Starting phenix.real_space_refine on Sun Aug 24 18:40:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jqm_36575/08_2025/8jqm_36575.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jqm_36575/08_2025/8jqm_36575.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jqm_36575/08_2025/8jqm_36575.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jqm_36575/08_2025/8jqm_36575.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jqm_36575/08_2025/8jqm_36575.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jqm_36575/08_2025/8jqm_36575.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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 9768 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 96 5.16 5 C 9044 2.51 5 N 2524 2.21 5 O 2712 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14376 Number of models: 1 Model: "" Number of chains: 8 Chain: "H" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 920 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "L" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 828 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "A" Number of atoms: 2837 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 352, 2816 Classifications: {'peptide': 352} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 332} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 352, 2816 Classifications: {'peptide': 352} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 332} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 2871 Chain: "B" Number of atoms: 2835 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 352, 2814 Classifications: {'peptide': 352} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 332} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 352, 2814 Classifications: {'peptide': 352} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 332} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 2869 Chain: "b" Number of atoms: 2627 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 332, 2606 Classifications: {'peptide': 332} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 312} Chain breaks: 3 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Conformer: "B" Number of residues, atoms: 332, 2606 Classifications: {'peptide': 332} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 312} Chain breaks: 3 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 2648 Chain: "M" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 914 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "N" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 817 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Chain: "a" Number of atoms: 2598 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 330, 2577 Classifications: {'peptide': 330} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 310} Chain breaks: 3 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 28 Conformer: "B" Number of residues, atoms: 330, 2577 Classifications: {'peptide': 330} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 310} Chain breaks: 3 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 28 bond proxies already assigned to first conformer: 2617 Residues with excluded nonbonded symmetry interactions: 12 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 AMET A 67 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET A 67 " occ=0.50 residue: pdb=" N ASER B 58 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER B 58 " 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 AMET B 67 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET B 67 " occ=0.50 residue: pdb=" N ASER b 58 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER b 58 " 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 AMET b 67 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET b 67 " occ=0.50 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 AMET a 67 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET a 67 " occ=0.50 Time building chain proxies: 4.11, per 1000 atoms: 0.29 Number of scatterers: 14376 At special positions: 0 Unit cell: (118.15, 116.45, 137.7, 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 96 16.00 O 2712 8.00 N 2524 7.00 C 9044 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=28, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " 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=2.03 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=2.04 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 97 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS a 313 " - pdb=" SG CYS a 316 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.61 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 715.3 nanoseconds 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3380 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 30 sheets defined 14.7% alpha, 29.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.676A 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 78 removed outlier: 3.652A pdb=" N ASN A 65 " --> pdb=" O SER A 61 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N GLY A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 5.353A 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: 3.848A 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 removed outlier: 3.507A pdb=" N HIS A 229 " --> pdb=" O PRO A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 241 removed outlier: 3.817A 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: 3.831A pdb=" N THR A 256 " --> pdb=" O HIS A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 345 removed outlier: 3.565A pdb=" N LEU A 345 " --> pdb=" O GLU A 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 52 Processing helix chain 'B' and resid 61 through 78 removed outlier: 3.565A pdb=" N ASN B 65 " --> pdb=" O SER B 61 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N GLY B 73 " --> pdb=" O ARG B 69 " (cutoff:3.500A) removed outlier: 5.420A 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: 3.909A 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: 3.824A pdb=" N THR B 256 " --> pdb=" O HIS B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 345 removed outlier: 3.749A pdb=" N LEU B 345 " --> pdb=" O GLU B 342 " (cutoff:3.500A) Processing helix chain 'b' and resid 40 through 52 Processing helix chain 'b' and resid 61 through 71 removed outlier: 3.648A pdb=" N ASN b 65 " --> pdb=" O SER b 61 " (cutoff:3.500A) Processing helix chain 'b' and resid 71 through 82 removed outlier: 3.509A pdb=" N ASN b 82 " --> pdb=" O ILE b 78 " (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: 3.810A 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: 3.527A pdb=" N THR b 256 " --> pdb=" O HIS b 253 " (cutoff:3.500A) Processing helix chain 'b' and resid 341 through 345 removed outlier: 3.571A pdb=" N LEU b 345 " --> pdb=" O GLU b 342 " (cutoff:3.500A) Processing helix chain 'M' and resid 88 through 92 Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.666A pdb=" N PHE N 83 " --> pdb=" O PRO N 80 " (cutoff:3.500A) Processing helix chain 'a' and resid 38 through 52 removed outlier: 3.950A pdb=" N ALA a 43 " --> pdb=" O PRO a 39 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ALA a 44 " --> pdb=" O ARG a 40 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASP a 52 " --> pdb=" O GLN a 48 " (cutoff:3.500A) Processing helix chain 'a' and resid 61 through 71 removed outlier: 3.638A pdb=" N ASN a 65 " --> pdb=" O SER a 61 " (cutoff:3.500A) Processing helix chain 'a' and resid 71 through 82 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: 3.879A 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: 