : angle 0.73301 (25128) *********************** 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 321 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 263 time to evaluate : 1.919 Fit side-chains revert: symmetry clash REVERT: H 29 VAL cc_start: 0.8996 (m) cc_final: 0.8725 (t) REVERT: a 40 ARG cc_start: 0.6827 (mtm-85) cc_final: 0.6535 (ttm110) REVERT: A 12 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7492 (mt-10) REVERT: A 116 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7819 (pttm) REVERT: A 128 LYS cc_start: 0.7991 (ttmm) cc_final: 0.7579 (tttt) REVERT: A 284 LYS cc_start: 0.7963 (mtpp) cc_final: 0.7427 (tttp) REVERT: A 286 HIS cc_start: 0.8068 (m-70) cc_final: 0.7796 (m-70) REVERT: A 309 GLU cc_start: 0.7102 (tm-30) cc_final: 0.6877 (tm-30) REVERT: M 3 GLN cc_start: 0.8359 (tt0) cc_final: 0.8112 (mm110) REVERT: B 63 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.8069 (ttp) REVERT: B 94 LYS cc_start: 0.8295 (mmmm) cc_final: 0.7531 (mtmt) REVERT: B 109 ASN cc_start: 0.7233 (m-40) cc_final: 0.6953 (m-40) REVERT: b 31 ARG cc_start: 0.6426 (ttm110) cc_final: 0.5951 (ttt90) REVERT: b 164 HIS cc_start: 0.6249 (OUTLIER) cc_final: 0.6040 (p90) REVERT: b 261 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.8212 (mtt-85) REVERT: b 274 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.7878 (tm-30) outliers start: 58 outliers final: 29 residues processed: 296 average time/residue: 1.3824 time to fit residues: 456.4637 Evaluate side-chains 264 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 230 time to evaluate : 1.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 100 GLN Chi-restraints excluded: chain h residue 54 SER 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 0 HIS Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 125 ARG Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain M residue 112 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 110 GLU Chi-restraints excluded: chain b residue 164 HIS Chi-restraints excluded: chain b residue 261 ARG Chi-restraints excluded: chain b residue 274 GLU 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 63 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 137 optimal weight: 0.8980 chunk 208 optimal weight: 0.9990 chunk 1 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 200 optimal weight: 7.9990 chunk 79 optimal weight: 1.9990 chunk 163 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 145 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 12 optimal weight: 0.0570 overall best weight: 0.9902 ------------------------------------------------------------------------------- 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 a 0 HIS a 263 GLN A 113 HIS N 100 GLN B 0 HIS b 131 ASN m 107 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.140881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.105747 restraints weight = 51122.940| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 3.28 r_work: 0.2962 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2968 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2968 r_free = 0.2968 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2968 r_free = 0.2968 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2968 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18548 Z= 0.112 Angle : 0.551 7.121 25192 Z= 0.293 Chirality : 0.042 0.168 2685 Planarity : 0.004 0.043 3216 Dihedral : 5.081 58.256 2517 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.24 % Favored : 96.71 % Rotamer: Outliers : 2.54 % Allowed : 12.42 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.18), residues: 2264 helix: 1.68 (0.41), residues: 153 sheet: -0.16 (0.21), residues: 657 loop : -0.51 (0.16), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP a 168 HIS 0.012 0.001 HIS A 113 PHE 0.009 0.001 PHE n 98 TYR 0.012 0.001 TYR A 175 ARG 0.007 0.000 ARG b 41 Details of bonding type rmsd hydrogen bonds : bond 0.03968 ( 555) hydrogen bonds : angle 5.65842 ( 1464) SS BOND : bond 0.00364 ( 32) SS BOND : angle 1.11756 ( 64) covalent geometry : bond 0.00256 (18516) covalent geometry : angle 0.54872 (25128) *********************** 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 291 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 244 time to evaluate : 2.060 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.7583 (mt0) REVERT: H 29 VAL cc_start: 0.8904 (m) cc_final: 0.8610 (t) REVERT: H 64 LYS cc_start: 0.9148 (ttmt) cc_final: 0.8908 (ttpt) REVERT: L 14 SER cc_start: 0.8312 (OUTLIER) cc_final: 0.7955 (m) REVERT: L 79 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.7230 (mp10) REVERT: h 19 ARG cc_start: 0.8721 (ttt-90) cc_final: 0.8502 (ttt180) REVERT: a 263 GLN cc_start: 0.8887 (mm-40) cc_final: 0.8663 (mm110) REVERT: A 12 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7367 (mt-10) REVERT: A 116 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7814 (pttm) REVERT: A 128 LYS cc_start: 0.7906 (ttmm) cc_final: 0.7555 (tttt) REVERT: A 220 MET cc_start: 0.8608 (OUTLIER) cc_final: 0.7213 (mmt) REVERT: A 284 LYS cc_start: 0.7890 (mtpp) cc_final: 0.7442 (tttp) REVERT: A 286 HIS cc_start: 0.7981 (m-70) cc_final: 0.7667 (m-70) REVERT: A 309 GLU cc_start: 0.6857 (tm-30) cc_final: 0.6634 (tm-30) REVERT: B 63 MET cc_start: 0.8226 (OUTLIER) cc_final: 0.7925 (ttp) REVERT: B 94 LYS cc_start: 0.8279 (mmmm) cc_final: 0.7482 (mtmt) REVERT: B 109 ASN cc_start: 0.7262 (m-40) cc_final: 0.6993 (m-40) REVERT: b 31 ARG cc_start: 0.6312 (ttm110) cc_final: 0.6003 (ttt90) REVERT: b 164 HIS cc_start: 0.6326 (OUTLIER) cc_final: 0.5906 (p90) REVERT: b 170 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.6811 (tppt) REVERT: m 76 ASN cc_start: 0.8673 (t0) cc_final: 0.8315 (t0) REVERT: n 103 LYS cc_start: 0.8198 (ttmm) cc_final: 0.7916 (tttp) outliers start: 47 outliers final: 21 residues processed: 271 average time/residue: 1.3239 time to fit residues: 400.1009 Evaluate side-chains 258 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 229 time to evaluate : 1.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain L residue 14 SER 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 h residue 6 GLU Chi-restraints excluded: chain l residue 22 THR 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 125 ARG Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 287 VAL 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 110 GLU Chi-restraints excluded: chain b residue 164 HIS Chi-restraints excluded: chain b residue 170 LYS 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 65 optimal weight: 0.3980 chunk 193 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 174 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 161 optimal weight: 9.9990 chunk 125 optimal weight: 6.9990 chunk 207 optimal weight: 5.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 35 ASN L 27 GLN L 100 GLN l 100 GLN a 0 HIS A 164 HIS N 100 GLN B 0 HIS m 107 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.138362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.103001 restraints weight = 52146.739| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 3.25 r_work: 0.2947 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2938 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2938 r_free = 0.2938 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2938 r_free = 0.2938 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2938 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18548 Z= 0.178 Angle : 0.626 8.255 25192 Z= 0.329 Chirality : 0.045 0.209 2685 Planarity : 0.005 0.044 3216 Dihedral : 5.320 53.587 2517 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.86 % Favored : 96.09 % Rotamer: Outliers : 3.35 % Allowed : 13.74 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.18), residues: 2264 helix: 1.62 (0.40), residues: 153 sheet: -0.25 (0.20), residues: 708 loop : -0.53 (0.17), residues: 1403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP a 168 HIS 0.010 0.001 HIS A 164 PHE 0.012 0.002 PHE b 163 TYR 0.015 0.002 TYR H 94 ARG 0.010 0.000 ARG b 41 Details of bonding type rmsd hydrogen bonds : bond 0.04674 ( 555) hydrogen bonds : angle 5.69398 ( 1464) SS BOND : bond 0.00508 ( 32) SS BOND : angle 1.40663 ( 64) covalent geometry : bond 0.00431 (18516) covalent geometry : angle 0.62278 (25128) *********************** 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 300 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 238 time to evaluate : 2.141 Fit side-chains revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8174 (OUTLIER) cc_final: 0.7615 (mt0) REVERT: H 29 VAL cc_start: 0.8953 (m) cc_final: 0.8643 (t) REVERT: L 14 SER cc_start: 0.8393 (OUTLIER) cc_final: 0.7987 (m) REVERT: L 79 GLN cc_start: 0.8046 (OUTLIER) cc_final: 0.7185 (mp10) REVERT: h 19 ARG cc_start: 0.8719 (ttt-90) cc_final: 0.8496 (ttt180) REVERT: a 40 ARG cc_start: 0.6869 (mtm-85) cc_final: 0.6591 (ttm110) REVERT: A -2 HIS cc_start: 0.6200 (OUTLIER) cc_final: 0.5748 (t-90) REVERT: A 12 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7367 (mt-10) REVERT: A 116 LYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7807 (pttm) REVERT: A 125 ARG cc_start: 0.6990 (mpp-170) cc_final: 0.6736 (tpp-160) REVERT: A 128 LYS cc_start: 0.7749 (ttmm) cc_final: 0.7384 (tttt) REVERT: A 284 LYS cc_start: 0.7905 (mtpp) cc_final: 0.7483 (tttp) REVERT: A 286 HIS cc_start: 0.8015 (m-70) cc_final: 0.7733 (m-70) REVERT: A 309 GLU cc_start: 0.6977 (tm-30) cc_final: 0.6703 (tm-30) REVERT: N 55 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.8053 (mm110) REVERT: B 40 ARG cc_start: 0.6291 (OUTLIER) cc_final: 0.5960 (mtm180) REVERT: B 63 MET cc_start: 0.8288 (OUTLIER) cc_final: 0.7941 (ttp) REVERT: B 94 LYS cc_start: 0.8235 (mmmm) cc_final: 0.7466 (mtmt) REVERT: B 109 ASN cc_start: 0.7273 (m-40) cc_final: 0.7048 (t0) REVERT: B 116 LYS cc_start: 0.8079 (OUTLIER) cc_final: 0.7789 (ttmm) REVERT: B 340 GLU cc_start: 0.6852 (OUTLIER) cc_final: 0.6542 (mt-10) REVERT: b 31 ARG cc_start: 0.6359 (ttm110) cc_final: 0.6000 (ttt90) REVERT: b 164 HIS cc_start: 0.6269 (OUTLIER) cc_final: 0.5993 (p90) REVERT: b 170 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.7800 (ttpp) REVERT: b 261 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.8184 (mtt-85) REVERT: m 76 ASN cc_start: 0.8722 (t0) cc_final: 0.8341 (t0) outliers start: 62 outliers final: 28 residues processed: 267 average time/residue: 1.3281 time to fit residues: 394.4065 Evaluate side-chains 274 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 233 time to evaluate : 1.911 ------------------------------------------------------------------------------- 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 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 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 19 VAL Chi-restraints excluded: chain l residue 22 THR 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 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 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 110 GLU Chi-restraints excluded: chain b residue 164 HIS Chi-restraints excluded: chain b residue 170 LYS 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 102 optimal weight: 5.9990 chunk 135 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 207 optimal weight: 4.9990 chunk 122 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 163 optimal weight: 10.0000 chunk 193 optimal weight: 4.9990 chunk 178 optimal weight: 0.6980 chunk 107 optimal weight: 5.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- 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 263 GLN A 164 HIS N 100 GLN B 0 HIS m 107 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.136002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.112646 restraints weight = 54118.763| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 4.68 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3285 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3285 r_free = 0.3285 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3285 r_free = 0.3285 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3285 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 18548 Z= 0.275 Angle : 0.721 9.735 25192 Z= 0.378 Chirality : 0.049 0.257 2685 Planarity : 0.005 0.051 3216 Dihedral : 5.775 59.811 2517 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.48 % Favored : 95.47 % Rotamer: Outliers : 3.96 % Allowed : 14.55 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.17), residues: 2264 helix: 1.19 (0.38), residues: 153 sheet: -0.42 (0.19), residues: 752 loop : -0.69 (0.17), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP a 168 HIS 0.011 0.002 HIS A 164 PHE 0.015 0.002 PHE A 323 TYR 0.019 0.002 TYR N 49 ARG 0.009 0.001 ARG b 41 Details of bonding type rmsd hydrogen bonds : bond 0.05522 ( 555) hydrogen bonds : angle 5.91692 ( 1464) SS BOND : bond 0.00657 ( 32) SS BOND : angle 1.74366 ( 64) covalent geometry : bond 0.00670 (18516) covalent geometry : angle 0.71629 (25128) *********************** 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 307 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 233 time to evaluate : 1.949 Fit side-chains revert: symmetry clash REVERT: H 3 GLN cc_start: 0.7895 (OUTLIER) cc_final: 0.7321 (mt0) REVERT: H 29 VAL cc_start: 0.8953 (m) cc_final: 0.8699 (t) REVERT: L 14 SER cc_start: 0.8266 (OUTLIER) cc_final: 0.7839 (m) REVERT: L 79 GLN cc_start: 0.8047 (OUTLIER) cc_final: 0.7272 (mp10) REVERT: A -2 HIS cc_start: 0.6102 (OUTLIER) cc_final: 0.5726 (t-90) REVERT: A 12 GLU cc_start: 0.7469 (mm-30) cc_final: 0.7204 (mt-10) REVERT: A 85 GLN cc_start: 0.8151 (mp10) cc_final: 0.7803 (mp10) REVERT: A 116 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7700 (pttm) REVERT: A 284 LYS cc_start: 0.7899 (mtpp) cc_final: 0.7519 (tttp) REVERT: N 45 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.8463 (ttpp) REVERT: N 55 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.7949 (mm110) REVERT: B 63 MET cc_start: 0.8047 (OUTLIER) cc_final: 0.7729 (ttp) REVERT: B 116 LYS cc_start: 0.7960 (OUTLIER) cc_final: 0.7622 (ttmm) REVERT: B 272 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7652 (tm-30) REVERT: B 309 GLU cc_start: 0.6758 (mm-30) cc_final: 0.6515 (tm-30) REVERT: B 340 GLU cc_start: 0.7001 (OUTLIER) cc_final: 0.6631 (mt-10) REVERT: b 31 ARG cc_start: 0.6422 (ttm110) cc_final: 0.6096 (ttt90) REVERT: b 33 LYS cc_start: 0.5919 (tmtt) cc_final: 0.4937 (tmmt) REVERT: b 110 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7412 (mt-10) REVERT: b 170 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7662 (ttpp) REVERT: b 261 ARG cc_start: 0.7789 (OUTLIER) cc_final: 0.7467 (mtt-85) REVERT: m 76 ASN cc_start: 0.8673 (t0) cc_final: 0.8292 (t0) outliers start: 74 outliers final: 37 residues processed: 270 average time/residue: 1.3581 time to fit residues: 408.4014 Evaluate side-chains 276 