3.569A pdb=" N THR a 256 " --> pdb=" O HIS a 253 " (cutoff:3.500A) Processing helix chain 'a' and resid 341 through 345 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 11 through 12 removed outlier: 6.529A pdb=" N TRP H 36 " --> pdb=" O TYR H 52 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N TYR H 52 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N TRP H 38 " --> pdb=" O ILE H 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 7 removed outlier: 5.802A pdb=" N THR L 69 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 10.301A pdb=" N GLN L 27 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 10.002A pdb=" N SER L 67 " --> pdb=" O GLN L 27 " (cutoff:3.500A) removed outlier: 11.983A pdb=" N ILE L 29 " --> pdb=" O SER L 65 " (cutoff:3.500A) removed outlier: 11.635A pdb=" N SER L 65 " --> pdb=" O ILE L 29 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 14 removed outlier: 6.555A pdb=" N LEU L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N LYS L 107 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N ALA L 13 " --> pdb=" O LYS L 107 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 14 removed outlier: 6.555A pdb=" N LEU L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N LYS L 107 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N ALA L 13 " --> pdb=" O LYS L 107 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 2 through 7 Processing sheet with id=AA8, first strand: chain 'A' and resid 33 through 35 removed outlier: 6.515A pdb=" N LYS A 33 " --> pdb=" O VAL A 167 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N LEU A 169 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N HIS A 35 " --> pdb=" O LEU A 169 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N VAL A 171 " --> pdb=" O HIS A 35 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N TRP A 168 " --> pdb=" O GLU A 156 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 87 through 90 removed outlier: 6.589A pdb=" N THR A 87 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N VAL A 135 " --> pdb=" O THR A 87 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N VAL A 89 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLY A 56 " --> pdb=" O ALA A 149 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 328 through 331 removed outlier: 4.680A pdb=" N PHE A 277 " --> pdb=" O LYS A 213 " (cutoff:3.500A) removed outlier: 9.208A pdb=" N LYS A 213 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N LEU A 212 " --> pdb=" O GLU A 205 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N GLU A 205 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU A 192 " --> pdb=" O LYS A 189 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG a 214 " --> pdb=" O GLU a 203 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N GLU a 205 " --> pdb=" O LEU a 212 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N LEU a 212 " --> pdb=" O GLU a 205 " (cutoff:3.500A) removed outlier: 9.135A pdb=" N LYS a 213 " --> pdb=" O PHE a 277 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N PHE a 277 " --> pdb=" O LYS a 213 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU a 274 " --> pdb=" O ARG a 324 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 284 through 287 removed outlier: 6.403A pdb=" N LYS A 284 " --> pdb=" O TRP A 311 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N CYS A 313 " --> pdb=" O LYS A 284 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N HIS A 286 " --> pdb=" O CYS A 313 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 2 through 7 Processing sheet with id=AB4, first strand: chain 'B' and resid 33 through 36 removed outlier: 6.578A pdb=" N LYS B 33 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU B 169 " --> pdb=" O LYS B 33 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N HIS B 35 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N VAL B 171 " --> pdb=" O HIS B 35 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP B 157 " --> pdb=" O TRP B 168 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LYS B 170 " --> pdb=" O VAL B 155 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N VAL B 155 " --> pdb=" O LYS B 170 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 87 through 89 removed outlier: 6.376A pdb=" N THR B 87 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N VAL B 135 " --> pdb=" O THR B 87 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N VAL B 89 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLY B 56 " --> pdb=" O ALA B 149 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 329 through 331 removed outlier: 4.621A pdb=" N PHE B 277 " --> pdb=" O LYS B 213 " (cutoff:3.500A) removed outlier: 9.042A pdb=" N LYS B 213 " --> pdb=" O PHE B 277 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLU B 203 " --> pdb=" O LYS B 213 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ALA B 215 " --> pdb=" O TRP B 201 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N TRP B 201 " --> pdb=" O ALA B 215 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N GLU b 205 " --> pdb=" O LEU b 212 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N LEU b 212 " --> pdb=" O GLU b 205 " (cutoff:3.500A) removed outlier: 9.145A pdb=" N LYS b 213 " --> pdb=" O PHE b 277 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N PHE b 277 " --> pdb=" O LYS b 213 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLY b 328 " --> pdb=" O ALA b 325 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 284 through 287 removed outlier: 6.218A pdb=" N LYS B 284 " --> pdb=" O TRP B 311 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N CYS B 313 " --> pdb=" O LYS B 284 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N HIS B 286 " --> pdb=" O CYS B 313 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'b' and resid 56 through 57 removed outlier: 6.819A pdb=" N GLY b 56 " --> pdb=" O ALA b 149 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'b' and resid 87 through 89 removed outlier: 6.411A pdb=" N THR b 87 " --> pdb=" O PHE b 133 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'b' and resid 153 through 157 removed outlier: 7.257A pdb=" N TRP b 168 " --> pdb=" O GLU b 156 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'b' and resid 284 through 287 removed outlier: 6.345A pdb=" N LYS b 284 " --> pdb=" O TRP b 311 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N CYS b 313 " --> pdb=" O LYS b 284 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N HIS b 286 " --> pdb=" O CYS b 313 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'M' and resid 3 through 7 removed outlier: 3.562A pdb=" N SER M 72 " --> pdb=" O SER M 81 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.508A pdb=" N ALA M 93 " --> pdb=" O VAL M 116 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N TRP M 36 " --> pdb=" O TYR M 52 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N TYR M 52 " --> pdb=" O TRP M 36 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N TRP M 38 " --> pdb=" O ILE M 50 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.508A pdb=" N ALA M 93 " --> pdb=" O VAL M 116 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'N' and resid 4 through 7 removed outlier: 5.636A pdb=" N THR N 69 " --> pdb=" O ALA N 25 " (cutoff:3.500A) removed outlier: 10.003A pdb=" N GLN N 27 " --> pdb=" O SER N 67 " (cutoff:3.500A) removed outlier: 9.890A pdb=" N SER N 67 " --> pdb=" O GLN N 27 " (cutoff:3.500A) removed outlier: 12.039A pdb=" N ILE N 29 " --> pdb=" O SER N 65 " (cutoff:3.500A) removed outlier: 11.678A pdb=" N SER N 65 " --> pdb=" O ILE N 29 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.360A pdb=" N GLN N 37 " --> pdb=" O LEU N 46 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N LEU N 46 " --> pdb=" O GLN N 37 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'N' and resid 10 through 13 removed outlier: 3.816A pdb=" N THR N 97 " --> pdb=" O GLN N 90 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'a' and resid 56 through 58 removed outlier: 6.872A pdb=" N GLY a 56 " --> pdb=" O ALA a 149 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'a' and resid 87 through 89 Processing sheet with id=AD2, first strand: chain 'a' and resid 153 through 157 removed outlier: 7.327A pdb=" N TRP a 168 " --> pdb=" O GLU a 156 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'a' and resid 284 through 287 removed outlier: 6.043A pdb=" N LYS a 284 " --> pdb=" O TRP a 311 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N CYS a 313 " --> pdb=" O LYS a 284 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N HIS a 286 " --> pdb=" O CYS a 313 " (cutoff:3.500A) 436 hydrogen bonds defined for protein. 1087 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.37 Time building geometry restraints manager: 2.09 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: 4720 1.34 - 1.46: 3628 1.46 - 1.59: 6278 1.59 - 1.71: 0 1.71 - 1.83: 136 Bond restraints: 14762 Sorted by residual: bond pdb=" N HIS A 2 " pdb=" CA HIS A 2 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.29e-02 6.01e+03 6.12e+00 bond pdb=" N GLY A 3 " pdb=" CA GLY A 3 " ideal model delta sigma weight residual 1.452 1.475 -0.023 1.03e-02 9.43e+03 4.95e+00 bond pdb=" CB CYS B 329 " pdb=" SG CYS B 329 " ideal model delta sigma weight residual 1.808 1.748 0.060 3.30e-02 9.18e+02 3.35e+00 bond pdb=" CE1 HIS A 2 " pdb=" NE2 HIS A 2 " ideal model delta sigma weight residual 1.321 1.337 -0.016 1.00e-02 1.00e+04 2.63e+00 bond pdb=" CE1 HIS A 1 " pdb=" NE2 HIS A 1 " ideal model delta sigma weight residual 1.321 1.337 -0.016 1.00e-02 1.00e+04 2.43e+00 ... (remaining 14757 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 19601 1.85 - 3.69: 403 3.69 - 5.54: 44 5.54 - 7.38: 10 7.38 - 9.23: 3 Bond angle restraints: 20061 Sorted by residual: angle pdb=" C HIS A 113 " pdb=" CA HIS A 113 " pdb=" CB HIS A 113 " ideal model delta sigma weight residual 116.54 109.68 6.86 1.15e+00 7.56e-01 3.56e+01 angle pdb=" C HIS B 113 " pdb=" CA HIS B 113 " pdb=" CB HIS B 113 " ideal model delta sigma weight residual 116.54 110.15 6.39 1.15e+00 7.56e-01 3.09e+01 angle pdb=" N ILE A 78 " pdb=" CA ILE A 78 " pdb=" C ILE A 78 " ideal model delta sigma weight residual 110.21 104.64 5.57 1.13e+00 7.83e-01 2.43e+01 angle pdb=" N ILE M 29 " pdb=" CA ILE M 29 " pdb=" C ILE M 29 " ideal model delta sigma weight residual 112.80 108.70 4.10 1.15e+00 7.56e-01 1.27e+01 angle pdb=" CA HIS A 113 " pdb=" C HIS A 113 " pdb=" N GLY A 114 " ideal model delta sigma weight residual 119.52 116.77 2.75 7.90e-01 1.60e+00 1.21e+01 ... (remaining 20056 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.05: 8081 18.05 - 36.09: 577 36.09 - 54.14: 127 54.14 - 72.18: 29 72.18 - 90.23: 13 Dihedral angle restraints: 8827 sinusoidal: 3558 harmonic: 5269 Sorted by residual: dihedral pdb=" CB CYS a 313 " pdb=" SG CYS a 313 " pdb=" SG CYS a 316 " pdb=" CB CYS a 316 " ideal model delta sinusoidal sigma weight residual -86.00 -176.23 90.23 1 1.00e+01 1.00e-02 9.64e+01 dihedral pdb=" CB CYS b 313 " pdb=" SG CYS b 313 " pdb=" SG CYS b 316 " pdb=" CB CYS b 316 " ideal model delta sinusoidal sigma weight residual 93.00 -178.65 -88.35 1 1.00e+01 1.00e-02 9.32e+01 dihedral pdb=" CB CYS B 313 " pdb=" SG CYS B 313 " pdb=" SG CYS B 316 " pdb=" CB CYS B 316 " ideal model delta sinusoidal sigma weight residual -86.00 -166.85 80.85 1 1.00e+01 1.00e-02 8.07e+01 ... (remaining 8824 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1433 0.037 - 0.075: 492 0.075 - 0.112: 171 0.112 - 0.149: 50 0.149 - 0.186: 5 Chirality restraints: 2151 Sorted by residual: chirality pdb=" CG LEU L 33 " pdb=" CB LEU L 33 " pdb=" CD1 LEU L 33 " pdb=" CD2 LEU L 33 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.68e-01 chirality pdb=" CA ILE H 109 " pdb=" N ILE H 109 " pdb=" C ILE H 109 " pdb=" CB ILE H 109 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.59e-01 chirality pdb=" CA VAL B 135 " pdb=" N VAL B 135 " pdb=" C VAL B 135 " pdb=" CB VAL B 135 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.54e-01 ... (remaining 2148 not shown) Planarity restraints: 2575 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE M 104 " -0.011 2.00e-02 2.50e+03 2.17e-02 4.71e+00 pdb=" C PHE M 104 " 0.038 2.00e-02 2.50e+03 pdb=" O PHE M 104 " -0.014 2.00e-02 2.50e+03 pdb=" N TYR M 105 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 117 " -0.007 2.00e-02 2.50e+03 1.48e-02 2.18e+00 pdb=" C ALA A 117 " 0.026 2.00e-02 2.50e+03 pdb=" O ALA A 117 " -0.009 2.00e-02 2.50e+03 pdb=" N TRP A 118 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS b 35 " 0.021 5.00e-02 4.00e+02 3.13e-02 1.57e+00 pdb=" N PRO b 36 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO b 36 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO b 36 " 0.017 5.00e-02 4.00e+02 ... (remaining 2572 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 281 2.69 - 3.24: 12771 3.24 - 3.80: 21358 3.80 - 4.35: 30153 4.35 - 4.90: 50004 Nonbonded interactions: 114567 Sorted by model distance: nonbonded pdb=" O LEU b 231 " pdb=" OG SER b 252 " model vdw 2.139 3.040 nonbonded pdb=" OG SER a 59 " pdb=" OD1 ASP a 136 " model vdw 2.171 3.040 nonbonded pdb=" O THR b 262 " pdb=" NH2 ARG b 294 " model vdw 2.173 3.120 nonbonded pdb=" O LEU a 231 " pdb=" OG SER a 252 " model vdw 2.195 3.040 nonbonded pdb=" OG SER A 297 " pdb=" O TYR A 331 " model vdw 2.218 3.040 ... (remaining 114562 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 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 26 or resid 34 through 39 or (resid \ 40 and (name N or name CA or name C or name O or name CB )) or resid 41 through \ 46 or (resid 47 and (name N or name CA or name C or name O or name CB )) or res \ id 48 through 57 or resid 59 or resid 61 through 66 or resid 68 through 107 or ( \ resid 108 and (name N or name CA or name C or name O or name CB )) or resid 109 \ through 112 or resid 124 or (resid 125 through 128 and (name N or name CA or nam \ e C or name O or name CB )) or resid 129 through 140 or (resid 141 and (name N o \ r name CA or name C or name O or name CB )) or resid 142 through 159 or resid 16 \ 5 through 172 or (resid 173 through 174 and (name N or name CA or name C or name \ O or name CB )) or resid 175 through 207 or (resid 208 and (name N or name CA o \ r name C or name O or name CB )) or resid 209 through 236 or (resid 237 and (nam \ e N or name CA or name C or name O or name CB )) or resid 238 through 270 or (re \ sid 271 and (name N or name CA or name C or name O or name CB )) or resid 272 th \ rough 288 or (resid 289 and (name N or name CA or name C or name O or name CB )) \ or resid 290 through 308 or (resid 309 through 310 and (name N or name CA or na \ me C or name O or name CB )) or resid 311 through 338 or (resid 339 and (name N \ or name CA or name C or name O or name CB )) or resid 340 through 352)) selection = (chain 'B' and (resid 1 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 26 or resid 34 through 39 or (resid \ 40 and (name N or name CA or name C or name O or name CB )) or resid 41 through \ 46 or (resid 47 and (name N or name CA or name C or name O or name CB )) or res \ id 48 through 57 or resid 59 or resid 61 through 66 or resid 68 through 107 or ( \ resid 108 and (name N or name CA or name C or name O or name CB )) or resid 109 \ through 112 or resid 124 or (resid 125 through 128 and (name N or name CA or nam \ e C or name O or name CB )) or resid 129 through 140 or (resid 141 and (name N o \ r name CA or name C or name O or name CB )) or resid 142 through 159 or resid 16 \ 5 through 172 or (resid 173 through 174 and (name N or name CA or name C or name \ O or name CB )) or resid 175 through 207 or (resid 208 and (name N or name CA o \ r name C or name O or name CB )) or resid 209 through 236 or (resid 237 and (nam \ e N or name CA or name C or name O or name CB )) or resid 238 through 270 or (re \ sid 271 and (name N or name CA or name C or name O or name CB )) or resid 272 th \ rough 309 or (resid 310 and (name N or name CA or name C or name O or name CB )) \ or resid 311 through 338 or (resid 339 and (name N or name CA or name C or name \ O or name CB )) or resid 340 through 352)) selection = (chain 'a' and (resid 1 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 57 or resid 59 or resid 61 through \ 66 or resid 68 through 112 or resid 124 through 140 or (resid 141 and (name N or \ name CA or name C or name O or name CB )) or resid 142 through 270 or (resid 27 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 272 through \ 288 or (resid 289 and (name N or name CA or name C or name O or name CB )) or re \ sid 290 through 308 or (resid 309 through 310 and (name N or name CA or name C o \ r name O or name CB )) or resid 311 through 352)) selection = (chain 'b' and (resid 1 through 46 or (resid 47 and (name N or name CA or name C \ or name O or name CB )) or resid 48 through 57 or resid 59 or resid 61 through \ 66 or resid 68 through 107 or (resid 108 and (name N or name CA or name C or nam \ e O or name CB )) or resid 109 through 112 or resid 124 through 159 or resid 165 \ through 207 or (resid 208 and (name N or name CA or name C or name O or name CB \ )) or resid 209 through 236 or (resid 237 and (name N or name CA or name C or n \ ame O or name CB )) or resid 238 through 308 or (resid 309 through 310 and (name \ N or name CA or name C or name O or name CB )) or resid 311 through 338 or (res \ id 339 and (name N or name CA or name C or name O or name CB )) or resid 340 thr \ ough 352)) } ncs_group { reference = (chain 'H' and resid 1 through 119) selection = chain 'M' } ncs_group { reference = (chain 'L' and resid 1 through 107) 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=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 18.450 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 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 : 0.004 0.060 14790 Z= 0.175 Angle : 0.657 9.226 20117 Z= 0.380 Chirality : 0.045 0.186 2151 Planarity : 0.003 0.031 2575 Dihedral : 13.525 89.095 5363 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.74 % Favored : 95.09 % Rotamer: Outliers : 1.40 % Allowed : 0.83 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.20), residues: 1824 helix: 1.42 (0.42), residues: 156 sheet: -0.20 (0.24), residues: 494 loop : -0.46 (0.18), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG b 14 TYR 0.016 0.002 TYR M 105 PHE 0.019 0.002 PHE M 104 TRP 0.015 0.001 TRP a 168 HIS 0.004 0.001 HIS b 216 Details of bonding type rmsd covalent geometry : bond 0.00388 (14762) covalent geometry : angle 0.64754 (20061) SS BOND : bond 0.00410 ( 28) SS BOND : angle 2.15290 ( 56) hydrogen bonds : bond 0.21690 ( 419) hydrogen bonds : angle 8.37160 ( 1087) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 225 time to evaluate : 0.389 Fit side-chains REVERT: L 61 ARG cc_start: 0.7494 (ptt-90) cc_final: 0.7291 (ptt90) REVERT: L 79 ARG cc_start: 0.7267 (mmm-85) cc_final: 0.6802 (mtp-110) REVERT: L 81 GLU cc_start: 0.6521 (pm20) cc_final: 0.6168 (pm20) REVERT: b 48 GLN cc_start: 0.7278 (tt0) cc_final: 0.7052 (tt0) REVERT: a 102 GLN cc_start: 0.7865 (mm-40) cc_final: 0.7608 (mm-40) REVERT: a 344 ASN cc_start: 0.8337 (m110) cc_final: 0.7959 (m110) outliers start: 11 outliers final: 0 residues processed: 231 average time/residue: 0.6409 time to fit residues: 160.8846 Evaluate side-chains 169 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN B 1 HIS B 82 ASN B 109 ASN b 1 HIS ** b 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 42 HIS a 1 HIS a 82 ASN ** a 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 286 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.127358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.094595 restraints weight = 86893.061| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 5.06 r_work: 0.2740 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2684 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2684 r_free = 0.2684 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2684 r_free = 0.2684 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2684 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 14790 Z= 0.195 Angle : 0.684 10.815 20117 Z= 0.361 Chirality : 0.047 0.168 2151 Planarity : 0.005 0.036 2575 Dihedral : 5.543 25.540 1995 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.19 % Favored : 94.70 % Rotamer: Outliers : 2.48 % Allowed : 8.00 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.20), residues: 1824 helix: 1.45 (0.42), residues: 157 sheet: -0.04 (0.24), residues: 503 loop : -0.50 (0.18), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG a 99 TYR 0.022 0.002 TYR M 105 PHE 0.019 0.002 PHE M 104 TRP 0.015 0.002 TRP b 330 HIS 0.015 0.002 HIS b 2 Details of bonding type rmsd covalent geometry : bond 0.00475 (14762) covalent geometry : angle 0.67482 (20061) SS BOND : bond 0.00517 ( 28) SS BOND : angle 2.20186 ( 56) hydrogen bonds : bond 0.05287 ( 419) hydrogen bonds : angle 6.14579 ( 1087) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 183 time to evaluate : 0.391 Fit side-chains REVERT: L 81 GLU cc_start: 0.6789 (pm20) cc_final: 0.6411 (pm20) REVERT: A 29 ARG cc_start: 0.7238 (OUTLIER) cc_final: 0.6050 (ptm-80) REVERT: B 220 MET cc_start: 0.9010 (mmt) cc_final: 0.8770 (mpp) REVERT: B 276 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.7895 (mtp180) REVERT: B 326 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8546 (tttp) REVERT: b 7 ASP cc_start: 0.8447 (t70) cc_final: 0.8176 (t0) REVERT: b 48 GLN cc_start: 0.7501 (tt0) cc_final: 0.7191 (tt0) REVERT: N 30 THR cc_start: 0.8808 (OUTLIER) cc_final: 0.8584 (p) REVERT: a 75 LEU cc_start: 0.7288 (tp) cc_final: 0.7054 (tp) REVERT: a 102 GLN cc_start: 0.8066 (mm-40) cc_final: 0.7693 (mm-40) REVERT: a 234 ASP cc_start: 0.8144 (p0) cc_final: 0.7915 (p0) REVERT: a 271 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8140 (tt0) REVERT: a 279 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7414 (mt-10) REVERT: a 340 GLU cc_start: 0.7620 (mm-30) cc_final: 0.7296 (mm-30) outliers start: 27 outliers final: 14 residues processed: 196 average time/residue: 0.6670 time to fit residues: 141.3837 Evaluate side-chains 191 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 171 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain b residue 55 CYS Chi-restraints excluded: chain b residue 78 ILE Chi-restraints excluded: chain b residue 132 SER Chi-restraints excluded: chain b residue 170 LYS Chi-restraints excluded: chain b residue 178 GLU Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain a residue 134 VAL Chi-restraints excluded: chain a residue 239 SER Chi-restraints excluded: chain a residue 271 GLU Chi-restraints excluded: chain a residue 279 GLU Chi-restraints excluded: chain a residue 287 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 105 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 61 optimal weight: 7.9990 chunk 101 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 136 optimal weight: 9.9990 chunk 1 optimal weight: 0.0270 chunk 88 optimal weight: 9.9990 chunk 155 optimal weight: 2.9990 overall best weight: 2.