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 225 time to evaluate : 2.103 ------------------------------------------------------------------------------- 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 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 79 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 19 VAL Chi-restraints excluded: chain l residue 22 THR Chi-restraints excluded: chain l residue 54 LEU Chi-restraints excluded: chain l residue 74 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 71 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 93 VAL 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 A residue 315 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 N residue 45 LYS Chi-restraints excluded: chain N residue 55 GLN 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 272 GLU 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 110 GLU Chi-restraints excluded: chain b residue 170 LYS 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 63 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 102 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 45 optimal weight: 0.5980 chunk 50 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 140 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 216 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** l 100 GLN a 0 HIS a 263 GLN A 164 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 = 0.138379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.103125 restraints weight = 56600.006| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 3.59 r_work: 0.2950 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2929 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2929 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18548 Z= 0.152 Angle : 0.597 8.126 25192 Z= 0.315 Chirality : 0.044 0.203 2685 Planarity : 0.004 0.047 3216 Dihedral : 5.340 59.635 2517 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.95 % Favored : 96.00 % Rotamer: Outliers : 3.40 % Allowed : 15.47 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.18), residues: 2264 helix: 1.61 (0.40), residues: 153 sheet: -0.30 (0.20), residues: 718 loop : -0.64 (0.16), residues: 1393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP a 168 HIS 0.010 0.001 HIS A 164 PHE 0.012 0.002 PHE n 98 TYR 0.012 0.001 TYR H 94 ARG 0.007 0.000 ARG b 41 Details of bonding type rmsd hydrogen bonds : bond 0.04283 ( 555) hydrogen bonds : angle 5.54477 ( 1464) SS BOND : bond 0.00445 ( 32) SS BOND : angle 1.27795 ( 64) covalent geometry : bond 0.00364 (18516) covalent geometry : angle 0.59390 (25128) *********************** 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 300 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 237 time to evaluate : 2.112 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7578 (mt0) REVERT: H 29 VAL cc_start: 0.8939 (m) cc_final: 0.8623 (t) REVERT: L 14 SER cc_start: 0.8421 (OUTLIER) cc_final: 0.7929 (m) REVERT: L 79 GLN cc_start: 0.8046 (OUTLIER) cc_final: 0.7215 (mp10) REVERT: A -2 HIS cc_start: 0.6109 (OUTLIER) cc_final: 0.5806 (t-90) REVERT: A 12 GLU cc_start: 0.7627 (mm-30) cc_final: 0.7221 (tt0) REVERT: A 85 GLN cc_start: 0.8411 (mp10) cc_final: 0.8076 (mp10) REVERT: A 116 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7819 (pttm) REVERT: A 125 ARG cc_start: 0.6861 (mpp-170) cc_final: 0.6517 (tpp-160) REVERT: A 284 LYS cc_start: 0.7820 (mtpp) cc_final: 0.7436 (tttp) REVERT: N 33 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8432 (tp) REVERT: N 55 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.8037 (mm110) REVERT: B 63 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.8002 (ttp) REVERT: B 94 LYS cc_start: 0.8214 (mmmm) cc_final: 0.7542 (mtmt) REVERT: B 272 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7767 (tm-30) REVERT: B 340 GLU cc_start: 0.6831 (OUTLIER) cc_final: 0.6506 (mt-10) REVERT: b 31 ARG cc_start: 0.6398 (ttm110) cc_final: 0.6086 (ttt90) REVERT: b 33 LYS cc_start: 0.5757 (tmtt) cc_final: 0.4823 (tmmt) REVERT: b 170 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.7779 (ttpp) REVERT: n 103 LYS cc_start: 0.8161 (ttpm) cc_final: 0.7769 (tttp) outliers start: 63 outliers final: 33 residues processed: 273 average time/residue: 1.3532 time to fit residues: 411.4376 Evaluate side-chains 280 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 236 time to evaluate : 1.910 ------------------------------------------------------------------------------- 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 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 79 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 19 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 84 VAL 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 A residue 315 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 N residue 55 GLN 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 272 GLU 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 170 LYS 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 6 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 111 optimal weight: 10.0000 chunk 134 optimal weight: 0.8980 chunk 140 optimal weight: 1.9990 chunk 161 optimal weight: 10.0000 chunk 123 optimal weight: 9.9990 chunk 75 optimal weight: 4.