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 16 GLN b 344 ASN a 1 HIS a 131 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.130041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.106257 restraints weight = 88185.672| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 6.31 r_work: 0.2648 rms_B_bonded: 6.14 restraints_weight: 2.0000 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2606 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2606 r_free = 0.2606 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2606 r_free = 0.2606 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2606 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 14790 Z= 0.160 Angle : 0.628 10.641 20117 Z= 0.331 Chirality : 0.045 0.161 2151 Planarity : 0.004 0.038 2575 Dihedral : 5.372 24.632 1995 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.97 % Favored : 94.92 % Rotamer: Outliers : 2.92 % Allowed : 9.78 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.20), residues: 1824 helix: 1.51 (0.42), residues: 158 sheet: 0.12 (0.24), residues: 494 loop : -0.53 (0.18), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG a 99 TYR 0.018 0.002 TYR M 105 PHE 0.013 0.002 PHE B 323 TRP 0.013 0.001 TRP b 168 HIS 0.011 0.001 HIS b 2 Details of bonding type rmsd covalent geometry : bond 0.00387 (14762) covalent geometry : angle 0.62083 (20061) SS BOND : bond 0.00445 ( 28) SS BOND : angle 1.85463 ( 56) hydrogen bonds : bond 0.04570 ( 419) hydrogen bonds : angle 5.75186 ( 1087) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 174 time to evaluate : 0.528 Fit side-chains REVERT: B 276 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.7989 (mtp180) REVERT: B 326 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8559 (tttp) REVERT: b 48 GLN cc_start: 0.7662 (tt0) cc_final: 0.7302 (tt0) REVERT: b 261 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.8490 (mpp-170) REVERT: N 30 THR cc_start: 0.8879 (OUTLIER) cc_final: 0.8650 (p) REVERT: a 75 LEU cc_start: 0.7349 (tp) cc_final: 0.7095 (tp) REVERT: a 102 GLN cc_start: 0.8116 (mm-40) cc_final: 0.7654 (mm-40) REVERT: a 157 ASP cc_start: 0.5814 (OUTLIER) cc_final: 0.5472 (t0) REVERT: a 224 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8386 (mt-10) REVERT: a 271 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8204 (tt0) REVERT: a 279 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7329 (mt-10) REVERT: a 340 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7292 (mm-30) outliers start: 34 outliers final: 13 residues processed: 194 average time/residue: 0.6467 time to fit residues: 135.5588 Evaluate side-chains 186 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 165 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain b residue 78 ILE Chi-restraints excluded: chain b residue 132 SER Chi-restraints excluded: chain b residue 170 LYS Chi-restraints excluded: chain b residue 178 GLU Chi-restraints excluded: chain b residue 261 ARG Chi-restraints excluded: chain b residue 287 VAL Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain a residue 129 THR Chi-restraints excluded: chain a residue 134 VAL Chi-restraints excluded: chain a residue 157 ASP Chi-restraints excluded: chain a residue 224 GLU Chi-restraints excluded: chain a residue 271 GLU Chi-restraints excluded: chain a residue 279 GLU Chi-restraints excluded: chain a residue 287 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 116 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 99 optimal weight: 0.9980 chunk 143 optimal weight: 6.9990 chunk 131 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 159 optimal weight: 10.0000 chunk 85 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 162 optimal weight: 7.9990 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 16 GLN L 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.128900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.104997 restraints weight = 91648.363| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 5.92 r_work: 0.2638 rms_B_bonded: 5.79 restraints_weight: 2.0000 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2605 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2605 r_free = 0.2605 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2605 r_free = 0.2605 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2605 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 14790 Z= 0.214 Angle : 0.694 11.566 20117 Z= 0.365 Chirality : 0.047 0.160 2151 Planarity : 0.005 0.040 2575 Dihedral : 5.661 26.201 1995 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.19 % Favored : 94.70 % Rotamer: Outliers : 3.17 % Allowed : 10.92 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.20), residues: 1824 helix: 1.40 (0.42), residues: 158 sheet: 0.07 (0.25), residues: 479 loop : -0.63 (0.18), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 62 TYR 0.022 0.002 TYR M 105 PHE 0.017 0.002 PHE B 323 TRP 0.016 0.002 TRP b 168 HIS 0.012 0.001 HIS b 2 Details of bonding type rmsd covalent geometry : bond 0.00527 (14762) covalent geometry : angle 0.68228 (20061) SS BOND : bond 0.00572 ( 28) SS BOND : angle 2.48389 ( 56) hydrogen bonds : bond 0.04971 ( 419) hydrogen bonds : angle 5.76312 ( 1087) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 166 time to evaluate : 0.578 Fit side-chains REVERT: A 29 ARG cc_start: 0.7213 (OUTLIER) cc_final: 0.6261 (ptm-80) REVERT: B 276 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.8009 (mtp180) REVERT: B 329 CYS cc_start: 0.8328 (m) cc_final: 0.8114 (t) REVERT: b 48 GLN cc_start: 0.7658 (tt0) cc_final: 0.7307 (tt0) REVERT: N 30 THR cc_start: 0.8914 (OUTLIER) cc_final: 0.8694 (p) REVERT: N 81 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.6066 (pm20) REVERT: a 102 GLN cc_start: 0.8143 (mm-40) cc_final: 0.7710 (mm-40) REVERT: a 224 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8391 (mt-10) REVERT: a 271 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8232 (tt0) REVERT: a 279 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7325 (mt-10) REVERT: a 340 GLU cc_start: 0.7587 (mm-30) cc_final: 0.7244 (mm-30) outliers start: 38 outliers final: 19 residues processed: 189 average time/residue: 0.6111 time to fit residues: 124.9170 Evaluate side-chains 189 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 163 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 143 CYS Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain b residue 71 VAL Chi-restraints excluded: chain b residue 78 ILE Chi-restraints excluded: chain b residue 132 SER Chi-restraints excluded: chain b residue 170 LYS Chi-restraints excluded: chain b residue 178 GLU Chi-restraints excluded: chain b residue 287 VAL Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 81 GLU Chi-restraints excluded: chain a residue 129 THR Chi-restraints excluded: chain a residue 134 VAL Chi-restraints excluded: chain a residue 224 GLU Chi-restraints excluded: chain a residue 239 SER Chi-restraints excluded: chain a residue 271 GLU Chi-restraints excluded: chain a residue 279 GLU Chi-restraints excluded: chain a residue 287 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 129 optimal weight: 0.7980 chunk 109 optimal weight: 0.5980 chunk 62 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 61 optimal weight: 4.9990 chunk 84 optimal weight: 0.5980 chunk 162 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 160 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 chunk 169 optimal weight: 8.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 16 GLN L 3 GLN a 147 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.131397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.107924 restraints weight = 90566.384| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 6.46 r_work: 0.2676 rms_B_bonded: 6.09 restraints_weight: 2.0000 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2637 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2637 r_free = 0.2637 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2637 r_free = 0.2637 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2637 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14790 Z= 0.112 Angle : 0.575 10.791 20117 Z= 0.303 Chirality : 0.043 0.156 2151 Planarity : 0.004 0.038 2575 Dihedral : 5.161 22.530 1995 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.52 % Favored : 95.37 % Rotamer: Outliers : 2.98 % Allowed : 11.24 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.20), residues: 1824 helix: 2.03 (0.43), residues: 151 sheet: 0.23 (0.25), residues: 481 loop : -0.43 (0.18), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG b 69 TYR 0.013 0.001 TYR M 35 PHE 0.011 0.001 PHE H 80 TRP 0.015 0.001 TRP b 168 HIS 0.006 0.001 HIS b 2 Details of bonding type rmsd covalent geometry : bond 0.00264 (14762) covalent geometry : angle 0.56668 (20061) SS BOND : bond 0.00346 ( 28) SS BOND : angle 1.91194 ( 56) hydrogen bonds : bond 0.03629 ( 419) hydrogen bonds : angle 5.38660 ( 1087) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 186 time to evaluate : 0.554 Fit side-chains REVERT: b 48 GLN cc_start: 0.7630 (tt0) cc_final: 0.7265 (tt0) REVERT: a 75 LEU cc_start: 0.7261 (tp) cc_final: 0.7038 (tp) REVERT: a 102 GLN cc_start: 0.8143 (mm-40) cc_final: 0.7688 (mm-40) REVERT: a 157 ASP cc_start: 0.5846 (OUTLIER) cc_final: 0.5513 (t0) REVERT: a 224 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8338 (mt-10) REVERT: a 279 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7579 (mt-10) REVERT: a 340 GLU cc_start: 0.7578 (mm-30) cc_final: 0.7317 (tp30) outliers start: 35 outliers final: 16 residues processed: 206 average time/residue: 0.6385 time to fit residues: 142.9677 Evaluate side-chains 186 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 167 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 143 CYS Chi-restraints excluded: chain b residue 55 CYS Chi-restraints excluded: chain b residue 132 SER Chi-restraints excluded: chain b residue 178 GLU Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain a residue 129 THR Chi-restraints excluded: chain a residue 134 VAL Chi-restraints excluded: chain a residue 157 ASP Chi-restraints excluded: chain a residue 224 GLU Chi-restraints excluded: chain a residue 236 ILE Chi-restraints excluded: chain a residue 239 SER Chi-restraints excluded: chain a residue 279 GLU Chi-restraints excluded: chain a residue 287 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 22 optimal weight: 8.9990 chunk 96 optimal weight: 0.9990 chunk 166 optimal weight: 6.9990 chunk 165 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 154 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 149 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 110 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 16 GLN L 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.127830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.104665 restraints weight = 94406.451| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 6.14 r_work: 0.2597 rms_B_bonded: 5.91 restraints_weight: 2.0000 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2576 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2576 r_free = 0.2576 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2576 r_free = 0.2576 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2576 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.105 14790 Z= 0.261 Angle : 0.746 13.036 20117 Z= 0.392 Chirality : 0.049 0.162 2151 Planarity : 0.005 0.041 2575 Dihedral : 5.773 25.290 1995 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.30 % Favored : 94.64 % Rotamer: Outliers : 3.24 % Allowed : 12.00 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.20), residues: 1824 helix: 1.35 (0.42), residues: 158 sheet: 0.04 (0.25), residues: 460 loop : -0.66 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 62 TYR 0.026 0.003 TYR M 105 PHE 0.020 0.002 PHE B 323 TRP 0.016 0.002 TRP b 168 HIS 0.013 0.002 HIS b 2 Details of bonding type rmsd covalent geometry : bond 0.00647 (14762) covalent geometry : angle 0.73020 (20061) SS BOND : bond 0.00650 ( 28) SS BOND : angle 2.95555 ( 56) hydrogen bonds : bond 0.05257 ( 419) hydrogen bonds : angle 5.73324 ( 1087) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 163 time to evaluate : 0.594 Fit side-chains REVERT: L 79 ARG cc_start: 0.7304 (mmm-85) cc_final: 0.6867 (mtp-110) REVERT: A 29 ARG cc_start: 0.7257 (OUTLIER) cc_final: 0.6227 (ptm-80) REVERT: B 340 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7685 (mm-30) REVERT: b 48 GLN cc_start: 0.7681 (tt0) cc_final: 0.7347 (tt0) REVERT: b 343 SER cc_start: 0.8449 (m) cc_final: 0.8197 (p) REVERT: N 81 GLU cc_start: 0.7147 (OUTLIER) cc_final: 0.6059 (pm20) REVERT: a 75 LEU cc_start: 0.7337 (tp) cc_final: 0.7086 (tp) REVERT: a 102 GLN cc_start: 0.8167 (mm-40) cc_final: 0.7733 (mm-40) REVERT: a 224 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8472 (mt-10) REVERT: a 261 ARG cc_start: 0.8923 (OUTLIER) cc_final: 0.8285 (mpp80) REVERT: a 279 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7323 (mt-10) REVERT: a 340 GLU cc_start: 0.7649 (mm-30) cc_final: 0.7317 (mm-30) outliers start: 39 outliers final: 22 residues processed: 185 average time/residue: 0.7587 time to fit residues: 151.4002 Evaluate side-chains 186 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 158 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 107 ASN Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 143 CYS Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain b residue 55 CYS Chi-restraints excluded: chain b residue 71 VAL Chi-restraints excluded: chain b residue 132 SER Chi-restraints excluded: chain b residue 178 GLU Chi-restraints excluded: chain b residue 287 VAL Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 81 GLU Chi-restraints excluded: chain a residue 129 THR Chi-restraints excluded: chain a residue 134 VAL Chi-restraints excluded: chain a residue 224 GLU Chi-restraints excluded: chain a residue 236 ILE Chi-restraints excluded: chain a residue 239 SER Chi-restraints excluded: chain a residue 261 ARG Chi-restraints excluded: chain a residue 279 GLU Chi-restraints excluded: chain a residue 287 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 4 optimal weight: 0.0270 chunk 14 optimal weight: 5.9990 chunk 166 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 176 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 121 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 142 optimal weight: 8.9990 overall best weight: 1.5442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.130862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.107297 restraints weight = 84685.687| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 5.70 