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 m 76 ASN m 107 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.137824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.103339 restraints weight = 54346.013| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 3.20 r_work: 0.2933 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- 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 = 0.20 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: 0.8622 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18548 Z= 0.170 Angle : 0.619 8.393 25192 Z= 0.325 Chirality : 0.044 0.217 2685 Planarity : 0.005 0.049 3216 Dihedral : 5.188 40.008 2514 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.26 % Favored : 95.69 % Rotamer: Outliers : 3.50 % Allowed : 15.62 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.18), residues: 2264 helix: 1.60 (0.40), residues: 153 sheet: -0.29 (0.20), residues: 718 loop : -0.63 (0.16), residues: 1393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP a 168 HIS 0.009 0.001 HIS A 164 PHE 0.012 0.002 PHE l 98 TYR 0.013 0.001 TYR H 94 ARG 0.007 0.000 ARG b 41 Details of bonding type rmsd hydrogen bonds : bond 0.04475 ( 555) hydrogen bonds : angle 5.55938 ( 1464) SS BOND : bond 0.00490 ( 32) SS BOND : angle 1.37531 ( 64) covalent geometry : bond 0.00409 (18516) covalent geometry : angle 0.61603 (25128) *********************** 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 294 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 229 time to evaluate : 1.930 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8157 (OUTLIER) cc_final: 0.7583 (mt0) REVERT: H 29 VAL cc_start: 0.8944 (m) cc_final: 0.8638 (t) REVERT: H 98 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8449 (tt0) REVERT: L 14 SER cc_start: 0.8411 (OUTLIER) cc_final: 0.7937 (m) REVERT: L 79 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7218 (mp10) REVERT: A -2 HIS cc_start: 0.6165 (OUTLIER) cc_final: 0.5850 (t-90) REVERT: A 12 GLU cc_start: 0.7615 (mm-30) cc_final: 0.7219 (tt0) REVERT: A 29 ARG cc_start: 0.7707 (mtm-85) cc_final: 0.7430 (tpp-160) REVERT: A 85 GLN cc_start: 0.8389 (mp10) cc_final: 0.8044 (mp10) REVERT: A 116 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7824 (pttm) REVERT: A 125 ARG cc_start: 0.6911 (mpp-170) cc_final: 0.6535 (tpp-160) REVERT: A 284 LYS cc_start: 0.7843 (mtpp) cc_final: 0.7461 (tttp) REVERT: N 45 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8507 (ttpp) REVERT: N 54 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8833 (mp) REVERT: N 55 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.8057 (mm110) REVERT: B 63 MET cc_start: 0.8386 (OUTLIER) cc_final: 0.8078 (ttp) REVERT: B 272 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7837 (tm-30) REVERT: B 340 GLU cc_start: 0.6797 (OUTLIER) cc_final: 0.6395 (mt-10) REVERT: b 31 ARG cc_start: 0.6378 (ttm110) cc_final: 0.6068 (ttt90) REVERT: b 170 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.7804 (ttpp) REVERT: b 274 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7709 (tm-30) REVERT: n 103 LYS cc_start: 0.8152 (ttpm) cc_final: 0.7772 (tttp) outliers start: 65 outliers final: 37 residues processed: 267 average time/residue: 1.3508 time to fit residues: 401.3767 Evaluate side-chains 277 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 226 time to evaluate : 1.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 98 GLU 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 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 h residue 54 SER Chi-restraints excluded: chain l residue 19 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 71 VAL Chi-restraints excluded: chain A residue 84 VAL 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 A residue 315 GLU Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 112 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 45 LYS Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 55 GLN 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 272 GLU 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 170 LYS 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 63 SER Chi-restraints excluded: chain n residue 74 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 165 optimal weight: 8.9990 chunk 210 optimal weight: 7.9990 chunk 176 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 156 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 114 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 8.9990 chunk 69 optimal weight: 5.9990 chunk 182 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 m 107 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.136330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.101456 