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3183 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3183 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 14790 Z= 0.131 Angle : 0.610 11.470 20117 Z= 0.321 Chirality : 0.044 0.154 2151 Planarity : 0.004 0.040 2575 Dihedral : 5.344 22.785 1995 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.58 % Favored : 95.37 % Rotamer: Outliers : 2.54 % Allowed : 13.08 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.20), residues: 1824 helix: 1.56 (0.42), residues: 159 sheet: 0.19 (0.25), residues: 477 loop : -0.55 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG b 69 TYR 0.014 0.002 TYR M 35 PHE 0.012 0.001 PHE H 80 TRP 0.016 0.001 TRP b 168 HIS 0.007 0.001 HIS b 2 Details of bonding type rmsd covalent geometry : bond 0.00316 (14762) covalent geometry : angle 0.60065 (20061) SS BOND : bond 0.00386 ( 28) SS BOND : angle 2.05730 ( 56) hydrogen bonds : bond 0.03869 ( 419) hydrogen bonds : angle 5.43624 ( 1087) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 168 time to evaluate : 0.591 Fit side-chains REVERT: A 29 ARG cc_start: 0.6923 (OUTLIER) cc_final: 0.5967 (ptm-80) REVERT: B 340 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7271 (mm-30) REVERT: b 48 GLN cc_start: 0.7364 (tt0) cc_final: 0.7109 (tt0) REVERT: b 343 SER cc_start: 0.8347 (m) cc_final: 0.8074 (p) REVERT: N 81 GLU cc_start: 0.6747 (OUTLIER) cc_final: 0.5529 (pm20) REVERT: a 75 LEU cc_start: 0.7469 (tp) cc_final: 0.7192 (tp) REVERT: a 102 GLN cc_start: 0.8035 (mm-40) cc_final: 0.7730 (mm-40) REVERT: a 157 ASP cc_start: 0.5691 (OUTLIER) cc_final: 0.5374 (t0) REVERT: a 224 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7374 (mt-10) REVERT: a 279 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.7030 (mt-10) REVERT: a 340 GLU cc_start: 0.7305 (mm-30) cc_final: 0.7000 (mm-30) outliers start: 28 outliers final: 19 residues processed: 184 average time/residue: 0.7896 time to fit residues: 157.8082 Evaluate side-chains 191 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 166 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 143 CYS Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain b residue 55 CYS Chi-restraints excluded: chain b residue 132 SER Chi-restraints excluded: chain b residue 178 GLU Chi-restraints excluded: chain b residue 287 VAL Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 81 GLU Chi-restraints excluded: chain a residue 129 THR Chi-restraints excluded: chain a residue 134 VAL Chi-restraints excluded: chain a residue 157 ASP Chi-restraints excluded: chain a residue 224 GLU Chi-restraints excluded: chain a residue 236 ILE Chi-restraints excluded: chain a residue 239 SER Chi-restraints excluded: chain a residue 279 GLU Chi-restraints excluded: chain a residue 287 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 57 optimal weight: 10.0000 chunk 87 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 80 optimal weight: 8.9990 chunk 167 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 chunk 153 optimal weight: 0.9980 chunk 144 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.129960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.107069 restraints weight = 99838.370| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 5.76 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3174 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3174 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 14790 Z= 0.182 Angle : 0.661 11.657 20117 Z= 0.347 Chirality : 0.046 0.155 2151 Planarity : 0.004 0.041 2575 Dihedral : 5.495 24.283 1995 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.19 % Favored : 94.75 % Rotamer: Outliers : 2.92 % Allowed : 12.95 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.20), residues: 1824 helix: 1.47 (0.42), residues: 159 sheet: 0.09 (0.25), residues: 483 loop : -0.58 (0.18), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 62 TYR 0.017 0.002 TYR M 105 PHE 0.015 0.002 PHE B 323 TRP 0.018 0.002 TRP b 168 HIS 0.010 0.001 HIS b 2 Details of bonding type rmsd covalent geometry : bond 0.00448 (14762) covalent geometry : angle 0.65022 (20061) SS BOND : bond 0.00496 ( 28) SS BOND : angle 2.36630 ( 56) hydrogen bonds : bond 0.04467 ( 419) hydrogen bonds : angle 5.51904 ( 1087) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 160 time to evaluate : 0.682 Fit side-chains REVERT: A 29 ARG cc_start: 0.6992 (OUTLIER) cc_final: 0.6014 (ptm-80) REVERT: B 340 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7368 (mm-30) REVERT: b 48 GLN cc_start: 0.7440 (tt0) cc_final: 0.7193 (tt0) REVERT: b 343 SER cc_start: 0.8374 (m) cc_final: 0.8104 (p) REVERT: N 81 GLU cc_start: 0.6762 (OUTLIER) cc_final: 0.5558 (pm20) REVERT: a 75 LEU cc_start: 0.7463 (tp) cc_final: 0.7178 (tp) REVERT: a 102 GLN cc_start: 0.8022 (mm-40) cc_final: 0.7753 (mm-40) REVERT: a 157 ASP cc_start: 0.5744 (OUTLIER) cc_final: 0.5409 (t0) REVERT: a 224 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7382 (mt-10) REVERT: a 261 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7371 (mpp80) REVERT: a 279 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.6721 (mt-10) REVERT: a 340 GLU cc_start: 0.7319 (mm-30) cc_final: 0.7012 (mm-30) outliers start: 34 outliers final: 20 residues processed: 180 average time/residue: 0.7994 time to fit residues: 155.3483 Evaluate side-chains 185 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 158 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain B residue 143 CYS Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain b residue 55 CYS Chi-restraints excluded: chain b residue 78 ILE Chi-restraints excluded: chain b residue 132 SER Chi-restraints excluded: chain b residue 178 GLU Chi-restraints excluded: chain b residue 287 VAL Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 81 GLU Chi-restraints excluded: chain a residue 129 THR Chi-restraints excluded: chain a residue 134 VAL Chi-restraints excluded: chain a residue 157 ASP Chi-restraints excluded: chain a residue 224 GLU Chi-restraints excluded: chain a residue 236 ILE Chi-restraints excluded: chain a residue 239 SER Chi-restraints excluded: chain a residue 261 ARG Chi-restraints excluded: chain a residue 279 GLU Chi-restraints excluded: chain a residue 287 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 119 optimal weight: 8.9990 chunk 160 optimal weight: 10.0000 chunk 107 optimal weight: 0.9980 chunk 104 optimal weight: 10.0000 chunk 127 optimal weight: 7.9990 chunk 145 optimal weight: 1.9990 chunk 38 optimal weight: 8.9990 chunk 55 optimal weight: 3.9990 chunk 169 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 chunk 72 optimal weight: 7.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.128959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.105404 restraints weight = 84926.716| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 5.58 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3124 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3124 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 14790 Z= 0.203 Angle : 0.692 12.675 20117 Z= 0.363 Chirality : 0.047 0.157 2151 Planarity : 0.005 0.042 2575 Dihedral : 5.628 24.765 1995 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.52 % Favored : 94.42 % Rotamer: Outliers : 2.79 % Allowed : 13.21 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.20), residues: 1824 helix: 1.40 (0.42), residues: 159 sheet: 0.04 (0.25), residues: 484 loop : -0.63 (0.18), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 62 TYR 0.019 0.002 TYR M 105 PHE 0.017 0.002 PHE B 323 TRP 0.021 0.002 TRP b 168 HIS 0.011 0.001 HIS b 2 Details of bonding type rmsd covalent geometry : bond 0.00502 (14762) covalent geometry : angle 0.68049 (20061) SS BOND : bond 0.00549 ( 28) SS BOND : angle 2.52523 ( 56) hydrogen bonds : bond 0.04715 ( 419) hydrogen bonds : angle 5.61328 ( 1087) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 155 time to evaluate : 0.602 Fit side-chains REVERT: L 79 ARG cc_start: 0.7100 (mmm-85) cc_final: 0.6759 (mtp-110) REVERT: A 29 ARG cc_start: 0.7014 (OUTLIER) cc_final: 0.6016 (ptm-80) REVERT: B 340 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7346 (mm-30) REVERT: b 48 GLN cc_start: 0.7375 (tt0) cc_final: 0.7102 (tt0) REVERT: b 343 SER cc_start: 0.8397 (m) cc_final: 0.8123 (p) REVERT: N 81 GLU cc_start: 0.6787 (OUTLIER) cc_final: 0.5566 (pm20) REVERT: a 75 LEU cc_start: 0.7444 (tp) cc_final: 0.7157 (tp) REVERT: a 102 GLN cc_start: 0.8033 (mm-40) cc_final: 0.7760 (mm-40) REVERT: a 157 ASP cc_start: 0.5722 (OUTLIER) cc_final: 0.5349 (t0) REVERT: a 224 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7427 (mt-10) REVERT: a 261 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7363 (mpp80) REVERT: a 279 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.6731 (mt-10) REVERT: a 340 GLU cc_start: 0.7368 (mm-30) cc_final: 0.7057 (mm-30) outliers start: 32 outliers final: 21 residues processed: 175 average time/residue: 0.8220 time to fit residues: 154.8393 Evaluate side-chains 181 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 153 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 143 CYS Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain b residue 55 CYS Chi-restraints excluded: chain b residue 78 ILE Chi-restraints excluded: chain b residue 132 SER Chi-restraints excluded: chain b residue 178 GLU Chi-restraints excluded: chain b residue 287 VAL Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 81 GLU Chi-restraints excluded: chain a residue 129 THR Chi-restraints excluded: chain a residue 134 VAL Chi-restraints excluded: chain a residue 157 ASP Chi-restraints excluded: chain a residue 224 GLU Chi-restraints excluded: chain a residue 236 ILE Chi-restraints excluded: chain a residue 239 SER Chi-restraints excluded: chain a residue 261 ARG Chi-restraints excluded: chain a residue 279 GLU Chi-restraints excluded: chain a residue 287 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 139 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 163 optimal weight: 7.9990 chunk 91 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 167 optimal weight: 4.9990 chunk 168 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 171 optimal weight: 4.9990 chunk 1 optimal weight: 0.4980 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.129368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.105799 restraints weight = 83156.980| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 5.50 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3154 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3154 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 14790 Z= 0.187 Angle : 0.672 12.002 20117 Z= 0.353 Chirality : 0.046 0.155 2151 Planarity : 0.004 0.041 2575 Dihedral : 5.562 24.516 1995 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.13 % Favored : 94.81 % Rotamer: Outliers : 2.73 % Allowed : 13.33 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.20), residues: 1824 helix: 1.46 (0.42), residues: 158 sheet: 0.09 (0.24), residues: 488 loop : -0.61 (0.18), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 62 TYR 0.017 0.002 TYR M 105 PHE 0.015 0.002 PHE B 323 TRP 0.021 0.002 TRP b 168 HIS 0.010 0.001 HIS b 2 Details of bonding type rmsd covalent geometry : bond 0.00460 (14762) covalent geometry : angle 0.66094 (20061) SS BOND : bond 0.00501 ( 28) SS BOND : angle 2.36863 ( 56) hydrogen bonds : bond 0.04503 ( 419) hydrogen bonds : angle 5.57360 ( 1087) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 152 time to evaluate : 0.611 Fit side-chains REVERT: H 112 GLN cc_start: 0.7239 (OUTLIER) cc_final: 0.6931 (mt0) REVERT: A 29 ARG cc_start: 0.7006 (OUTLIER) cc_final: 0.6018 (ptm-80) REVERT: B 340 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7314 (mm-30) REVERT: b 48 GLN cc_start: 0.7381 (tt0) cc_final: 0.7125 (tt0) REVERT: b 343 SER cc_start: 0.8379 (m) cc_final: 0.8110 (p) REVERT: N 81 GLU cc_start: 0.6755 (OUTLIER) cc_final: 0.5517 (pm20) REVERT: a 75 LEU cc_start: 0.7474 (tp) cc_final: 0.7191 (tp) REVERT: a 102 GLN cc_start: 0.8019 (mm-40) cc_final: 0.7756 (mm-40) REVERT: a 157 ASP cc_start: 0.5751 (OUTLIER) cc_final: 0.5423 (t0) REVERT: a 224 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7423 (mt-10) REVERT: a 279 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7059 (mt-10) REVERT: a 340 GLU cc_start: 0.7333 (mm-30) cc_final: 0.7026 (mm-30) outliers start: 31 outliers final: 22 residues processed: 171 average time/residue: 0.8135 time to fit residues: 150.5618 Evaluate side-chains 180 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 151 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 143 CYS Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain b residue 55 CYS Chi-restraints excluded: chain b residue 78 ILE Chi-restraints excluded: chain b residue 132 SER Chi-restraints excluded: chain b residue 178 GLU Chi-restraints excluded: chain b residue 287 VAL Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 81 GLU Chi-restraints excluded: chain a residue 134 VAL Chi-restraints excluded: chain a residue 157 ASP Chi-restraints excluded: chain a residue 224 GLU Chi-restraints excluded: chain a residue 236 ILE Chi-restraints excluded: chain a residue 239 SER Chi-restraints excluded: chain a residue 279 GLU Chi-restraints excluded: chain a residue 287 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 155 optimal weight: 8.9990 chunk 128 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 73 optimal weight: 7.9990 chunk 74 optimal weight: 3.9990 chunk 178 optimal weight: 7.9990 chunk 51 optimal weight: 0.4980 chunk 8 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 110 optimal weight: 0.7980 chunk 41 optimal weight: 7.9990 overall best weight: 3.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 16 GLN L 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.128567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.104965 restraints weight = 74676.827| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 5.18 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3106 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3106 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.103 14790 Z= 0.251 Angle : 0.747 13.893 20117 Z= 0.391 Chirality : 0.049 0.162 2151 Planarity : 0.005 0.042 2575 Dihedral : 5.836 25.575 1995 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.52 % Favored : 94.42 % Rotamer: Outliers : 2.73 % Allowed : 13.52 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.20), residues: 1824 helix: 1.22 (0.42), residues: 160 sheet: -0.02 (0.25), residues: 480 loop : -0.70 (0.18), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 62 TYR 0.023 0.003 TYR M 105 PHE 0.019 0.002 PHE B 323 TRP 0.024 0.002 TRP b 168 HIS 0.012 0.001 HIS b 2 Details of bonding type rmsd covalent geometry : bond 0.00620 (14762) covalent geometry : angle 0.73378 (20061) SS BOND : bond 0.00648 ( 28) SS BOND : angle 2.75898 ( 56) hydrogen bonds : bond 0.05202 ( 419) hydrogen bonds : angle 5.76183 ( 1087) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4699.56 seconds wall clock time: 80 minutes 50.84 seconds (4850.84 seconds total)