restraints weight = 64477.668| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 3.51 r_work: 0.2897 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2893 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2893 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 18548 Z= 0.251 Angle : 0.702 9.462 25192 Z= 0.367 Chirality : 0.048 0.258 2685 Planarity : 0.005 0.052 3216 Dihedral : 5.509 41.673 2514 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.48 % Favored : 95.47 % Rotamer: Outliers : 3.55 % Allowed : 16.13 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.17), residues: 2264 helix: 1.28 (0.38), residues: 153 sheet: -0.43 (0.19), residues: 752 loop : -0.72 (0.17), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP a 168 HIS 0.009 0.002 HIS A 164 PHE 0.015 0.002 PHE A 323 TYR 0.018 0.002 TYR N 49 ARG 0.011 0.001 ARG b 41 Details of bonding type rmsd hydrogen bonds : bond 0.05227 ( 555) hydrogen bonds : angle 5.76585 ( 1464) SS BOND : bond 0.00621 ( 32) SS BOND : angle 1.67765 ( 64) covalent geometry : bond 0.00612 (18516) covalent geometry : angle 0.69760 (25128) *********************** 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 296 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 230 time to evaluate : 1.971 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7620 (mt0) REVERT: H 29 VAL cc_start: 0.8957 (m) cc_final: 0.8641 (t) REVERT: H 98 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8493 (tt0) REVERT: L 14 SER cc_start: 0.8461 (OUTLIER) cc_final: 0.7949 (m) REVERT: L 79 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.7184 (mp10) REVERT: A 12 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7413 (mt-10) REVERT: A 29 ARG cc_start: 0.7713 (mtm-85) cc_final: 0.7426 (tpp-160) REVERT: A 85 GLN cc_start: 0.8441 (mp10) cc_final: 0.8064 (mp10) REVERT: A 97 MET cc_start: 0.8903 (OUTLIER) cc_final: 0.8413 (mtt) REVERT: A 116 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7844 (pttm) REVERT: A 284 LYS cc_start: 0.7903 (mtpp) cc_final: 0.7499 (tttp) REVERT: N 45 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8568 (ttpp) REVERT: N 55 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.8078 (mm110) REVERT: B 63 MET cc_start: 0.8390 (OUTLIER) cc_final: 0.8084 (ttp) REVERT: B 272 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7835 (tm-30) REVERT: B 309 GLU cc_start: 0.7005 (mm-30) cc_final: 0.6663 (tm-30) REVERT: B 340 GLU cc_start: 0.6829 (OUTLIER) cc_final: 0.6406 (mt-10) REVERT: b 31 ARG cc_start: 0.6411 (ttm110) cc_final: 0.6075 (ttt90) REVERT: b 164 HIS cc_start: 0.6366 (OUTLIER) cc_final: 0.6140 (p90) REVERT: b 170 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.7850 (ttpp) REVERT: b 261 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.8203 (mtt-85) REVERT: b 274 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.7751 (tm-30) REVERT: m 76 ASN cc_start: 0.8732 (t0) cc_final: 0.8409 (t0) REVERT: n 75 ILE cc_start: 0.7616 (mm) cc_final: 0.7337 (mm) REVERT: n 103 LYS cc_start: 0.8174 (ttpm) cc_final: 0.7795 (tttp) outliers start: 66 outliers final: 40 residues processed: 268 average time/residue: 1.3471 time to fit residues: 403.9723 Evaluate side-chains 282 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 227 time to evaluate : 1.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 98 GLU 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 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 h residue 54 SER Chi-restraints excluded: chain l residue 19 VAL Chi-restraints excluded: chain l residue 22 THR Chi-restraints excluded: chain l residue 54 LEU 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 97 MET Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 112 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 45 LYS Chi-restraints excluded: chain N residue 55 GLN 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 165 THR Chi-restraints excluded: chain B residue 272 GLU 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 170 LYS 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 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 74 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 135 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 189 optimal weight: 0.7980 chunk 162 optimal weight: 7.9990 chunk 179 optimal weight: 0.0980 chunk 192 optimal weight: 4.9990 chunk 150 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** l 100 GLN a 0 HIS a 147 HIS a 263 GLN A 164 HIS N 100 GLN m 107 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.141078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.105938 restraints weight = 43189.294| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.96 r_work: 0.3016 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2908 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2908 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18548 Z= 0.111 Angle : 0.554 9.321 25192 Z= 0.292 Chirality : 0.042 0.188 2685 Planarity : 0.004 0.044 3216 Dihedral : 4.917 38.176 2514 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.60 % Favored : 96.36 % Rotamer: Outliers : 2.43 % Allowed : 17.70 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.18), residues: 2264 helix: 1.84 (0.40), residues: 153 sheet: -0.15 (0.21), residues: 675 loop : -0.57 (0.16), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP a 168 HIS 0.007 0.001 HIS A 164 PHE 0.018 0.001 PHE L 98 TYR 0.010 0.001 TYR A 175 ARG 0.007 0.000 ARG b 41 Details of bonding type rmsd hydrogen bonds : bond 0.03657 ( 555) hydrogen bonds : angle 5.31233 ( 1464) SS BOND : bond 0.00342 ( 32) SS BOND : angle 1.05323 ( 64) covalent geometry : bond 0.00257 (18516) covalent geometry : angle 0.55183 (25128) *********************** 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 277 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 233 time to evaluate : 1.947 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.7715 (mt0) REVERT: H 29 VAL cc_start: 0.8994 (m) cc_final: 0.8673 (t) REVERT: L 14 SER cc_start: 0.8449 (OUTLIER) cc_final: 0.7979 (m) REVERT: L 70 ASP cc_start: 0.7760 (m-30) cc_final: 0.6939 (t70) REVERT: a 263 GLN cc_start: 0.8759 (mm-40) cc_final: 0.8488 (mm110) REVERT: A -2 HIS cc_start: 0.6299 (OUTLIER) cc_final: 0.5948 (t-90) REVERT: A 12 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7227 (tt0) REVERT: A 85 GLN cc_start: 0.8496 (mp10) cc_final: 0.8112 (mp10) REVERT: A 97 MET cc_start: 0.8917 (OUTLIER) cc_final: 0.8522 (mtt) REVERT: A 116 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7888 (pttm) REVERT: A 125 ARG cc_start: 0.7020 (mpp-170) cc_final: 0.6669 (tpp-160) REVERT: A 284 LYS cc_start: 0.7874 (mtpp) cc_final: 0.7470 (tttp) REVERT: N 33 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8417 (tp) REVERT: N 55 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.8097 (mm110) REVERT: B 63 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.8246 (ttp) REVERT: B 94 LYS cc_start: 0.8158 (mmmm) cc_final: 0.7374 (mtmt) REVERT: b 31 ARG cc_start: 0.6388 (ttm110) cc_final: 0.6037 (ttt90) REVERT: b 170 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.7897 (ttpp) REVERT: b 274 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.7931 (tm-30) REVERT: m 76 ASN cc_start: 0.8701 (t0) cc_final: 0.8370 (t0) REVERT: n 75 ILE cc_start: 0.7499 (mm) cc_final: 0.7251 (mm) REVERT: n 103 LYS cc_start: 0.8056 (ttpm) cc_final: 0.7779 (tttp) outliers start: 44 outliers final: 24 residues processed: 259 average time/residue: 1.3290 time to fit residues: 383.7514 Evaluate side-chains 264 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 230 time to evaluate : 1.966 ------------------------------------------------------------------------------- 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 14 SER Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain h residue 2 VAL Chi-restraints excluded: chain l residue 19 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 71 VAL Chi-restraints excluded: chain A residue 97 MET 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 12 ILE Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 55 GLN 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 170 LYS 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 112 THR Chi-restraints excluded: chain n residue 5 THR Chi-restraints excluded: chain n residue 21 ILE Chi-restraints excluded: chain n residue 74 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 194 optimal weight: 0.8980 chunk 73 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 150 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 148 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 chunk 46 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 chunk 94 optimal weight: 0.3980 chunk 108 optimal weight: 0.0980 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 164 HIS m 107 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.140017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.105590 restraints weight = 51229.217| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 3.15 r_work: 0.2974 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2950 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2950 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18548 Z= 0.139 Angle : 0.588 9.170 25192 Z= 0.308 Chirality : 0.043 0.205 2685 Planarity : 0.004 0.047 3216 Dihedral : 4.960 37.165 2514 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.73 % Favored : 96.23 % Rotamer: Outliers : 2.69 % Allowed : 17.70 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.18), residues: 2264 helix: 1.80 (0.40), residues: 153 sheet: -0.13 (0.21), residues: 676 loop : -0.53 (0.16), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP a 168 HIS 0.007 0.001 HIS A 164 PHE 0.011 0.001 PHE L 98 TYR 0.013 0.001 TYR H 94 ARG 0.010 0.000 ARG b 41 Details of bonding type rmsd hydrogen bonds : bond 0.04058 ( 555) hydrogen bonds : angle 5.35426 ( 1464) SS BOND : bond 0.00420 ( 32) SS BOND : angle 1.20812 ( 64) covalent geometry : bond 0.00331 (18516) covalent geometry : angle 0.58558 (25128) ********************** 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 280 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 231 time to evaluate : 1.890 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7606 (mt0) REVERT: H 29 VAL cc_start: 0.8957 (m) cc_final: 0.8664 (t) REVERT: L 14 SER cc_start: 0.8390 (OUTLIER) cc_final: 0.7883 (m) REVERT: L 79 GLN cc_start: 0.8149 (OUTLIER) cc_final: 0.7502 (tp40) REVERT: A -2 HIS cc_start: 0.6281 (OUTLIER) cc_final: 0.5948 (t-90) REVERT: A 12 GLU cc_start: 0.7618 (mm-30) cc_final: 0.7218 (tt0) REVERT: A 85 GLN cc_start: 0.8403 (mp10) cc_final: 0.8088 (mp10) REVERT: A 97 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.8463 (mtt) REVERT: A 116 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.7849 (pttm) REVERT: A 125 ARG cc_start: 0.6986 (mpp-170) cc_final: 0.6661 (tpp-160) REVERT: A 284 LYS cc_start: 0.7874 (mtpp) cc_final: 0.7523 (tttp) REVERT: N 33 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8423 (tp) REVERT: N 55 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.8047 (mm110) REVERT: B 63 MET cc_start: 0.8406 (OUTLIER) cc_final: 0.8091 (ttp) REVERT: B 128 LYS cc_start: 0.7577 (tmmt) cc_final: 0.6643 (tmtt) REVERT: B 141 LYS cc_start: 0.8169 (mppt) cc_final: 0.7857 (mppt) REVERT: b 31 ARG cc_start: 0.6410 (ttm110) cc_final: 0.6127 (ttt90) REVERT: b 164 HIS cc_start: 0.6369 (OUTLIER) cc_final: 0.6132 (p90) REVERT: b 170 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.7874 (ttpp) REVERT: b 274 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7673 (tm-30) REVERT: m 76 ASN cc_start: 0.8658 (t0) cc_final: 0.8320 (t0) REVERT: n 75 ILE cc_start: 0.7586 (mm) cc_final: 0.7342 (mm) REVERT: n 103 LYS cc_start: 0.8104 (ttpm) cc_final: 0.7827 (tttp) outliers start: 49 outliers final: 29 residues processed: 260 average time/residue: 1.2502 time to fit residues: 363.1382 Evaluate side-chains 270 residues out of total 1969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 229 time to evaluate : 2.108 ------------------------------------------------------------------------------- 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 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 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 19 VAL Chi-restraints excluded: chain l residue 22 THR 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 97 MET 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 12 ILE Chi-restraints excluded: chain M residue 112 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 55 GLN 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 165 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain b residue 164 HIS Chi-restraints excluded: chain b residue 170 LYS 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 112 THR Chi-restraints excluded: chain n residue 5 THR Chi-restraints excluded: chain n residue 9 SER Chi-restraints excluded: chain n residue 21 ILE Chi-restraints excluded: chain n residue 74 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 10 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 206 optimal weight: 1.9990 chunk 157 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 169 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 A 164 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 = 0.3635 r_free = 0.3635 target = 0.138174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.115409 restraints weight = 51679.296| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 4.52 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3323 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3323 r_free = 0.3323 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3323 r_free = 0.3323 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3323 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 18548 Z= 0.198 Angle : 0.654 9.331 25192 Z= 0.341 Chirality : 0.046 0.236 2685 Planarity : 0.005 0.047 3216 Dihedral : 5.214 38.185 2514 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.26 % Favored : 95.69 % Rotamer: Outliers : 2.89 % Allowed : 17.70 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.18), residues: 2264 helix: 1.54 (0.39), residues: 153 sheet: -0.28 (0.20), residues: 726 loop : -0.63 (0.17), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP a 168 HIS 0.008 0.001 HIS A 164 PHE 0.012 0.002 PHE b 163 TYR 0.015 0.002 TYR H 94 ARG 0.011 0.000 ARG b 41 Details of bonding type rmsd hydrogen bonds : bond 0.04697 ( 555) hydrogen bonds : angle 5.55488 ( 1464) SS BOND : bond 0.00533 ( 32) SS BOND : angle 1.47997 ( 64) covalent geometry : bond 0.00479 (18516) covalent geometry : angle 0.65018 (25128) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12479.42 seconds wall clock time: 215 minutes 30.45 seconds (12930.45 seconds total)